# # ChangeLog for / # # Generated by Trac 1.4.4 # Apr 11, 2025, 5:48:55 PM Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [4a6ef3] * src/Graph/BreadthFirstSearchGatherer.hpp (modified) * src/Graph/unittests/BoostGraphCreatorUnitTest.cpp (modified) Moved AlwaysTruePredicate from BoostGraphCreatorUnitTest into ... Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [e0b960] * src/Graph/BoostGraphCreator.cpp (modified) * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/unittests/BoostGraphCreatorUnitTest.cpp (modified) * src/Graph/unittests/BoostGraphCreatorUnitTest.hpp (modified) Edges may be added and removed in BoostGraphCreator. - TESTS: added ... Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [966ce7] * src/Graph/BreadthFirstSearchGatherer.cpp (modified) * src/Graph/BreadthFirstSearchGatherer.hpp (modified) BreadthFirstSearchGatherer::getDistances() added. Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [e3ec8a8] * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/BreadthFirstSearchGatherer.cpp (modified) * src/Graph/BreadthFirstSearchGatherer.hpp (modified) * src/Graph/unittests/BreadthFirstSearchGathererUnitTest.cpp (modified) * src/Graph/unittests/BreadthFirstSearchGathererUnitTest.hpp (modified) Extended BreadthFirstSearchGatherer to allow BFS with limited ... Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [0dc8bf2] * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/unittests/BoostGraphCreatorUnitTest.cpp (added) * src/Graph/unittests/BoostGraphCreatorUnitTest.hpp (added) * src/Graph/unittests/Makefile.am (modified) Added unit test for BoostGraphCreator. Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [1356af] * src/Graph/BoostGraphCreator.cpp (modified) * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/BoostGraphCreator_impl.hpp (added) * src/Graph/Makefile.am (modified) Moved BoostGraphCreator::createFromRange into extra impl module. Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [6e5b8d] * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/unittests/BreadthFirstSearchGathererUnitTest.cpp (added) * src/Graph/unittests/BreadthFirstSearchGathererUnitTest.hpp (added) * src/Graph/unittests/Makefile.am (modified) Added BreadthFirstSearchGathererUnitTest. Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [bccbe9] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.def (modified) * src/Graph/BoostGraphCreator.cpp (modified) * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/BoostGraphHelpers.hpp (added) * src/Graph/BreadthFirstSearchGatherer.cpp (added) * src/Graph/BreadthFirstSearchGatherer.hpp (added) * src/Graph/Makefile.am (modified) Extracted extraction (subset of) nodes from BoostGraph into ... Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [d24ef58] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Graph/BoostGraphCreator.cpp (added) * src/Graph/BoostGraphCreator.hpp (added) * src/Graph/Makefile.am (modified) Extracted conversion to boost::graph into distinct struct. - ... Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [3b74fa] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.def (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/StretchBond/post/benzene.pdb (added) * tests/regression/Molecules/StretchBond/pre/benzene.pdb (added) * tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond-cyclic_bond.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Rewrite of StretchBondAction to take bondgraph into account. - i.e. ... Wed, 12 Jul 2017 19:10:22 GMT Frederik Heber [0716eac] * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.def (modified) SelectMoleculeByOrder and SelectionAtomByOrder now allows multiple ... Wed, 12 Jul 2017 19:10:21 GMT Frederik Heber [f56e14] * tests/Examples/Makefile.am (modified) * tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz (added) * tests/Examples/ManyWaysTranslateAtom/pre/water.xyz (added) * tests/Examples/ManyWaysTranslateAtom/testsuite-examples-many-ways-translate-atom.at (added) * tests/Examples/testsuite-examples.at (modified) Added Examples testcase for the many ways to translate an atom blog ... Wed, 12 Jul 2017 19:10:07 GMT Frederik Heber [70f2a1] * doc/userguide/userguide.xml (modified) DOCU: Added restrictions of file formats to userguide. Wed, 12 Jul 2017 19:10:07 GMT Frederik Heber [33af20] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiple-timesteps.at (modified) TremoloParser::save() now supports multiple time steps. - TESTS: ... Wed, 12 Jul 2017 19:10:07 GMT Frederik Heber [0e894a] * src/Parser/FormatParser_common.cpp (modified) * src/Parser/FormatParser_common.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) Extracted getMinMaxTrajectories() into FormatParser_common. Wed, 12 Jul 2017 19:10:07 GMT Frederik Heber [220d2c] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo/post/water_multipletimesteps.data (added) * tests/regression/Parser/Tremolo/post/water_multipletimesteps_fail.data (added) * tests/regression/Parser/Tremolo/pre/water_multipletimesteps.data (added) * tests/regression/Parser/Tremolo/pre/water_multipletimesteps_fail.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiple-timesteps.at (added) * tests/regression/Parser/testsuite-parser.at (modified) TremoloParser::load() can deal with multiple time steps. - TESTS: ... Mon, 03 Jul 2017 15:07:28 GMT Frederik Heber [95b64f] * src/Atom/atom_atominfo.cpp (modified) Implemented missing AtomInfo::setAtStep(). Mon, 03 Jul 2017 15:06:53 GMT Frederik Heber [3cfb31] * src/documentation/constructs/potentials.dox (modified) DOCU: Updated potentials.dox. Mon, 03 Jul 2017 15:06:53 GMT Frederik Heber [b52710e] * doc/userguide/userguide.xml (modified) DOCU: Enhanced documentation of fit-potential to explain new ... Mon, 03 Jul 2017 15:06:34 GMT Frederik Heber [8f2f4e] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLWorldScene::removeShape() invalidated iter before delete. Mon, 03 Jul 2017 15:06:31 GMT Frederik Heber [3f6aac] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomByNameAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomByNameAction.def (added) * src/Actions/SelectionAction/Atoms/AtomByNameAction.hpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.cpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.def (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomByName/post/ethane-H5_missing.pdb (added) * tests/regression/Selection/Atoms/AtomByName/pre/ethane.pdb (added) * tests/regression/Selection/Atoms/AtomByName/testsuite-selection-select-atoms-by-name.at (added) * tests/regression/Selection/Atoms/AtomByName/testsuite-selection-unselect-atoms-by-name.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added (Un)selectAtomByName. - Descriptor for AtomByName was already ... Mon, 03 Jul 2017 15:01:38 GMT Frederik Heber [9a4772] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) AnalyseFragmentResults now always prints energy table, verbosity 1. Mon, 03 Jul 2017 15:01:38 GMT Frederik Heber [f1cacb] * doc/userguide/userguide.xml (modified) Fixed several small issues with the userguide. - additional ... Mon, 03 Jul 2017 15:00:00 GMT Frederik Heber [4dfe724] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) FIX: QtGui again reacts to WorldTime changes. - QtObservedAtom now ... Mon, 03 Jul 2017 15:00:00 GMT Frederik Heber [70fee0] * ThirdParty/CodePatterns/src/CodePatterns/ObservedValue.hpp (modified) * ThirdParty/CodePatterns/src/Patterns/unittests/ObservedValueUnitTest.cpp (modified) ObservedValue has forceUpdate() public function to externally force ... Mon, 03 Jul 2017 14:59:32 GMT Frederik Heber [8e9217] * configure.ac (modified) Changed email address to bug@molecuilder.com. Thu, 22 Jun 2017 22:28:16 GMT Frederik Heber [310445] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/RandomPerturbationAction.cpp (added) * src/Actions/AtomAction/RandomPerturbationAction.def (added) * src/Actions/AtomAction/RandomPerturbationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Atoms/RandomPerturbation/post/water.xyz (added) * tests/regression/Atoms/RandomPerturbation/pre/water.xyz (added) * tests/regression/Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added RandomPerturbationAction. - this should be when doing ... Wed, 21 Jun 2017 22:02:50 GMT Frederik Heber [78ea3c] * doc/userguide/userguide.xml (modified) * src/Actions/Action.hpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundBondAction.def (added) * src/Actions/MoleculeAction/RotateAroundBondAction.hpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.def (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/World.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/RotateAroundBond/post/test-195-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-90-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-95-false.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test_cycle.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (added) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/regression/Molecules/testsuite-molecules.at (modified) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (modified) Merge branch 'Docu_Python_wait' into Candidate_v1.6.1 Conflicts: ... Wed, 21 Jun 2017 22:02:14 GMT Frederik Heber [be848d] * doc/userguide/userguide.xml (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.def (added) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.def (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.def (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.def (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryRemoveAction.cpp (added) * src/Actions/GeometryAction/GeometryRemoveAction.def (added) * src/Actions/GeometryAction/GeometryRemoveAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/Values.hpp (modified) * src/Geometry/GeometryObject.cpp (added) * src/Geometry/GeometryObject.hpp (added) * src/Geometry/GeometryRegistry.cpp (added) * src/Geometry/GeometryRegistry.hpp (added) * src/Geometry/Makefile.am (added) * src/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Parameter.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Specifics/Parameter_vector.cpp (added) * src/Parameters/Specifics/Parameter_vector.hpp (added) * src/Parameters/Specifics/Value_vector.cpp (added) * src/Parameters/Specifics/Value_vector.hpp (added) * src/Parameters/Validators/Specific/GeometryNameValidator.cpp (added) * src/Parameters/Validators/Specific/GeometryNameValidator.hpp (added) * src/Parameters/Validators/Specific/PresentGeometryNameValidator.cpp (added) * src/Parameters/Validators/Specific/PresentGeometryNameValidator.hpp (added) * src/Parameters/Value.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * src/Parameters/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/GlobalListOfParameterQueries.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/TextUI/Query/TextQuery.hpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/Views/Qt4/QtGeometryList.cpp (added) * src/UIElements/Views/Qt4/QtGeometryList.hpp (added) * src/cleanUp.cpp (modified) * tests/GuiChecks/Geometry/DistanceToVector/testsuite-geometry-distance-to-vector.at (added) * tests/GuiChecks/Geometry/InputToVector/testsuite-geometry-input-to-vector.at (added) * tests/GuiChecks/Geometry/PlaneToVector/testsuite-geometry-plane-to-vector.at (added) * tests/GuiChecks/Geometry/PositionToVector/testsuite-geometry-position-to-vector.at (added) * tests/GuiChecks/Geometry/Remove/testsuite-geometry-remove.at (added) * tests/GuiChecks/Geometry/testsuite-geometry-common.at (added) * tests/GuiChecks/Geometry/testsuite-geometry.at (added) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/testsuite.at (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Geometry/DistanceToVector/post/test.xyz (added) * tests/regression/Geometry/DistanceToVector/pre/test.xyz (added) * tests/regression/Geometry/DistanceToVector/testsuite-geometry-distance-to-vector.at (added) * tests/regression/Geometry/InputToVector/post/test.xyz (added) * tests/regression/Geometry/InputToVector/pre/test.xyz (added) * tests/regression/Geometry/InputToVector/testsuite-geometry-input-to-vector.at (added) * tests/regression/Geometry/PlaneToVector/post/test.xyz (added) * tests/regression/Geometry/PlaneToVector/pre/test.xyz (added) * tests/regression/Geometry/PlaneToVector/testsuite-geometry-plane-to-vector.at (added) * tests/regression/Geometry/PositionToVector/post/test.xyz (added) * tests/regression/Geometry/PositionToVector/pre/test.xyz (added) * tests/regression/Geometry/PositionToVector/testsuite-geometry-position-to-vector.at (added) * tests/regression/Geometry/Remove/post/test.xyz (added) * tests/regression/Geometry/Remove/pre/test.xyz (added) * tests/regression/Geometry/Remove/testsuite-geometry-remove.at (added) * tests/regression/Geometry/testsuite-geometry-common.at (added) * tests/regression/Geometry/testsuite-geometry.at (added) * tests/regression/Makefile.am (modified) * tests/regression/Options/DryRun/post/session.py (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/pre/complextest.py (modified) * tests/regression/testsuite.at (modified) Merge branch 'GeometryObjects' into Candidate_v1.6.1 Wed, 21 Jun 2017 21:52:01 GMT Frederik Heber [101d2d] * doc/userguide/userguide.xml (modified) DOCU: Added note on necessity of wait() to Python section. Wed, 21 Jun 2017 21:51:24 GMT Frederik Heber [7294dc] * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.hpp (modified) * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/testsuite-analysis-dipole-angular-correlation-periodic-boundaries.at (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) FIX: Fixing the use of the trajectories that were changed to maps. ... Wed, 21 Jun 2017 21:15:15 GMT Frederik Heber [9f2071] * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/testsuite-analysis-dipole-angular-correlation-periodic-boundaries.at (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) FIX: World::setTime() now correctly copies the current state to the ... Tue, 20 Jun 2017 20:02:18 GMT Frederik Heber [137845] * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (modified) StepWorldTime now has a single argument. - this was not possible ... Tue, 20 Jun 2017 20:02:18 GMT Frederik Heber [15d21e] * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) CommandLineParser is now able to parse negative numbers. - before ... Tue, 20 Jun 2017 20:01:46 GMT Frederik Heber [da7ef9] * src/Actions/Action.hpp (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) FIX: STATUS msg only pushed to GUI, now also always in log. Tue, 20 Jun 2017 20:01:31 GMT Frederik Heber [536b13] * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) RotateToPrincipalAxisSystemAction now has Undo/Redo working. - ... Tue, 20 Jun 2017 19:58:37 GMT Frederik Heber [5e17bf] * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (modified) * tests/regression/Molecules/RotateAroundBond/pre/test_cycle.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (modified) Added test in RotateAroundBondAction whether given bond is cyclic. ... Tue, 20 Jun 2017 19:58:36 GMT Frederik Heber [788dce] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundBondAction.def (added) * src/Actions/MoleculeAction/RotateAroundBondAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/RotateAroundBond/post/test-195-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-90-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-95-false.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added RotateAroundBondAction. - TESTS: added regression test. - ... Mon, 19 Jun 2017 08:24:17 GMT Frederik Heber [6116df] * src/UIElements/Views/Qt4/QtGeometryList.cpp (modified) * src/UIElements/Views/Qt4/QtGeometryList.hpp (modified) QtGeometryList now shows length or angle of stored vectors via tooltips. Mon, 19 Jun 2017 08:24:17 GMT Frederik Heber [5776cb] * tests/GuiChecks/Geometry/DistanceToVector/testsuite-geometry-distance-to-vector.at (added) * tests/GuiChecks/Geometry/InputToVector/testsuite-geometry-input-to-vector.at (added) * tests/GuiChecks/Geometry/PlaneToVector/testsuite-geometry-plane-to-vector.at (added) * tests/GuiChecks/Geometry/PositionToVector/testsuite-geometry-position-to-vector.at (added) * tests/GuiChecks/Geometry/Remove/testsuite-geometry-remove.at (added) * tests/GuiChecks/Geometry/testsuite-geometry-common.at (added) * tests/GuiChecks/Geometry/testsuite-geometry.at (added) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/testsuite.at (modified) Recreated all GuiCheck tests. - new Geometry tests are added. - ... Mon, 19 Jun 2017 08:24:17 GMT Frederik Heber [836972] * doc/userguide/userguide.xml (modified) * src/Actions/GeometryAction/GeometryRemoveAction.cpp (added) * src/Actions/GeometryAction/GeometryRemoveAction.def (added) * src/Actions/GeometryAction/GeometryRemoveAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Geometry/Remove/post/test.xyz (added) * tests/regression/Geometry/Remove/pre/test.xyz (added) * tests/regression/Geometry/Remove/testsuite-geometry-remove.at (added) * tests/regression/Geometry/testsuite-geometry.at (modified) * tests/regression/Makefile.am (modified) Added GeometryRemoveAction. - TESTS: Also added regression test. Mon, 19 Jun 2017 08:24:17 GMT Frederik Heber [fd4e8c] * src/Geometry/GeometryRegistry.cpp (modified) * src/Geometry/GeometryRegistry.hpp (modified) GeometryRegistry knows a list of protected names. Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [1ba51c] * doc/userguide/userguide.xml (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) Updated userguide with lots of notes on using geometry object. Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [f79d65] * src/Actions/Values.cpp (modified) * src/Actions/Values.hpp (modified) * src/Parameters/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * tests/regression/Geometry/DistanceToVector/testsuite-geometry-distance-to-vector.at (modified) * tests/regression/Geometry/InputToVector/testsuite-geometry-input-to-vector.at (modified) * tests/regression/Geometry/PlaneToVector/testsuite-geometry-plane-to-vector.at (modified) * tests/regression/Geometry/PositionToVector/post/test.xyz (modified) * tests/regression/Geometry/PositionToVector/testsuite-geometry-position-to-vector.at (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Vector(s) are now stored as strings in Querys intermediately. - ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [2eded3e] * src/Parameters/Makefile.am (modified) * src/Parameters/Parameter.hpp (modified) * src/Parameters/Specifics/Parameter_vector.cpp (added) * src/Parameters/Specifics/Parameter_vector.hpp (added) * src/Parameters/Specifics/Value_vector.cpp (added) * src/Parameters/Specifics/Value_vector.hpp (added) * src/Parameters/Value.hpp (modified) * src/Parameters/unittests/Makefile.am (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) Added specific Value and Parameter implemenations for Vector. - for ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [6d78b6f] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Parameters/Parameter.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) Action::outputAsPython() access Parameters via ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [db1048] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/pre/complextest.py (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Moved toPythonString() from Action::outputAsPython() to ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [467b2b] * tests/regression/Geometry/DistanceToVector/post/test.xyz (added) * tests/regression/Geometry/DistanceToVector/pre/test.xyz (added) * tests/regression/Geometry/DistanceToVector/testsuite-geometry-distance-to-vector.at (added) * tests/regression/Geometry/InputToVector/post/test.xyz (added) * tests/regression/Geometry/InputToVector/pre/test.xyz (added) * tests/regression/Geometry/InputToVector/testsuite-geometry-input-to-vector.at (added) * tests/regression/Geometry/PlaneToVector/post/test.xyz (added) * tests/regression/Geometry/PlaneToVector/pre/test.xyz (added) * tests/regression/Geometry/PlaneToVector/testsuite-geometry-plane-to-vector.at (added) * tests/regression/Geometry/PositionToVector/post/test.xyz (added) * tests/regression/Geometry/PositionToVector/pre/test.xyz (added) * tests/regression/Geometry/PositionToVector/testsuite-geometry-position-to-vector.at (added) * tests/regression/Geometry/testsuite-geometry-common.at (added) * tests/regression/Geometry/testsuite-geometry.at (added) * tests/regression/Makefile.am (modified) * tests/regression/testsuite.at (modified) Added regression test for all four geometry Actions and common ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [987145] * doc/userguide/userguide.xml (modified) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.def (added) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.def (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.def (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.def (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/Python/AllActions/options.dat (modified) Added four GeometryActions to convert atom positions into vectors. ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [97c364] * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/Specific/GeometryNameValidator.cpp (added) * src/Parameters/Validators/Specific/GeometryNameValidator.hpp (added) * src/Parameters/Validators/Specific/PresentGeometryNameValidator.cpp (added) * src/Parameters/Validators/Specific/PresentGeometryNameValidator.hpp (added) Added Validator for name of a GeometryObject. - added ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [48eab8] * doc/userguide/userguide.xml (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/QtGeometryList.cpp (added) * src/UIElements/Views/Qt4/QtGeometryList.hpp (added) Added QtGeometryList to QtMainWindow. - this list shows the name ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [d8c6c7] * src/Geometry/GeometryObject.cpp (added) * src/Geometry/GeometryObject.hpp (added) * src/Geometry/GeometryRegistry.cpp (added) * src/Geometry/GeometryRegistry.hpp (added) * src/Geometry/Makefile.am (added) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/cleanUp.cpp (modified) Added GeometryObject and GeometryRegistry. - GeometryObject ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [6af6470] * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/GlobalListOfParameterQueries.hpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/TextUI/Query/TextQuery.hpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) Removed Vector and Vectors from boost preprocessor magic. - this is ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [d6d2129] * tests/regression/Options/DryRun/post/session.py (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) TESTFIX: Regression tests DryRun store-session used wrong option key. Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [b5bdb9] * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) FIX: Vector(s)TextQuery was still asserting vector to be valid inside ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [61003d] * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value.hpp (modified) FIX: Parameter is now longer friend of class Value. - Parameter ... Mon, 19 Jun 2017 08:23:19 GMT Frederik Heber [9a9f847] * ThirdParty/CodePatterns/src/CodePatterns/Chronos.hpp (modified) * ThirdParty/CodePatterns/src/Helpers/Chronos.cpp (modified) Chronos can now be safely used in multithread environements. - this ... Fri, 12 May 2017 21:15:04 GMT Frederik Heber [51a013] * ThirdParty/JobMarket/tests/regression/testsuite-addingjobs.at (modified) * ThirdParty/JobMarket/tests/regression/testsuite-checkalive.at (modified) * ThirdParty/JobMarket/tests/regression/testsuite-checkstate.at (modified) * ThirdParty/JobMarket/tests/regression/testsuite-completerun.at (modified) * ThirdParty/JobMarket/tests/regression/testsuite-enrollinpool.at (modified) * ThirdParty/JobMarket/tests/regression/testsuite-falsehost.at (modified) * ThirdParty/JobMarket/tests/regression/testsuite-getresults.at (modified) * ThirdParty/JobMarket/tests/regression/testsuite-resubmitjobs.at (modified) * ThirdParty/JobMarket/tests/regression/testsuite-server-shutdown.at (modified) * ThirdParty/JobMarket/tests/regression/testsuite-server-worker.at (modified) Ports used by regression tests are now between 11000 and 11999. - ... Wed, 10 May 2017 19:30:31 GMT Frederik Heber [2945e6] * tests/Calculations/molecuilder_poolworker.in (modified) * tests/Examples/molecuilder_poolworker.in (modified) * tests/integration/molecuilder_poolworker.in (modified) * tests/integration/testsuite-integration-mpqc-jobs.at (modified) * tests/integration/testsuite-integration-vmg-jobs.at (modified) FIX: integration tests killed worker script not worker in error case. ... Mon, 08 May 2017 18:43:40 GMT Frederik Heber [ae14a1] * tests/Calculations/testsuite-calculations-jobmarket-1_2-dimethoxyethane.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-1_2-dimethylbenzene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-2-methylcyclohexanone.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-N_N-dimethylacetamide.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-anthracene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-benzene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-cholesterol.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-coronene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-cycloheptane.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-dimethyl_bromomalonate.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-glucose.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-heptan.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-isoleucine.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-mpqc.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-naphthalene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-neohexane.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-phenanthrene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-proline.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-putrescine.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-tartaric_acid.at (modified) * tests/Examples/PartialChargeFitting/testsuite-examples-partialchargefitting-h2o.at (modified) * tests/Examples/Simple/testsuite-examples-simple-h2o.at (modified) * tests/JobMarket/testsuite-jobmarket-molecuilderrun.at (modified) * tests/JobMarket/testsuite-jobmarket-mpqc-jobs.at (modified) * tests/integration/testsuite-integration-mpqc-jobs.at (modified) * tests/integration/testsuite-integration-vmg-jobs.at (modified) Ports used by regression tests are now between 11024 and 19999. - ... Mon, 08 May 2017 13:51:00 GMT Frederik Heber [ce254c] * ThirdParty/mpqc_open/src/lib/chemistry/qc/basis/gpetite.cc (modified) FIX: Enforce template instantation in mpqc's gpetite.cc to avoid ... Mon, 08 May 2017 13:51:00 GMT Frederik Heber [23ad4f] * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler.hpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler_ControllerListener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/CheckResultsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/GetNextJobIdOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/ReceiveResultsOperation.cpp (modified) FIX: boost::serialization change requires clear before async_read. ... Mon, 08 May 2017 13:51:00 GMT Frederik Heber [557b39] * configure.ac (modified) * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (modified) * tests/regression/DiffFragmentResultContainer.cpp (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/difffragmentresultcontainer.in (added) boost::serialization changed text output format. - needed to write ... Fri, 05 May 2017 14:17:49 GMT Frederik Heber [4a38b9] * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) FIX: needed static_cast in QtObservedBond for stating which ... Fri, 05 May 2017 14:17:48 GMT Frederik Heber [3aa204] * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) FIX: Default values in function implementation not allowed. Fri, 05 May 2017 14:17:48 GMT Frederik Heber [5fea7d] * src/Graph/BondGraph.cpp (modified) FIX: boost::tuple prefix was needed for tie in boost::graph usage. Fri, 05 May 2017 14:17:48 GMT Frederik Heber [184d89] * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/MatrixContainer.hpp (modified) FIX: MatrixContainer's serialize() was broken because default cstor ... Fri, 05 May 2017 14:17:23 GMT Frederik Heber [dde50d] * ThirdParty/JobMarket/src/JobMarket/Results/FragmentResult.hpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (modified) * src/Fragmentation/KeySet.hpp (modified) * src/Fragmentation/Summation/IndexSet.hpp (modified) * src/Jobs/JobMarket/FragmentResult.hpp (modified) FIX: boost::serialization 1.58 introduced changes which breaks stand- ... Fri, 05 May 2017 14:17:23 GMT Frederik Heber [33a694] * ThirdParty/vmg/src/thirdparty/pugixml/pugiconfig.hpp (modified) * ThirdParty/vmg/src/thirdparty/pugixml/pugixml.cpp (modified) * ThirdParty/vmg/src/thirdparty/pugixml/pugixml.hpp (modified) * ThirdParty/vmg/src/thirdparty/pugixml/readme.txt (modified) * src/Parser/pugixml/pugiconfig.hpp (modified) * src/Parser/pugixml/pugixml.cpp (modified) * src/Parser/pugixml/pugixml.hpp (modified) * src/Parser/pugixml/readme.txt (modified) Updated pugixml in ThirdParty/vmg and src from 1.0 to 1.8. - this ... Fri, 05 May 2017 14:17:23 GMT Frederik Heber [6798a5] * ThirdParty/vmg/m4/ax_prog_fc_mpi.m4 (modified) FIX: vmg's ax_prog_fc_mpi did not find mpif. Fri, 05 May 2017 14:17:23 GMT Frederik Heber [dabe63] * ThirdParty/JobMarket/m4/ltsugar.m4 (deleted) * ThirdParty/levmar/m4/libtool.m4 (deleted) * ThirdParty/levmar/m4/ltoptions.m4 (deleted) * ThirdParty/levmar/m4/ltsugar.m4 (deleted) * ThirdParty/levmar/m4/ltversion.m4 (deleted) * ThirdParty/levmar/m4/lt~obsolete.m4 (deleted) * ThirdParty/mpqc_open/lib/autoconf/acinclude.m4 (deleted) * ThirdParty/mpqc_open/lib/autoconf/cca.m4 (deleted) * ThirdParty/mpqc_open/lib/autoconf/libtool.m4 (deleted) * ThirdParty/vmg/m4/libtool.m4 (deleted) * ThirdParty/vmg/m4/ltoptions.m4 (deleted) * ThirdParty/vmg/m4/ltsugar.m4 (deleted) * ThirdParty/vmg/m4/ltversion.m4 (deleted) * ThirdParty/vmg/m4/lt~obsolete.m4 (deleted) Updated libtool m4 macros. - also removed unneeded m4 macros of ... Fri, 05 May 2017 14:17:22 GMT Frederik Heber [aed262] * ThirdParty/CodePatterns/m4/boost.m4 (modified) * ThirdParty/JobMarket/m4/boost.m4 (modified) * ThirdParty/vmg/m4/boost.m4 (modified) * m4/boost.m4 (modified) Upgraded boost.m4 from serial 22 to 26. Fri, 05 May 2017 14:17:22 GMT Frederik Heber [ac9dc8] * ThirdParty/vmg/configure.ac (modified) FIX: LT_INIT came too late for boost in ThirdParty's vmg. Fri, 05 May 2017 14:08:59 GMT Frederik Heber [9eb71b3] * ThirdParty/CodePatterns/src/Helpers/Assert.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Chronos.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Info.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Log.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Verbose.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/errorlogger.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/logger.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Channels.cpp (modified) * ThirdParty/CodePatterns/src/Observer/GlobalObservableInfo.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Graveyard.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Notification.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Observable.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Observer.cpp (modified) * ThirdParty/CodePatterns/src/Observer/ObserverLog.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Relay.cpp (modified) * ThirdParty/CodePatterns/src/Patterns/unittests/stubs/Cacheable_threeNumbers.cpp (modified) * ThirdParty/CodePatterns/src/Patterns/unittests/stubs/ObservedValue_threeNumbers.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/ControllerCommandRegistry.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/ControllerOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/ControllerOptions_SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/FragmentController.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/FragmentController_JobIdProxy.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller_AddOn_SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller_SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller_main.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/DefaultOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentQueue.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler_ControllerListener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler_WorkerListener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/GlobalJobId.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/JobId.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Jobs/FragmentJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Jobs/NoOpJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Jobs/SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Listener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/AsyncOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/CheckResultsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/GetNextJobIdOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/ReceiveResultsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/RemoveAllJobsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/RemoveAllResultsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/RemoveAllWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/SendJobsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/ShutdownOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/OperationQueue.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/OperationRegistry.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Servers/CheckAliveWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Servers/SendJobToWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Servers/ShutdownWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/SyncOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/EnrollInPoolOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/ObtainJobOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/RemoveFromPoolOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/SubmitResultOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Pool/PoolGuard.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Pool/PoolWorker.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Pool/WorkerPool.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Results/FragmentResult.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/ServerOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/SignalHandler.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/SignalOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/WorkerAddress.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/WorkerOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/atexit.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/poolworker.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/poolworker_main.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/server.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/server_main.cpp (modified) * ThirdParty/JobMarket/src/unittests/stubs/FragmentJobStub.cpp (modified) * ThirdParty/JobMarket/src/unittests/stubs/FragmentResultStub.cpp (modified) * ThirdParty/JobMarket/src/unittests/stubs/ObserverStub.cpp (modified) * ThirdParty/JobMarket/tests/CodeChecks/testsuite-memdebug.at (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Plane.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Space.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Vector.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (modified) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionStatusList.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/MirrorAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateToOriginAction.cpp (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/BondAction/BondSetDegreeAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/DryRunAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (modified) * src/Actions/CommandAction/LoadSessionAction.cpp (modified) * src/Actions/CommandAction/NoDryRunAction.cpp (modified) * src/Actions/CommandAction/StoreSessionAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FillAction/FillVolumeAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (modified) * src/Actions/FragmentationAction/SaveFragmentResultsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/GraphAction/CorrectBondDegreeAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RemoveAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParseAtomFragmentsAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Actions/PotentialAction/ParseParticleParametersAction.cpp (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Actions/PotentialAction/SaveAtomFragmentsAction.cpp (modified) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (modified) * src/Actions/PotentialAction/SaveParticleParametersAction.cpp (modified) * src/Actions/PotentialAction/SavePotentialsAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/PushAtomsAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/AllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotAllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.cpp (modified) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.cpp (modified) * src/Actions/ShapeAction/CombineShapesAction.cpp (modified) * src/Actions/ShapeAction/CreateShapeAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/RotateShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Actions/ShapeAction/TranslateShapeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) * src/Actions/toCLIString.cpp (modified) * src/Actions/toPythonString.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_SaturateDanglingBonds.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_graphnode.cpp (modified) * src/Atom/atom_graphnodeinfo.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/AtomIdSet.cpp (modified) * src/Bond/AdjacencyMatcher/AdjacencyMatcher.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Box_BoundaryConditions.cpp (modified) * src/ControllerOptions_MPQCCommandJob.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomNameDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomOrderDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/ion.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Filling/Cluster.cpp (modified) * src/Filling/ClusterInterface.cpp (modified) * src/Filling/Filler.cpp (modified) * src/Filling/Generators/NodeGenerator.cpp (modified) * src/Filling/Inserter/Inserter.cpp (modified) * src/Filling/Inserter/RandomInserter.cpp (modified) * src/Filling/Inserter/SimpleInserter.cpp (modified) * src/Filling/Inserter/SurfaceInserter.cpp (modified) * src/Filling/Inserter/SurfaceRandomInserter.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Filling/Mesh/Mesh.cpp (modified) * src/Filling/Predicates/AnyFillPredicate.cpp (modified) * src/Filling/Predicates/FillPredicate.cpp (modified) * src/Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideSurface_FillPredicate.cpp (modified) * src/Filling/Predicates/IsValidInDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsVoidNode_FillPredicate.cpp (modified) * src/Filling/Predicates/Ops_FillPredicate.cpp (modified) * src/Filling/Preparators/BaseFillerPreparator.cpp (modified) * src/Filling/Preparators/BoxFillerPreparator.cpp (modified) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.cpp (modified) * src/Filling/Preparators/ShapeVolumeFillerPreparator.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/SpecificFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToAtomFragments.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/SaturatedBond.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution_getConnections.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution_getPoints.cpp (modified) * src/Fragmentation/Exporters/unittests/stubs/SaturatedBondStub.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeysetStub.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/SortIndex.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/GridDownsampler.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (modified) * src/Fragmentation/Summation/IndexSet.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/FragmentForces.cpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/parseKeySetFile.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionArgument.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Graph/AdjacencyList.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Helpers/defs.cpp (modified) * src/Jobs/ChargeSmearer.cpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/JobMarket/FragmentJob.cpp (modified) * src/Jobs/JobMarket/FragmentResult.cpp (modified) * src/Jobs/JobMarket/JobId.cpp (modified) * src/Jobs/JobMarket/SystemCommandJob.cpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/tripleIndex.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/MoleculeObserver.cpp (modified) * src/Parameters/Specifics/Value_atom.cpp (modified) * src/Parameters/Specifics/Value_element.cpp (modified) * src/Parameters/Specifics/Value_elements.cpp (modified) * src/Parameters/Specifics/Value_molecule.cpp (modified) * src/Parameters/Specifics/Value_string.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomDataValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomIdValidator.cpp (modified) * src/Parameters/Validators/Specific/BoundaryConditionValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxLengthValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxVectorValidator.cpp (modified) * src/Parameters/Validators/Specific/FileSuffixValidator.cpp (modified) * src/Parameters/Validators/Specific/FormulaValidator.cpp (modified) * src/Parameters/Validators/Specific/KeyValueValidator.cpp (modified) * src/Parameters/Validators/Specific/MoleculeIdValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserFileValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/PotentialTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/RandomNumberValidators.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixInvertibleValidator.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixSymmetricValidator.cpp (modified) * src/Parameters/Validators/Specific/SessionTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/ShapeNameValidator.cpp (modified) * src/Parameters/Validators/Specific/ShapeOpValidator.cpp (modified) * src/Parameters/Validators/Specific/ShapeTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorNotZeroValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorPositiveComponentsValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorZeroOneComponentsValidator.cpp (modified) * src/Parameters/unittests/stubs/ActionNameValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxLengthValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxVectorValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/TimeStepPresentValidatorStub.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Potentials/BindingModel.cpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/InternalCoordinates/CoordinatorFactory.cpp (modified) * src/Potentials/InternalCoordinates/FourBody_ImproperAngle.cpp (modified) * src/Potentials/InternalCoordinates/FourBody_TorsionAngle.cpp (modified) * src/Potentials/InternalCoordinates/OneBody_Constant.cpp (modified) * src/Potentials/InternalCoordinates/ThreeBody_Angle.cpp (modified) * src/Potentials/InternalCoordinates/TwoBody_Length.cpp (modified) * src/Potentials/PartialNucleiChargeFitter.cpp (modified) * src/Potentials/ParticleTypeCheckers.cpp (modified) * src/Potentials/Particles/Particle.cpp (modified) * src/Potentials/Particles/ParticleFactory.cpp (modified) * src/Potentials/Particles/ParticleRegistry.cpp (modified) * src/Potentials/Particles/StreamFactory_Particle.cpp (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/RegistryDeserializer_impl.hpp (modified) * src/Potentials/RegistrySerializer_Particle.cpp (modified) * src/Potentials/RegistrySerializer_impl.hpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PotentialTypes.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/StreamFactory_EmpiricalPotential.cpp (modified) * src/Potentials/TremoloPotentialFileParser.cpp (modified) * src/Potentials/TremoloPotentialTypes.cpp (modified) * src/Potentials/unittests/stubs/SerializablePotentialMock.cpp (modified) * src/Python/PythonScripting.cpp (modified) * src/Python/exit.cpp (modified) * src/Python/getBoundingBox.cpp (modified) * src/Python/getDomainVolume.cpp (modified) * src/Python/getSelectedMolarMass.cpp (modified) * src/Python/reinit.cpp (modified) * src/Python/wait.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/Server.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeFactory.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp (modified) * src/Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp (modified) * src/Shapes/unittests/stubs/moleculeStub.cpp (modified) * src/Tesselation/ApproximateShapeArea.cpp (modified) * src/Tesselation/ApproximateShapeVolume.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/TriangleMatcher/TriangleMatcher.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FilesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/KeyValuePairCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/KeyValuePairsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RealSpaceMatrixCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/getLastPosition.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FilesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/KeyValuePairQtQuery.cpp (modified) * src/UIElements/Qt4/Query/KeyValuePairsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.cpp (modified) * src/UIElements/Qt4/Query/RealSpaceMatrixQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FilesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/KeyValuePairTextQuery.cpp (modified) * src/UIElements/TextUI/Query/KeyValuePairsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QListWidgetCurveItem.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QScrollZoomer/ScrollBar.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QScrollZoomer/ScrollZoomer.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisCurveRegistry.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisData.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPageRegistry.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotCurve.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser.cpp (modified) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser_plotcurve.cpp (modified) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser_plottype.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtLogBox.cpp (modified) * src/UIElements/Views/Qt4/QtNumericalItem.cpp (modified) * src/UIElements/Views/Qt4/QtShapeController.cpp (modified) * src/UIElements/Views/Qt4/QtShapeList.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/controller.cpp (modified) * src/controller_AddOn_MPQCCommandJob.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/poolworker.cpp (modified) * src/unittests/stubs/AtomStub.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-memdebug.at (modified) * tests/JobMarket/mpqc.cpp (modified) Commented out MemDebug include and Memory::ignore. - MemDebug ... Fri, 05 May 2017 14:08:57 GMT Frederik Heber [aa91de0] * ThirdParty/JobMarket/src/JobMarket/types.hpp (modified) * src/Atom/CopyAtoms/CopyAtomsInterface.hpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Filling/Preparators/BaseFillerPreparator.hpp (modified) * src/Fragmentation/UniqueFragments.hpp (modified) * src/Parser/ParserTypes.hpp (modified) * src/Potentials/Specifics/PotentialTypes.hpp (modified) * src/RandomNumbers/RandomNumberDistribution.hpp (modified) FIX: size_t definition missing and other fixes. - cstddef defines ... Fri, 17 Mar 2017 10:11:35 GMT Frederik Heber [eca0d7] * configure.ac (modified) * debian/changelog (modified) Set version to 1.6.0. - MoleCuilder library is now 17:0:1. - ... Fri, 17 Mar 2017 10:11:35 GMT Frederik Heber [c4c113] * src/Parameters/Specifics/Value_elements.cpp (modified) * src/Parameters/Specifics/Value_elements.hpp (modified) * src/Parameters/Value.hpp (modified) * tests/CodeChecks/testsuite-specifics_present_in_value_header.at (added) * tests/CodeChecks/testsuite.at (modified) FIX: Value_elements was broken from copy&paste. - inclusion guard ... Fri, 17 Mar 2017 10:11:35 GMT Frederik Heber [917c46] * src/UIElements/Qt4/QtUIFactory.cpp (modified) FIX: Gui tests would not abort if an intermediate action failed. - ... Thu, 16 Mar 2017 06:48:58 GMT Frederik Heber [d50b91] * tests/GuiChecks/Atoms/Saturate/testsuite-atoms-saturate-atoms-bonded_atoms.at (added) * tests/GuiChecks/Atoms/Saturate/testsuite-atoms-saturate-atoms-carbon.at (added) * tests/GuiChecks/Atoms/Saturate/testsuite-atoms-saturate-atoms-nitrogen.at (added) * tests/GuiChecks/Atoms/testsuite-atoms.at (modified) * tests/GuiChecks/Bond/SetDegree/testsuite-bond-set-degree.at (added) * tests/GuiChecks/Bond/SetDegree/testsuite-bond-set-degree_multiple.at (added) * tests/GuiChecks/Bond/testsuite-bond.at (modified) * tests/GuiChecks/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) * tests/GuiChecks/Filling/FillSurface/testsuite-fill-surface-micelle.at (modified) * tests/GuiChecks/Filling/RegularGrid/testsuite-fill-regular-grid-with-surface.at (modified) * tests/GuiChecks/Filling/RegularGrid/testsuite-fill-regular-grid.at (modified) * tests/GuiChecks/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/GuiChecks/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (added) * tests/GuiChecks/Fragmentation/testsuite-fragmentation.at (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/GuiChecks/Options/testsuite-options.at (modified) * tests/GuiChecks/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-load.at (modified) * tests/GuiChecks/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-save.at (modified) * tests/GuiChecks/Parser/Tremolo/testsuite-parser-tremolo-improper.at (modified) * tests/GuiChecks/Parser/testsuite-parser.at (modified) * tests/GuiChecks/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (modified) * tests/GuiChecks/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) * tests/GuiChecks/Potential/SaveParseParticleParameters/testsuite-potential-save-parse-particle-parameters.at (added) * tests/GuiChecks/Potential/SaveParsePotentials/testsuite-potential-save-parse-potentials.at (added) * tests/GuiChecks/Potential/testsuite-potential.at (modified) * tests/GuiChecks/WorldTime/SetWorldTime/testsuite-worldtime-set-world-time.at (added) * tests/GuiChecks/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (added) * tests/GuiChecks/WorldTime/testsuite-worldtime.at (added) Recreated all GuiChecks. Wed, 15 Mar 2017 18:16:47 GMT Frederik Heber [cb20c0] * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) MEMFIX: StepWorldTimeAction leaked mem on failure. Wed, 15 Mar 2017 18:16:22 GMT Frederik Heber [bd4f83] * doc/Makefile.am (modified) DISTFIX: molecuilder.pdf was included with top_builddir. Wed, 15 Mar 2017 18:16:22 GMT Frederik Heber [6ec999] * ThirdParty/JobMarket/tests/CodeChecks/Makefile.am (modified) * ThirdParty/JobMarket/tests/regression/Makefile.am (modified) * ThirdParty/LinearAlgebra/tests/CodeChecks/Makefile.am (modified) DISTFIX: package.m4 must not be prefixed with srcdir in Makefile.am. Wed, 15 Mar 2017 18:15:56 GMT Frederik Heber [ef7b4b] * src/Jobs/MPQCJob_Work.cpp (modified) * src/Jobs/Makefile.am (modified) * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_empty_jobmarkt_disabled.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_jobmarkt_disabled.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (modified) ENABLEFIX: disable-jobmarket is now working. - needed to add ... Wed, 15 Mar 2017 08:45:32 GMT Frederik Heber [86f27c] * python/Makefile.am (modified) * python/cleanUp.cpp (added) DISTFIX: deps for cleanUp.cpp was removed in both src and python ... Wed, 15 Mar 2017 08:45:32 GMT Frederik Heber [de51d2] * tests/integration/Makefile.am (modified) DISTFIX: molecuilder_mpqc still listed in tests/integration/Makefile.am. Wed, 15 Mar 2017 08:45:32 GMT Frederik Heber [0b738b] * configure.ac (modified) * src/poolworker.cpp (modified) ENABLEFIX: Fixes to vmg and jobmarket enables. - ... Thu, 09 Mar 2017 22:17:15 GMT Frederik Heber [854a1e] * ThirdParty/JobMarket/tests/CodeChecks/Makefile.am (modified) * ThirdParty/JobMarket/tests/regression/Makefile.am (modified) * ThirdParty/LinearAlgebra/tests/CodeChecks/Makefile.am (modified) * ThirdParty/mpqc_open/src/bin/mpqc/validate/Makefile.am (modified) * tests/Calculations/Makefile.am (modified) * tests/CodeChecks/Makefile.am (modified) * tests/Examples/Makefile.am (modified) * tests/Fragmentations/Makefile.am (modified) * tests/GuiChecks/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) * tests/Python/Makefile.am (modified) * tests/Tesselations/Makefile.am (modified) * tests/integration/Makefile.am (modified) * tests/regression/Makefile.am (modified) Increased max_jobs to 8 for all testsuite's Makefiles.am. - running ... Thu, 09 Mar 2017 22:17:15 GMT Frederik Heber [755fb1] * tests/regression/Makefile.am (modified) DISTFIX: Worldtime was missing in EXTRA_DIST. Thu, 09 Mar 2017 22:17:15 GMT Frederik Heber [4e8108] * Makefile.am (modified) * ThirdParty/CodePatterns/Makefile.am (modified) * ThirdParty/CodePatterns/configure.ac (modified) * ThirdParty/JobMarket/Makefile.am (modified) * ThirdParty/JobMarket/configure.ac (modified) * ThirdParty/LinearAlgebra/Makefile.am (modified) * ThirdParty/LinearAlgebra/configure.ac (modified) * ThirdParty/levmar/Makefile.am (modified) * ThirdParty/levmar/configure.ac (modified) * ThirdParty/mpqc_open/Makefile.am (modified) * ThirdParty/mpqc_open/configure.ac (modified) * ThirdParty/vmg/Makefile.am (modified) * ThirdParty/vmg/configure.ac (modified) * configure.ac (modified) Libtool consolidates and updates itself through LIBTOOL_DEPS for all ... Thu, 09 Mar 2017 22:16:58 GMT Frederik Heber [f67dfb] * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/OperationQueue.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/OperationQueue.hpp (modified) * ThirdParty/JobMarket/src/JobMarket/Pool/PoolWorker.cpp (modified) * ThirdParty/JobMarket/tests/regression/testsuite-falsehost.at (modified) FIX: FragmentScheduler and PoolWorker now handle unresolvable ... Thu, 09 Mar 2017 22:16:58 GMT Frederik Heber [8e7a1b] * ThirdParty/JobMarket/src/JobMarket/Operations/AsyncOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Operation.hpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/SyncOperation.cpp (modified) AsyncOperation now sets a status code to indicate resolver failure. ... Thu, 09 Mar 2017 22:16:58 GMT Frederik Heber [c300e2] * ThirdParty/JobMarket/tests/regression/Makefile.am (modified) * ThirdParty/JobMarket/tests/regression/testsuite-falsehost.at (added) * ThirdParty/JobMarket/tests/regression/testsuite.at (modified) Adding JobMarket test when worker has unresolvable hostname. - so ... Thu, 09 Mar 2017 22:16:58 GMT Frederik Heber [89b42d] * ThirdParty/JobMarket/src/JobMarket/WorkerAddress.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/WorkerAddress.hpp (modified) Added assignment op to WorkerAddress. Thu, 09 Mar 2017 22:16:58 GMT Frederik Heber [c79d7a] * ThirdParty/JobMarket/src/JobMarket/WorkerOptions.cpp (modified) FIX: JobMarket's PoolWorker now uses ip addresses as hostname. - ... Thu, 09 Mar 2017 22:16:01 GMT Frederik Heber [fed1ae] * src/Parser/Makefile.am (modified) FIX: Removed Parameters' headers from libmolecuilderparser's. - ... Thu, 09 Mar 2017 22:16:01 GMT Frederik Heber [0ee9cb3] * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Plotting/Makefile.am (modified) FIX: Removed multiple instances of libmolecuilder_config.h in ... Thu, 09 Mar 2017 22:16:01 GMT Frederik Heber [7672284] * Makefile.am (modified) * configure.ac (modified) * python/Makefile.am (added) * src/Makefile.am (modified) * tests/Python/run.in (modified) * tests/regression/runpython.in (modified) FIX: install target now works with multiple threads. - the problem ... Thu, 09 Mar 2017 09:43:23 GMT Frederik Heber [fbf005] * Makefile.am (modified) * ThirdParty/Makefile.am (modified) * ThirdParty/mpqc_open/src/bin/mpqc/Makefile.am (modified) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc.cc (modified) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc.h (added) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc_extract.h (added) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc_extract_dummy.cc (added) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc_main.cc (added) * configure.ac (modified) * src/Jobs/MPQCJob_Work.cpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/mpqc_extract.cc (added) * src/Makefile.am (modified) * src/poolworker.cpp (modified) * tests/Calculations/molecuilder_mpqc.in (deleted) * tests/Calculations/molecuilder_poolworker.in (added) * tests/Calculations/testsuite-calculations-jobmarket-1_2-dimethoxyethane.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-1_2-dimethylbenzene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-2-methylcyclohexanone.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-N_N-dimethylacetamide.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-anthracene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-benzene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-cholesterol.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-coronene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-cycloheptane.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-dimethyl_bromomalonate.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-glucose.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-heptan.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-isoleucine.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-mpqc.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-naphthalene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-neohexane.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-phenanthrene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-proline.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-putrescine.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-tartaric_acid.at (modified) * tests/CodeChecks/testsuite-memdebug.at (modified) * tests/Examples/PartialChargeFitting/testsuite-examples-partialchargefitting-h2o.at (modified) * tests/Examples/Simple/testsuite-examples-simple-h2o.at (modified) * tests/Examples/molecuilder_mpqc.in (deleted) * tests/Examples/molecuilder_poolworker.in (added) * tests/integration/molecuilder_mpqc.in (deleted) * tests/integration/molecuilder_poolworker.in (added) * tests/integration/testsuite-integration-mpqc-jobs.at (modified) * tests/integration/testsuite-integration-vmg-jobs.at (modified) HUGE: Extracted libmolecuilder_mpqc that is now linked to poolworker. ... Wed, 08 Mar 2017 21:46:42 GMT Frederik Heber [ba1152] * ThirdParty/mpqc_open/configure.ac (modified) Removed libfl dependence in mpqc. - this fixes "undefined reference ... Wed, 08 Mar 2017 21:46:36 GMT Frederik Heber [69682a] * ThirdParty/LinearAlgebra/src/LinearAlgebra/Vector.cpp (modified) * src/cleanUp.cpp (modified) LinearAlgebra's static Vectors are now ignore Memory::ignore()'d ...