# # ChangeLog for src/Actions # # Generated by Trac 1.6 # May 24, 2025, 11:01:00 AM Wed, 10 Sep 2014 19:10:26 GMT Frederik Heber [16c7dd] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (deleted) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (deleted) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (deleted) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (modified) * tests/regression/Filling/FillVoidWithMolecule/post/propane.xyz (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/test.conf (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/test.xyz (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.potentials (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/test.conf (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/water.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (deleted) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (deleted) * tests/regression/Filling/FillWithMolecule/post/propane.xyz (deleted) * tests/regression/Filling/FillWithMolecule/post/test.conf (deleted) * tests/regression/Filling/FillWithMolecule/pre/test.conf (deleted) * tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (deleted) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Removed FillVoidWithMolecule and FillWithMolecule actions. - these ... Wed, 10 Sep 2014 19:00:56 GMT Frederik Heber [df9f20] * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.def (modified) * src/Filling/Inserter/SurfaceRandomInserter.cpp (added) * src/Filling/Inserter/SurfaceRandomInserter.hpp (added) * src/Filling/Makefile.am (modified) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.cpp (added) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.hpp (added) * tests/regression/Filling/FillSurface/post/tensid-undo.data (moved) * tests/regression/Filling/FillSurface/post/tensid.data (moved) * tests/regression/Filling/FillSurface/post/water_cube.xyz (added) * tests/regression/Filling/FillSurface/post/water_cylinder.xyz (added) * tests/regression/Filling/FillSurface/post/water_sphere.xyz (added) * tests/regression/Filling/FillSurface/post/water_undo.xyz (added) * tests/regression/Filling/FillSurface/pre/tensid.data (moved) * tests/regression/Filling/FillSurface/pre/tensid.potentials (moved) * tests/regression/Filling/FillSurface/pre/water.xyz (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-cube.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-cylinder.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-everywhere.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-micelle.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-nowhere.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-sphere.at (added) * tests/regression/Filling/SphericalSurface/testsuite-fill-spherical-surface.at (deleted) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Refactored FillSurfaceAction to also use FillerPreparators. - added ... Wed, 10 Sep 2014 18:59:16 GMT Frederik Heber [6801f4] * src/Actions/FillAction/FillVolumeAction.cpp (added) * src/Actions/FillAction/FillVolumeAction.def (added) * src/Actions/FillAction/FillVolumeAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Filling/Makefile.am (modified) * src/Filling/Mesh/MeshAdaptor.hpp (modified) * src/Filling/Preparators/ShapeVolumeFillerPreparator.cpp (added) * src/Filling/Preparators/ShapeVolumeFillerPreparator.hpp (added) * tests/regression/Filling/FillVolume/post/water_cylinder.xyz (added) * tests/regression/Filling/FillVolume/post/water_undo.xyz (added) * tests/regression/Filling/FillVolume/pre/water.xyz (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-cube.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-cylinder.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-everywhere.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-nowhere.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-sphere.at (added) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Added FillVolumeAction for filling a Shape's volume. - added ... Wed, 10 Sep 2014 07:55:12 GMT Frederik Heber [cae614] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Filling/Makefile.am (modified) * src/Filling/Preparators/BaseFillerPreparator.cpp (added) * src/Filling/Preparators/BaseFillerPreparator.hpp (added) * src/Filling/Preparators/BoxFillerPreparator.cpp (added) * src/Filling/Preparators/BoxFillerPreparator.hpp (added) * src/documentation/constructs/filling.dox (modified) Extracted filler preparing functionality from FillRegularGridAction. ... Wed, 10 Sep 2014 07:45:55 GMT Frederik Heber [a090e3] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * tests/regression/Filling/RegularGrid/post/solved_double_sles.data (modified) * tests/regression/Filling/RegularGrid/post/solved_single_sles.data (modified) FIX: FillRegularGridAction requires filler molecule at origin. - ... Tue, 09 Sep 2014 19:42:32 GMT Frederik Heber [833b15] * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/moleculelist.cpp (modified) FIX: Changes to function signatures in molecule_geometry. - no more ... Thu, 21 Aug 2014 06:43:48 GMT Frederik Heber [07ecc5] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) FIX: FragmentationAutomationAction did not fail correctly with ... Thu, 21 Aug 2014 06:43:46 GMT Frederik Heber [748fc7] * src/Actions/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/builder_init.cpp (modified) * src/unittests/Makefile.am (modified) libMolecuilder is now a shared library. - linking error ... Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [d93b4b3] * src/Actions/ActionQueue.cpp (modified) FIX: ActionQueue::run() did not use boost::thread::sleep_for() correctly. Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [e9e86f] * src/Actions/unittests/Makefile.am (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) FIX: UnitTestMain placed into convenience libUnitTest. - removed ... Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [0c74aa] * src/Actions/Action_impl_python.hpp (modified) FIX: Fixes to Action_impl_python, lacked boost preprocessor includes. Wed, 20 Aug 2014 12:58:30 GMT Frederik Heber [45cdce6] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (modified) MPQCCommandFragmentController supports FragmentationAutomationAction ... Wed, 20 Aug 2014 12:58:30 GMT Frederik Heber [e5f61ba] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (added) * src/Actions/FragmentationAction/StructuralOptimizationAction.def (added) * src/Actions/FragmentationAction/StructuralOptimizationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Added MakroAction StructureOptimizationAction. - performs similarly ... Wed, 20 Aug 2014 12:58:30 GMT Frederik Heber [ff3edf] * src/Actions/ActionRegistry.cpp (modified) FIX: MolecularDynamicsAction works also without JobMarket. - since ... Wed, 20 Aug 2014 12:58:30 GMT Frederik Heber [1a48d2] * src/Actions/AtomAction/RemoveAction.def (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (added) * src/Actions/MoleculeAction/ForceAnnealingAction.def (added) * src/Actions/MoleculeAction/ForceAnnealingAction.hpp (added) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (added) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (added) * tests/regression/Molecules/ForceAnnealing/post/test.conf (added) * tests/regression/Molecules/ForceAnnealing/pre/test.conf (added) * tests/regression/Molecules/ForceAnnealing/pre/test.forces (added) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added ForceAnnealingAction. - also added regression test. - ... Wed, 20 Aug 2014 12:58:29 GMT Frederik Heber [1e45f1f] * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * tests/regression/Molecules/VerletIntegration/post/test-undo.conf (added) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) Extended VerletIntegrationAction wirth Undo/Redo. - using new ... Wed, 20 Aug 2014 12:58:29 GMT Frederik Heber [7e51e1] * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/TesselPoint.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) Extended UndoRedoHelpers. - added removeLastStep(), addNewStep(). ... Wed, 20 Aug 2014 12:58:29 GMT Frederik Heber [442495] * src/Actions/GlobalListOfActions.hpp (modified) Sorted GlobalListOfActions. - note that Redo must remain at the ... Wed, 20 Aug 2014 12:58:28 GMT Frederik Heber [51cdfd] * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Dynamics/AtomicForceManipulator.hpp (added) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Makefile.am (modified) Extracted common functions from VerletForceIntegration into ... Sat, 16 Aug 2014 15:52:31 GMT Frederik Heber [343c5a] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/CorrectBondDegreeAction.cpp (added) * src/Actions/GraphAction/CorrectBondDegreeAction.def (added) * src/Actions/GraphAction/CorrectBondDegreeAction.hpp (added) * src/Actions/Makefile.am (modified) * tests/Calculations/testsuite-calculations-anthracene.at (modified) * tests/Calculations/testsuite-calculations-coronene.at (modified) * tests/Calculations/testsuite-calculations-naphthalene.at (modified) * tests/Calculations/testsuite-calculations-phenanthrene.at (modified) Added CorrectBondDegreeAction and fixed Calculation tests. - pdb ... Sat, 16 Aug 2014 15:52:30 GMT Frederik Heber [5d5550] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) FragmentationAction now compiles global saturation positions information. Sat, 16 Aug 2014 15:52:30 GMT Frederik Heber [98a293b] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) SaturatedFragment can deal with a global saturation position map. - ... Mon, 14 Jul 2014 11:16:23 GMT Frederik Heber [d8821e] * Makefile.am (modified) * configure.ac (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Element/Makefile.am (modified) * src/Element/element.hpp (modified) * src/Element/ion.cpp (added) * src/Element/ion.hpp (added) * src/Element/periodentafel.cpp (modified) * src/Element/periodentafel.hpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/IonUnitTest.cpp (added) * src/Element/unittests/IonUnitTest.hpp (added) * src/Element/unittests/Makefile.am (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (added) * src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (added) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/ResultContainer.hpp (added) * src/Fragmentation/Automation/ResultContainer_impl.hpp (added) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/SpecificFragmentController_ReceiveResultContainer_impl.hpp (added) * src/Fragmentation/Automation/SpecificFragmentController_ResultContainer_impl.hpp (deleted) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Fragmentation/analyzer.cpp (deleted) * src/Fragmentation/datacreator.cpp (deleted) * src/Fragmentation/datacreator.hpp (deleted) * src/Fragmentation/joiner.cpp (deleted) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/Jobs/JobMarket/FragmentJob.cpp (added) * src/Jobs/JobMarket/FragmentJob.hpp (added) * src/Jobs/JobMarket/FragmentResult.cpp (added) * src/Jobs/JobMarket/FragmentResult.hpp (added) * src/Jobs/JobMarket/JobId.cpp (added) * src/Jobs/JobMarket/JobId.hpp (added) * src/Jobs/JobMarket/SystemCommandJob.cpp (added) * src/Jobs/JobMarket/SystemCommandJob.hpp (added) * src/Jobs/JobMarket/types.hpp (added) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp (modified) * src/Potentials/helpers.hpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) * src/Potentials/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/cleanUp.cpp (modified) * src/documentation/constructs/potentials.dox (modified) * tests/Calculations/Makefile.am (added) * tests/Calculations/atlocal.in (added) * tests/Calculations/molecuilder.in (moved) * tests/Calculations/testsuite-calculations-1_2-dimethoxyethane.at (added) * tests/Calculations/testsuite-calculations-1_2-dimethylbenzene.at (added) * tests/Calculations/testsuite-calculations-2-methylcyclohexanone.at (added) * tests/Calculations/testsuite-calculations-N_N-dimethylacetamide.at (added) * tests/Calculations/testsuite-calculations-anthracene.at (added) * tests/Calculations/testsuite-calculations-benzene.at (added) * tests/Calculations/testsuite-calculations-cholesterol.at (added) * tests/Calculations/testsuite-calculations-coronene.at (added) * tests/Calculations/testsuite-calculations-cycloheptane.at (added) * tests/Calculations/testsuite-calculations-dimethyl_bromomalonate.at (added) * tests/Calculations/testsuite-calculations-glucose.at (added) * tests/Calculations/testsuite-calculations-heptan.at (added) * tests/Calculations/testsuite-calculations-isoleucine.at (added) * tests/Calculations/testsuite-calculations-mpqc.at (added) * tests/Calculations/testsuite-calculations-naphthalene.at (added) * tests/Calculations/testsuite-calculations-neohexane.at (added) * tests/Calculations/testsuite-calculations-phenanthrene.at (added) * tests/Calculations/testsuite-calculations-proline.at (added) * tests/Calculations/testsuite-calculations-putrescine.at (added) * tests/Calculations/testsuite-calculations-tartaric_acid.at (added) * tests/Calculations/testsuite.at (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaEnergies-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaEnergies-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaForces-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMaxForces-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMaxForces-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMeanForces-Order.dat (deleted) * 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tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragmentForces-Factors.dat (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragmentKeySets.dat (deleted) * tests/Fragmentations/Joining/heptan/pre/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/testsuite-joining-heptan.at (deleted) * tests/Fragmentations/Makefile.am (modified) * tests/Fragmentations/joiner.in (deleted) * tests/Fragmentations/testsuite.at (modified) * tests/Makefile.am (modified) * tests/regression/Fragmentation/FragmentationAutomation/pre/test.conf (added) * tests/regression/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable ... Mon, 14 Jul 2014 11:15:18 GMT Frederik Heber [a61dbb] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * tests/regression/Fragmentation/FragmentationAutomation/pre/test.conf (added) * tests/regression/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) In CommandLineUI actions are skipped after failing action. - ... Sun, 13 Jul 2014 18:04:51 GMT Frederik Heber [d6a7b9] * configure.ac (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (modified) * src/Jobs/JobMarket/SystemCommandJob.cpp (modified) * src/Jobs/JobMarket/SystemCommandJob.hpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) Specifying executable and suffix in SystemCommandJob with ... Sun, 13 Jul 2014 07:41:15 GMT Frederik Heber [18ed8c] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Jobs/Makefile.am (modified) All HAVE_VMG also check for HAVE_JOBMARKET. - right now VMG is not ... Sun, 13 Jul 2014 07:41:14 GMT Frederik Heber [bf0ff3] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) Using MPQCCommandFragmentController in FragmentationAutomationAction. ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [786d28] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Lib..FragmentationAutomation and lib..Jobs now also compiled without ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [1dfe00] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) Added inclusion switch on HAVE_JOBMARKET for files depending on ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [37ef6d] * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/periodentafel.hpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) Changed element class and periodentafel to have and use functions ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [9b68fc] * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) FitParticleChargesAction now averages over all fitted partial ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [550f2a] * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) Enhanced error messages in FitParticleChargesAction. Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [e1fe7e] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp (modified) * src/Potentials/helpers.hpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FunctionModel now uses list_of_arguments to split sequence of subsets ... Fri, 27 Jun 2014 21:32:29 GMT Frederik Heber [f4496d] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) Extracted associating each configuration with its L2 error into ... Fri, 27 Jun 2014 21:32:29 GMT Frederik Heber [4e009d] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) Extracted function from PotentialFitPotentialAction::performCall(). ... Fri, 27 Jun 2014 21:32:03 GMT Frederik Heber [26b4d62] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/LoadSessionAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.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/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.cpp (modified) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.cpp (modified) * src/Actions/ShapeAction/CombineShapesAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) All Actions now give correct failure status via STATUS() macro. Fri, 27 Jun 2014 21:32:03 GMT Frederik Heber [0b6b77] * src/Actions/ActionQueue.cpp (modified) ActionQueue gives caught failure of Action and success via pushStatus(). Fri, 27 Jun 2014 21:32:03 GMT Frederik Heber [378f2d5] * src/Actions/ActionStatusList.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.hpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.hpp (modified) Updated all UI's StatusIndicator classes to use ActionStatusList. - ... Fri, 27 Jun 2014 21:32:02 GMT Frederik Heber [26b4eb4] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionStatusList.cpp (added) * src/Actions/ActionStatusList.hpp (added) * src/Actions/Makefile.am (modified) Added observable ActionStatusList to ActionQueue. - this allows to ... Tue, 20 May 2014 09:14:56 GMT Frederik Heber [74459a] * configure.ac (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Python/wait.cpp (modified) * src/builder.cpp (modified) * src/cleanUp.cpp (modified) * src/cleanUp.hpp (modified) Added --disable-action-thread to allow disabling of extra run thread. ... Tue, 20 May 2014 09:14:56 GMT Frederik Heber [415ddd] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Python/Makefile.am (modified) * src/Python/PythonScripting_impl.hpp (modified) * src/Python/wait.cpp (added) * src/UIElements/UIFactory.hpp (modified) * src/builder.cpp (modified) * src/builder_init.hpp (modified) * src/cleanUp.cpp (modified) * src/cleanUp.hpp (modified) * src/documentation/Makefile.am (modified) * src/documentation/userinterfaces/python.dox (modified) * tests/regression/Options/Session/pre/complexwait.py (added) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * utils/Python/boxmaker.py.in (modified) ActionQueue now contains a run thread. - otherwise the progress bar ... Tue, 20 May 2014 09:11:52 GMT Frederik Heber [975b83] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Python/PythonScripting_impl.hpp (modified) * tests/Python/AllActions/moltest.py (modified) Added ActionQueue::insertAction(). - this is preparatory for ... Tue, 20 May 2014 08:47:10 GMT Frederik Heber [cc6e5c] * src/Actions/AnalysisAction/CalculateBoundingBoxAction.def (deleted) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.hpp (deleted) * src/Actions/AnalysisAction/CalculateCellVolumeAction.def (deleted) * src/Actions/AnalysisAction/CalculateCellVolumeAction.hpp (deleted) * src/Actions/AnalysisAction/CalculateMolarMassAction.def (deleted) * src/Actions/AnalysisAction/CalculateMolarMassAction.hpp (deleted) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/Reaction.hpp (deleted) * src/Actions/Reaction_impl.hpp (deleted) * src/Actions/Reaction_impl_header.hpp (deleted) * src/Actions/Reaction_impl_pre.hpp (deleted) * src/Actions/pyMoleCuilder.cpp (deleted) * src/Makefile.am (modified) * src/Python/Makefile.am (modified) * src/Python/PythonScripting_impl.hpp (modified) * src/Python/exit.cpp (added) * src/Python/getBoundingBox.cpp (moved) * src/Python/getDomainVolume.cpp (moved) * src/Python/getSelectedMolarMass.cpp (moved) * src/Python/modules.hpp (added) * src/Python/reinit.cpp (added) * tests/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (modified) * tests/regression/Analysis/CalculateBoundingBox/testsuite-analysis-calculate-bounding-box.at (deleted) * tests/regression/Analysis/CalculateCellVolume/testsuite-analysis-calculate-cell-volume.at (deleted) * tests/regression/Analysis/CalculateMolarMass/pre/argon.xyz (deleted) * tests/regression/Analysis/CalculateMolarMass/pre/water.xyz (deleted) * tests/regression/Analysis/CalculateMolarMass/testsuite-analysis-calculate-molar-mass.at (deleted) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * utils/Python/boxmaker.py.in (modified) Replaced Reactions by simple function exported to pyMoleCuilder. - ... Tue, 20 May 2014 08:47:03 GMT Frederik Heber [0d4168] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * src/Parameters/unittests/ContinuousValueTest.cpp (modified) * src/Parameters/unittests/DiscreteValueTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/builder_init.cpp (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Allow setting of invalid values in Value class, Action::performCall() ... Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [c09f94] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) Transformed FragmentationAutomationAction into a Process. - Removed ... Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [7fc447] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) Renamed ActionsQueue's queue -> actionqueue. Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [af5384] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl_header.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) Actions can now clone() and split off prepare() from call(). - ... Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [36053c] * src/Actions/Action.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) OptionRegistry is now filled by ActionRegistry() not by Action's ... Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [ec43a2] * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) FIX: Process's getters are now const member functions. Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [5eaa23] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) Added sensible default values to MolecularDynamics sequence of Actions. Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [d76d65] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) FIX: MPQCDataFragmentMap_t can be summed up in ... Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [5c78e3] * src/Actions/CommandAction/VersionAction.cpp (modified) FIX: Implemented VersionAction. - yes, it never printed the actual ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [5f364e] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) FIX: Fix typo in error msg of FillRegularGridAction. Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [a2a2f7] * src/Actions/ActionSequence.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Box.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) Huge warning fix. - fixed unused variables. - fixed set but unused ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [9bac15] * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) FIX: MolecularDynamicsAction needs to clear fragment results after ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [f47e00b] * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.def (modified) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/post/complextest.sh (modified) FIX: SubgraphDissectionAction is now a MakroAction, fixed store- ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [237f93] * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) FIX: MolecularDynamicsAction now prepares normally not inside ... Wed, 05 Mar 2014 19:47:43 GMT Frederik Heber [afbbfeb] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * tests/Python/AllActions/options.dat (modified) FIX: Some python commands with default values threw asserts. - ... Thu, 17 Oct 2013 07:24:42 GMT Frederik Heber [d29b31] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_LongRangeEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_LongRangeEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults_OBC.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults_PBC.dat (modified) Longrange energy is now also calculated for level 1. - level 1 sum ... Thu, 17 Oct 2013 07:24:25 GMT Frederik Heber [16893f] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.cpp (added) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.def (added) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Added ClearFragmentationResultsAction. - As we retain summed ... Thu, 17 Oct 2013 07:24:25 GMT Frederik Heber [c8d13f5] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) * src/Fragmentation/Summation/IndexSet.hpp (modified) * src/Fragmentation/Summation/writeIndexedTable.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_IndexedEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_IndexedEnergy.dat (modified) Summed up results are now handed-over to FragmentationResultContainer ... Thu, 17 Oct 2013 07:24:25 GMT Frederik Heber [47cee7] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/HeaderPrinter.hpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/ValuePrinter.hpp (modified) * src/Fragmentation/Summation/writeIndexedTable.hpp (added) * src/Fragmentation/Summation/writeTable.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_IndexedEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_IndexedEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Writing out energy file with value and contribution per index set - ... Thu, 17 Oct 2013 07:24:06 GMT Frederik Heber [f58e56] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) Extracted cycle contribution calculation into distinct function. Thu, 17 Oct 2013 07:24:06 GMT Frederik Heber [0588e9] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FragmentMolecule/pre/benzene.pdb (added) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) AnalyseFragmentationResultsAction now also calculates and prints ... Mon, 14 Oct 2013 23:42:04 GMT Frederik Heber [e0ae58d] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.hpp (modified) createMatrixNrLookup now requires a ValueMask. - adapted all ... Mon, 14 Oct 2013 23:42:04 GMT Frederik Heber [adb51ab] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Helpers/defs.cpp (modified) * src/Helpers/defs.hpp (modified) FragmentationAction stores cycles to file and in ... Mon, 14 Oct 2013 23:42:03 GMT Frederik Heber [fe0cb8] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added option DoCyclesFull to FragmentationAction. - FIX: ... Sat, 05 Oct 2013 09:31:54 GMT Frederik Heber [c34711] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) FIX: FitPotentialAction did not check whether potential already exists. Sat, 05 Oct 2013 09:31:54 GMT Frederik Heber [f130d4] * src/Actions/unittests/stubs/DummyUI.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (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/CommandLineQuery.hpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FilesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RealSpaceMatrixCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FilesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RealSpaceMatrixQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FilesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/TextQuery.hpp (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/TextDialog.hpp (modified) Qt's labels now show description as tool text. - had to streamline ... Thu, 19 Sep 2013 20:24:28 GMT Frederik Heber [87ec81] * src/Actions/ShapeAction/CombineShapesAction.cpp (modified) * src/Actions/ShapeAction/CreateShapeAction.cpp (modified) * src/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Shapes/ShapeRegistry.hpp (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp (added) * src/Shapes/unittests/stubs/moleculeStub.cpp (added) ShapeFactory removed from libMolecuilderShapes. - Factory is right ... Thu, 19 Sep 2013 20:24:28 GMT Frederik Heber [aeb694] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/unittests/MoleculeUnitTest.cpp (modified) * src/unittests/MoleculeUnitTest.hpp (modified) Added molecule::getBoundingShape() (renamed old to ...Sphere()). - ... Thu, 19 Sep 2013 20:23:53 GMT Frederik Heber [12d946] * src/Actions/ActionQueue.cpp (modified) * src/Actions/CommandAction/LoadSessionAction.cpp (added) * src/Actions/CommandAction/LoadSessionAction.def (added) * src/Actions/CommandAction/LoadSessionAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (added) * tests/regression/Options/testsuite-options.at (modified) Implemented LoadSessionAction. - this it also used in ... Thu, 19 Sep 2013 20:23:53 GMT Frederik Heber [992839] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/toPythonString.cpp (added) * src/Actions/toPythonString.hpp (added) * tests/regression/Options/Session/post/complextest.py (added) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Added more complex python example to regression test of store ... Thu, 19 Sep 2013 20:23:53 GMT Frederik Heber [9e4655] * src/Actions/ActionQueue.cpp (modified) * src/Actions/CommandAction/StoreSessionAction.cpp (modified) * src/Actions/CommandAction/StoreSessionAction.def (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/Specific/SessionTypeValidator.cpp (added) * src/Parameters/Validators/Specific/SessionTypeValidator.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Options/Session/post/test.py (added) Added sessiontype option to StoreSessionAction. - added ... Thu, 19 Sep 2013 20:23:53 GMT Frederik Heber [f6ff216] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * tests/regression/Options/Session/post/test.sh (modified) FIX: Removed " " around every printed parameter. Thu, 19 Sep 2013 20:23:53 GMT Frederik Heber [27d0bc] * src/Actions/toCLIString.cpp (modified) * src/Actions/toCLIString.hpp (modified) Extended and fixed toCLIString for RealSpaceMatrix, element and vector<>. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [477012] * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/Reaction_impl_header.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) Added Action::outputAsPython() and ActionQueue::outputAsPython(). - ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [9b56f34] * src/Actions/ActionSequence.cpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/toCLIString.cpp (added) * src/Actions/toCLIString.hpp (added) ActionParameters need special format when given to CLI. - ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [bad589] * src/Actions/ActionQueue.cpp (modified) * src/Actions/CommandAction/StoreSessionAction.cpp (added) * src/Actions/CommandAction/StoreSessionAction.def (added) * src/Actions/CommandAction/StoreSessionAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/Session/post/test.sh (added) * tests/regression/Options/Session/testsuite-options-store-session.at (added) * tests/regression/Options/testsuite-options.at (modified) Added StoreSessionAction to store the current session to file. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [46b181] * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/Reaction_impl_header.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) Added Action::outputAsCLI() and ActionQueue::outputAsCLI(). - ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [f54cda] * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) Action::call() is private, replaced by ActionQueue::queueAction(). Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [c5177f] * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) FIX: Reaction's hasResult() and getResult() are const member functions. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [05c989] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) Actions are now called through ActionQueue. - Action::call() is ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [126867] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/OptionRegistry.hpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/World.cpp (modified) Actions no longer register themselves, ActionQueue::addAction() ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [d649b7] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/getLastPosition.cpp (added) * src/UIElements/Menu/getLastPosition.hpp (added) Added functor getLastPosition, extracted from ActionRegistry. - ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [6367dd] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) ActionHistory now is part of ActionQueue. - TESTFIX: changes to ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [b5b01e] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionParameters.hpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/ActionState.hpp (added) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Shapes/AllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotAllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.cpp (modified) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.cpp (modified) * src/Actions/ShapeAction/CombineShapesAction.cpp (modified) * src/Actions/ShapeAction/CreateShapeAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/RotateShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Actions/ShapeAction/TranslateShapeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) ActionState extracted into own header file, rename Action::state_ptr ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [f92ef3] * src/Actions/Action.hpp (modified) * src/Actions/ActionParameters.hpp (added) * src/Actions/Makefile.am (modified) Extracted ActionParameters into own header file. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [ed3944] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) ActionQueue contains now ptr to ActionRegistry to allow forward ref ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [0c8056] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Action_impl_python.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/World.cpp (modified) Actions now get ptr to ActionRegistry in cstor. - this is the last ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [a6ceab] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) FIX: ActionRegistry's function now get ref to token string. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [690741] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.hpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.hpp (modified) * src/cleanUp.cpp (modified) Added getListOfActions() and getActionsTrait() to completely wrap ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [1d3563] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) Main functions of ActionRegistry are now tunneled through ActionQueue. Thu, 19 Sep 2013 20:23:51 GMT Frederik Heber [628577] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (added) * src/Actions/ActionQueue.hpp (added) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/PythonScripting.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/cleanUp.cpp (modified) Introduced ActionQueue which contains internal ActionRegistry. - ... Thu, 19 Sep 2013 20:21:37 GMT Frederik Heber [1e5f84] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) FragmentationAutomationAction does long-range jobs now depending on ... Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [f5724f] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (moved) * src/Actions/PotentialAction/FitParticleChargesAction.def (moved) * src/Actions/PotentialAction/FitParticleChargesAction.hpp (moved) * src/Actions/PotentialAction/FitPotentialAction.cpp (moved) * src/Actions/PotentialAction/FitPotentialAction.def (moved) * src/Actions/PotentialAction/FitPotentialAction.hpp (moved) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (moved) * src/Actions/PotentialAction/ParseHomologiesAction.def (moved) * src/Actions/PotentialAction/ParseHomologiesAction.hpp (moved) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (moved) * src/Actions/PotentialAction/SaveHomologiesAction.def (moved) * src/Actions/PotentialAction/SaveHomologiesAction.hpp (moved) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/FitParticleCharges/pre/homology_grid.dat (moved) * tests/regression/Potential/FitParticleCharges/pre/water.pdb (moved) * tests/regression/Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at (moved) * tests/regression/Potential/FitPotential/pre/angle_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/harmonic_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/improper_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/length_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/lj_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/torsion_homology.dat (moved) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (moved) * tests/regression/Potential/testsuite-potential.at (added) * tests/regression/testsuite.at (modified) Moved all FragmentationActions related to potentials into own menu ... Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [474c62] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FIX: Typo in FragmentationAction. Mon, 12 Aug 2013 11:30:31 GMT Frederik Heber [321470] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) FIX: Fragmentation's OrderAtSite was written per molecule and with ... Fri, 09 Aug 2013 14:26:27 GMT Frederik Heber [3e93bd4] * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) FIX: SetOutputFormatsAction fails on unknown parser type. Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [2a8731] * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) World now has channel TimeChanged. - FIX: SetWorldTimeAction uses ...