# # ChangeLog for src # # Generated by Trac 1.6 # May 24, 2025, 3:10:11 PM 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 [31bd9c] * src/Element/Makefile.am (modified) * src/Element/element.hpp (modified) * src/Element/ion.cpp (added) * src/Element/ion.hpp (added) * src/Element/unittests/IonUnitTest.cpp (added) * src/Element/unittests/IonUnitTest.hpp (added) * src/Element/unittests/Makefile.am (modified) Added ion class, derived from element. 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 21:32:55 GMT Frederik Heber [16227a] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.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/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) Removed FunctionModel::getSpecificExtractor() that is not needed ... 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 21:32:29 GMT Frederik Heber [1ba8a1] * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/documentation/constructs/potentials.dox (modified) DOCU: Extended documentation on FunctionApproximation and potential ... Fri, 27 Jun 2014 11:43:27 GMT Frederik Heber [0932c2] * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (modified) * src/documentation/constructs/potentials.dox (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) FIX: RandomNumberEngine_Encapsulation::clone() did not set the seed ... Mon, 26 May 2014 09:15:08 GMT Frederik Heber [6029a6] * configure.ac (modified) * doc/Makefile.am (modified) * doc/userguide.xml (deleted) * doc/userguide/Makefile.am (added) * doc/userguide/catalog.xml.in (added) * doc/userguide/createguide.sh (added) * doc/userguide/css/html.css (added) * doc/userguide/pictures/dialog_add-atom_tooltip.png (added) * doc/userguide/pictures/dialog_box.png (added) * doc/userguide/pictures/dialog_complex.png (added) * doc/userguide/pictures/dialog_exit.png (added) * doc/userguide/pictures/example_basic_view.png (added) * doc/userguide/pictures/molecuilder_logo.png (moved) * doc/userguide/userguide.xml (added) * m4/ax_check_docbook.m4 (added) * src/documentation/mainpage.dox (modified) * src/documentation/userguide.dox (added) Added largely extended userguide with some images into subfolder of ... Tue, 20 May 2014 09:14:56 GMT Frederik Heber [caece4] * src/Fragmentation/Fragmentation.cpp (modified) * src/documentation/code.dox (modified) * src/documentation/constructs/actions.dox (modified) * src/documentation/constructs/atoms.dox (modified) * src/documentation/constructs/bondgraph.dox (modified) * src/documentation/constructs/filling.dox (modified) * src/documentation/constructs/fragmentation.dox (modified) * src/documentation/constructs/potentials.dox (modified) * src/documentation/constructs/serialization.dox (modified) * src/documentation/constructs/shaperegistry.dox (modified) * src/documentation/constructs/shapes.dox (modified) * src/documentation/constructs/tesselation.dox (modified) * src/documentation/constructs/validators.dox (modified) * src/documentation/copyright.dox (modified) * src/documentation/fileformats.dox (modified) * src/documentation/future.dox (modified) * src/documentation/install.dox (modified) * src/documentation/launch.dox (modified) * src/documentation/mainpage.dox (modified) * src/documentation/tests/code-tests.dox (modified) * src/documentation/tests/regression-tests.dox (modified) * src/documentation/userinterfaces/commandline.dox (modified) * src/documentation/userinterfaces/graphical.dox (modified) * src/documentation/userinterfaces/python.dox (modified) * src/documentation/userinterfaces/textmenu.dox (modified) Enhanced documentation significantly. - went through all of the ... 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 [d9f2b3] * src/Fragmentation/Automation/SpecificFragmentController.cpp (modified) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/SpecificFragmentController_ResultContainer_impl.hpp (modified) SpecificFragmentController has a ref to an updatehandler to call in ... 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 12:42:44 GMT Frederik Heber [0b3cf47] * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) FIX: CommandLineWindow::display() did not use present ActionQueue ref. Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [e3f9b8] * src/WorldTime.hpp (modified) FIX: WorldTime's dstor is now virtual. Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [606c24] * src/Atom/atom_atominfo.cpp (modified) FIX: Newly created default atom has element hydrogen. - also when ... 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 [ae68b5] * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) Fixed some boost serialization static warnings. 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 ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [ec7511] * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * tests/Fragmentations/Fragmenting/anthracene/pre/anthracene.pdb (added) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at (added) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at (added) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at (added) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at (added) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at (added) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at (added) * tests/Fragmentations/Fragmenting/coronene/pre/coronene.pdb (added) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order1.at (added) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order2.at (added) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order3.at (added) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order4.at (added) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order5.at (added) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order6.at (added) * tests/Fragmentations/Fragmenting/naphthalene/pre/naphthalene.pdb (added) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order1.at (added) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order2.at (added) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order3.at (added) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order4.at (added) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order5.at (added) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order6.at (added) * tests/Fragmentations/Fragmenting/phenanthrene/pre/phenanthrene.pdb (added) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order1.at (added) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order2.at (added) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order3.at (added) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order4.at (added) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order5.at (added) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order6.at (added) * tests/Fragmentations/Makefile.am (modified) * tests/Fragmentations/testsuite.at (modified) FIX: CyclicStructureAnalysis falsely used DFS, skipped some cycles. ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [4b10fd] * src/Parser/XmlParser.cpp (modified) XmlParser::load() now gives each different charge a different ... Tue, 29 Apr 2014 12:42:22 GMT Frederik Heber [57388c9] * src/Python/PythonScripting.cpp (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) FIX: Test on skipping load/store session from python script was wrong ... 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. - ... Tue, 04 Mar 2014 23:24:56 GMT Frederik Heber [cb32aa] * src/UIElements/Makefile.am (modified) DISTFIX: libMolecuilderFragmentationAutomation.la was included ... Tue, 04 Mar 2014 23:24:56 GMT Frederik Heber [6497a3] * src/UIElements/Views/Qt4/Plotting/Makefile.am (modified) DISTFIX: QwtPlotting had extra _ in QWTHEADER declaration. - this ... Mon, 03 Mar 2014 14:06:36 GMT Frederik Heber [eddab7] * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) FIX: getSummedShortRangeResults() usage of typename incompatible with ... Sun, 20 Oct 2013 11:45:34 GMT Frederik Heber [b47f9c] * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) FIX: WindowGrid_converter::addWindowOntoGrid() never used ... Sun, 20 Oct 2013 11:45:34 GMT Frederik Heber [e0cf82] * src/Fragmentation/Automation/SpecificFragmentController.cpp (modified) Cut down verbosity of SpecificFragmentController with ... 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 07:24:40 GMT Frederik Heber [958312] * src/Graph/CyclicStructureAnalysis.cpp (modified) FIX: CyclicStructureAnalysis::InitializeToRoot() did not reset some ... Thu, 17 Oct 2013 07:24:25 GMT Frederik Heber [174f8b] * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.hpp (modified) Extending QtFragmentList to show value and contribution of summed ... 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 ... Thu, 17 Oct 2013 07:24:06 GMT Frederik Heber [675cd6] * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/Summation_impl.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) (Orthogonal)Summator are notified via out-of-range matrixnr to omit ... Thu, 17 Oct 2013 07:24:06 GMT Frederik Heber [58952a] * src/Fragmentation/Summation/SetValue.hpp (modified) * src/Fragmentation/Summation/ZeroInstance.hpp (modified) SetValue treats ZeroInstance as value special. - ZeroInstance in ... Thu, 17 Oct 2013 07:14:21 GMT Frederik Heber [955051] * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.hpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.hpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties_inline.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.cpp (added) * src/Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.hpp (added) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (modified) Added (in)equality operators to all SetValues. - only Fragment and ... 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 [7d507c] * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) FIX: Histogram::superposeOtherHistogram() could not deal with empty ... 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: ... Mon, 14 Oct 2013 23:42:03 GMT Frederik Heber [8dbcaf] * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) FIX: CyclicStructureAnalysis did not work correctly. - many errors ... Mon, 14 Oct 2013 23:42:03 GMT Frederik Heber [fb9f6d] * src/Atom/atom_graphnode.cpp (modified) FIX: GraphNode's operator<<() omitted commata between components. Mon, 14 Oct 2013 23:41:38 GMT Frederik Heber [b677ab] * src/UIElements/Views/Qt4/Plotting/QSeisPageRegistry.hpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlot.hpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.hpp (modified) Added QSeisPlotPage to QtHomologyList. - spawning QSeisPlotCurves ... Mon, 14 Oct 2013 23:41:38 GMT Frederik Heber [f0964c] * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialRegistry.hpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.hpp (modified) QtHomologyList also observes PotentialRegistry. - PotentialRegistry ... Mon, 14 Oct 2013 23:41:37 GMT Frederik Heber [4b2e05] * src/Potentials/CompoundPotential.hpp (modified) Made models of CompoundPotential const_iterable. Mon, 14 Oct 2013 23:41:35 GMT Frederik Heber [35302b] * m4/qwt.m4 (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Plotting/Makefile.am (added) * src/UIElements/Views/Qt4/Plotting/QListWidgetCurveItem.cpp (added) * src/UIElements/Views/Qt4/Plotting/QListWidgetCurveItem.hpp (added) * src/UIElements/Views/Qt4/Plotting/QScrollZoomer/ScrollBar.cpp (added) * src/UIElements/Views/Qt4/Plotting/QScrollZoomer/ScrollBar.hpp (added) * src/UIElements/Views/Qt4/Plotting/QScrollZoomer/ScrollZoomer.cpp (added) * src/UIElements/Views/Qt4/Plotting/QScrollZoomer/ScrollZoomer.hpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisCurveRegistry.cpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisCurveRegistry.hpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisData.cpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisData.hpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisPageRegistry.cpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisPageRegistry.hpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisPlot.hpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisPlotCurve.cpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisPlotCurve.hpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (added) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.hpp (added) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser.cpp (added) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser.hpp (added) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser_plotcurve.cpp (added) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser_plotcurve.hpp (added) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser_plottype.cpp (added) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser_plottype.hpp (added) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) Added many files from project Seismolo. - we either had the choice ... Sun, 06 Oct 2013 08:45:10 GMT Frederik Heber [c76b8b] * configure.ac (modified) * m4/qwt.m4 (added) * src/UIElements/Makefile.am (modified) Added check for qwt. - this is taken from the SIM project, i.e. ... Sun, 06 Oct 2013 08:45:08 GMT Frederik Heber [94453f1] * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.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) Added getCoordinator() to EmpiricalPotential interface. - ... Sat, 05 Oct 2013 09:33:18 GMT Frederik Heber [4e6a60] * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Potentials/InternalCoordinates/Coordinator.hpp (modified) * src/Potentials/InternalCoordinates/CoordinatorFactory.cpp (modified) * src/Potentials/InternalCoordinates/CoordinatorFactory.hpp (added) * src/Potentials/Makefile.am (modified) Added CoordinatorFactory that returns the correct Coordinator for a ... Sat, 05 Oct 2013 09:33:18 GMT Frederik Heber [291eca] * src/Potentials/InternalCoordinates/Coordinator.hpp (added) * src/Potentials/InternalCoordinates/CoordinatorFactory.cpp (added) * src/Potentials/InternalCoordinates/FourBody_ImproperAngle.cpp (added) * src/Potentials/InternalCoordinates/FourBody_ImproperAngle.hpp (added) * src/Potentials/InternalCoordinates/FourBody_TorsionAngle.cpp (added) * src/Potentials/InternalCoordinates/FourBody_TorsionAngle.hpp (added) * src/Potentials/InternalCoordinates/OneBody_Constant.cpp (added) * src/Potentials/InternalCoordinates/OneBody_Constant.hpp (added) * src/Potentials/InternalCoordinates/ThreeBody_Angle.cpp (added) * src/Potentials/InternalCoordinates/ThreeBody_Angle.hpp (added) * src/Potentials/InternalCoordinates/TwoBody_Length.cpp (added) * src/Potentials/InternalCoordinates/TwoBody_Length.hpp (added) * src/Potentials/Makefile.am (modified) Extracted all length,angle, ... function inside potentials into ... Sat, 05 Oct 2013 09:32:58 GMT Frederik Heber [a8f5d94] * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.hpp (modified) QtHomologyList is now a split with QTreeWidget and another widget. Sat, 05 Oct 2013 09:32:45 GMT Frederik Heber [d20ded] * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (added) * src/UIElements/Views/Qt4/QtFragmentList.hpp (added) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FragmentResultContainer is Observable and displayed by ... Sat, 05 Oct 2013 09:32:07 GMT Frederik Heber [c792e0] * data/icons/Makefile.am (modified) * data/icons/molecuilder_logo.png (added) * data/icons/molecuildergui_logo.png (added) * src/UIElements/Qt4/QtMainWindow.cpp (modified) Added molecuilder logo to QApplication. Sat, 05 Oct 2013 09:31:54 GMT Frederik Heber [76e224] * src/UIElements/Qt4/QtMainWindow.cpp (modified) FIX: QTimeLine does not grow vertically anymore. Sat, 05 Oct 2013 09:31:54 GMT Frederik Heber [592d42] * data/icons/Makefile.am (modified) * data/icons/icon_domain.png (added) * data/icons/icon_dreiBein.png (added) * data/icons/icons.qrc (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) Added enable/disable for DreiBein and domain box. Sat, 05 Oct 2013 09:31:54 GMT Frederik Heber [5e4bfd] * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) QtInfoBox shows name of atom. 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 [38112d] * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) FIX: StringQtQuery did not use default value. Sat, 05 Oct 2013 09:31:54 GMT Frederik Heber [25ce49] * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.hpp (modified) FIX: QtTimeLine was not notified of TimeChanged of WorldTime. - ... 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 ... Sat, 05 Oct 2013 09:31:33 GMT Frederik Heber [07414d7] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Changed atom ptr into atomicId_t param for atomInserted of GLWorld... ... Sat, 05 Oct 2013 09:30:38 GMT Frederik Heber [c60665] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Rewrote Observer structure of GLMoleculeObject_bond. - renamed ... Sun, 29 Sep 2013 11:40:49 GMT Frederik Heber [917659] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLMoleculeObject_atom just stores the atom's id, now ptr. Sun, 29 Sep 2013 11:40:49 GMT Frederik Heber [beadd0] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) Changed atom ptr into atomicId_t param for atomInserted of GLWorld... ... Sun, 29 Sep 2013 11:40:48 GMT Frederik Heber [8481f5] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) FIX: Using signal/slots to notify other thread of new or removed shapes. Sun, 29 Sep 2013 11:40:48 GMT Frederik Heber [426c84] * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.hpp (modified) QtStatusBar::updateProcess() replaced by signal/slot mechanism. - ... Sun, 29 Sep 2013 11:40:48 GMT Frederik Heber [c48ac12] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) FIX: GLWorldScene and GLWorldView have atomRemoved with id not atom ... Sat, 21 Sep 2013 08:58:26 GMT Frederik Heber [4d4caf] * src/Potentials/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) DISTFIX: Did not delete csv files PartialNucleiChargeFitterUnitTest ... Thu, 19 Sep 2013 20:24:28 GMT Frederik Heber [27888f] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) Using Normals from tesselated surface instead of from Shapes. - ... Thu, 19 Sep 2013 20:24:28 GMT Frederik Heber [00eda9] * src/Shapes/ShapeFactory.cpp (modified) * src/Shapes/ShapeFactory.hpp (modified) Added ShapeFactory::isBaseShape() to discern between BaseShapes. - ... Thu, 19 Sep 2013 20:24:28 GMT Frederik Heber [192397] * src/Shapes/ShapeFactory.cpp (modified) * src/Shapes/ShapeType.hpp (modified) Added new ShapeType molecule-surface. - uses getBoundingShape() of ... 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 [d5521e] * src/Shapes/ShapeFactory.cpp (modified) * src/Shapes/ShapeFactory.hpp (modified) FIX: Made most ShapeFactory member function const. 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 20:24:28 GMT Frederik Heber [f06cbb] * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape_impl.hpp (modified) AndShape and OrShape now use Cacheable to store center and radius ... Thu, 19 Sep 2013 20:24:28 GMT Frederik Heber [52bb5a] * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.hpp (modified) Added clearing flag to QtHomologyList. Thu, 19 Sep 2013 20:24:28 GMT Frederik Heber [4d6662] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) FIX: Using signal/slots to notify other thread of new or removed shapes. Thu, 19 Sep 2013 20:24:28 GMT Frederik Heber [95c4e2] * src/Tesselation/ApproximateShapeArea.cpp (modified) FIX: ApproximateShapeArea::operator() needs to set the number of ... Thu, 19 Sep 2013 20:24:28 GMT Frederik Heber [25e18e7] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) FIX: Required qRegisterMetaType of bond::ptr. 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 [7e3f11a] * src/Makefile.am (modified) * src/Python/Makefile.am (added) * src/Python/PythonScripting.cpp (added) * src/Python/PythonScripting.hpp (added) * src/Python/PythonScripting_impl.hpp (moved) * src/UIElements/Makefile.am (modified) * src/builder_init.cpp (modified) Moved PythonScripting into own folder and created convenience ...