# # ChangeLog for src # # Generated by Trac 1.6 # May 23, 2025, 3:51:12 PM Fri, 09 Aug 2013 14:26:27 GMT Frederik Heber [d7e931] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (added) * src/UIElements/Views/Qt4/QtTimeLine.hpp (added) Added Timeline slider to QtMainWindow. - this allows quick setting ... Fri, 09 Aug 2013 14:26:27 GMT Frederik Heber [89b992] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) GLWorldView now listens to World::TimeChanged() and updates view. - ... 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 ... Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [cd9a59] * src/Atom/AtomObserver.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_observable.hpp (modified) Added TrajectoryChanged channel to atom_observable. - this lets us ... Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [13c5c1] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * tests/Python/AllActions/options.dat (modified) FragmentationAction uses Interfragmenter to add non-bonded fragments. Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [0331ee] * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/Interfragmenter.cpp (added) * src/Fragmentation/Interfragmenter.hpp (added) * src/Fragmentation/Makefile.am (modified) Added functor to add non-bonded union of fragments. - this is done ... Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [c1353f5] * src/AtomIdSet.cpp (modified) * src/AtomIdSet.hpp (modified) Added AtomIdSet cstor that converts from a KeySet. - as this ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [ff90e3] * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/PotentialTypes.def (modified) Renamed potential token harmonic to harmonic_bond. Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [791a12] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (added) * src/Potentials/Specifics/FourBodyPotential_Improper.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (added) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) * tests/regression/Fragmentation/FitPotential/pre/improper_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added improper potential based on torsion potential with flipped ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [a74a96] * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (modified) Made function_theta of FourBodyPotential_Torsion virtual. - also ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [e2037e] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (added) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (added) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) * tests/regression/Fragmentation/FitPotential/pre/torsion_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added FourBodyPotential_Torsion. - also added regression test to ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [484e2a] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (moved) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (moved) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp (moved) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.hpp (moved) Renamed PairPotential_Angle -> ThreeBodyPotential_Angle and also ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [1413f4] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (added) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp (added) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.hpp (added) * tests/regression/Fragmentation/FitPotential/pre/lj_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added LennardJones pair potential. - this is for later fitting ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [4792ab] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added set-threshold option to FitPotentialAction. - TESTFIX: ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [af4318] * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/GenericValidators.hpp (modified) * src/Parameters/Validators/GenericValidators_impl.hpp (added) Implemented GenericValidators. Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [c4a323] * src/Actions/FragmentationAction/FitParticleChargesAction.cpp (added) * src/Actions/FragmentationAction/FitParticleChargesAction.def (added) * src/Actions/FragmentationAction/FitParticleChargesAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Fragmentation/FitParticleCharges/pre/homology_grid.dat (added) * tests/regression/Fragmentation/FitParticleCharges/pre/water.pdb (added) * tests/regression/Fragmentation/FitParticleCharges/testsuite-fragmentation-fit-particle-charges.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added FitParticleChargesAction for fitting partial nuclei charges to ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [e355b31] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added both_sampled_potential to VMGData, analogous to ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [bf1d1b] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * tests/Python/AllActions/options.dat (modified) HomologyContainer now stores full struct as value to HomologyGraph ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [ff09f3] * src/Potentials/Makefile.am (modified) * src/Potentials/Particles/Particle.cpp (added) * src/Potentials/Particles/Particle.hpp (added) * src/Potentials/Particles/ParticleRegistry.cpp (added) * src/Potentials/Particles/ParticleRegistry.hpp (added) Added Particle and ParticleRegistry class. - Paricle class contains ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [f60d95] * src/Potentials/PartialNucleiChargeFitter.cpp (modified) * src/Potentials/PartialNucleiChargeFitter.hpp (modified) PartialNucleiChargeFitter writes potential, solution, and residuum to ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [58fcbe5] * src/Potentials/Makefile.am (modified) * src/Potentials/PartialNucleiChargeFitter.cpp (added) * src/Potentials/PartialNucleiChargeFitter.hpp (added) * src/Potentials/unittests/Makefile.am (modified) * src/Potentials/unittests/PartialNucleiChargeFitterUnitTest.cpp (added) * src/Potentials/unittests/PartialNucleiChargeFitterUnitTest.hpp (added) Added functor for fitting partial nuclear charges. - is simply via ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [3f64ee] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) Extracted SamplingGrid::getDiscreteWindowIndices() from ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [b5f548] * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties_inline.hpp (added) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (modified) FIX: Shifted all helper functions from SamplingGrid to ..Properties. ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [af2c7ec] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) TrainingData now generates internal list of all arguments. - ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [31a2be] * src/FunctionApproximation/Extractors.cpp (modified) FIX: Extractors::filterArgumentsByParticleTypes() did wrongly break ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [a633f6] * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) Added splitUpArgumentsByModelsFilter() to CompoundPotential. - this ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [51e0e3] * configure.ac (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) Added two filter functions to Extractors. - renamed ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [0f5d38] * 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/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/helpers.hpp (modified) Added getSpecificFilter() and getSpecificArgumentCount() to ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [f0025d] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * 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/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Renamed getFragmentSpecificExtractor() -> getSpecificExtractor(). Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [d449a9] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * src/Actions/FragmentationAction/ParseHomologiesAction.cpp (added) * src/Actions/FragmentationAction/ParseHomologiesAction.def (added) * src/Actions/FragmentationAction/ParseHomologiesAction.hpp (added) * src/Actions/FragmentationAction/SaveHomologiesAction.cpp (added) * src/Actions/FragmentationAction/SaveHomologiesAction.def (added) * src/Actions/FragmentationAction/SaveHomologiesAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Split off parsing and saving of homologies into new Actions. Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [1e1098] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (added) * src/UIElements/Views/Qt4/QtHomologyList.hpp (added) Added table of all present HomologyGraph keys to QtMainWindow. Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [98dbee] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) World now maintains HomologyContainer instance. Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [bcc24f] * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) Made HomologyContainer observable. - added clear() and getNextKey() ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [a8bc27a] * src/Fragmentation/Homology/HomologyContainer.hpp (modified) FIX: HomologyContainer::getHomologousGraphs() is actually const ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [0afe00] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) Extracted printNodes() and printEdges from HomologyGraph's output ... Fri, 09 Aug 2013 14:20:18 GMT Frederik Heber [39986b] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (added) * src/Actions/FragmentationAction/MolecularDynamicsAction.def (added) * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) Added new MakroAction MolecularDynamicsAction. - this resides ... Thu, 11 Jul 2013 21:44:01 GMT Frederik Heber [9c1324] * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (added) * src/Actions/MakroAction_impl_pre.hpp (added) Equipped MakroAction with some boost::preprocessor magic, ... Thu, 11 Jul 2013 21:43:31 GMT Frederik Heber [bcb593] * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Molecules/VerletIntegration/post/test.conf (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) FIX: VerletIntegrationAction now assumes forces have just been ... Tue, 09 Jul 2013 06:21:28 GMT Frederik Heber [11f0fa] * src/Atom/atom.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.hpp (modified) FIX: Newly created atoms must have trajectories reaching out till ... Tue, 09 Jul 2013 06:21:28 GMT Frederik Heber [f73351] * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * tests/regression/Atoms/Add/post/empty.conf (modified) * tests/regression/Domain/ChangeBox/post/test-undo.conf (modified) * tests/regression/Domain/ChangeBox/post/test.conf (modified) FIX: Some Thermostats would cause NaN on zero temperature. - ... Tue, 09 Jul 2013 06:21:05 GMT Frederik Heber [e5ebaf] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Forces obtained from fragmentation summation are now set. - i.e. ... Mon, 08 Jul 2013 14:22:04 GMT Frederik Heber [62164d] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) Writing final parameters to potential-file. Mon, 08 Jul 2013 14:22:04 GMT Frederik Heber [a315e8] * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/Specific/EmptyStringValidator.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Potential type is given via extra option not "fit-potential". - ... Mon, 08 Jul 2013 14:22:04 GMT Frederik Heber [a504946] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) Training data can now be written to optional file. Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [49dcf7] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) Added catching of SerializablePotentialException in FitPotentialAction. Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [baccf6] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) FitPotentialAction now uses new CompoundPotential to fit. - ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [7c1091] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) Extended CompoundPotential for multiple occurences of argument ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [c5e63a] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialDeserializer.cpp (added) * src/Potentials/PotentialDeserializer.hpp (added) * src/Potentials/PotentialSerializer.cpp (added) * src/Potentials/PotentialSerializer.hpp (added) * src/Potentials/SerializablePotential.cpp (modified) Added De(serializer) functors for instanting potentials from stream info. Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [3723f0] * src/Potentials/SerializablePotential.cpp (modified) FIX: SerializablePotential prints no comma following empty ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [6d9073] * src/Potentials/SerializablePotential.cpp (modified) FIX: SerializablePotential::stream_from() wrongly used ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [b3b31e] * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) Added PotentialFactory::createInstance() that uses default cstors. ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [a82d33] * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) FIX: Default cstor of specific potentials did not allocate parameter ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [713888] * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/SerializablePotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Made PotentialFactory friend of all specific potentials and added ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [acc9b1] * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PotentialTypes.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) FIX: Added new copyright lines to files in src/Potentials, too. Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [b15ae7] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) Removed energy_offset from ManyBodyPotential_Tersoff. Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [1e242a] * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Removed energy_offset from PairPotential_Angle. - regression test ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [065a16] * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) Removed energy_offset from PairPotential_Harmonic. Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [919c8a] * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Removed energy_offset from PairPotential_Morse. - regression test ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [1e565c] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/SaturationPotential.cpp (deleted) * src/Potentials/Specifics/SaturationPotential.hpp (deleted) Removed SaturationPotential. - SaturationPotential can be seen as a ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [7e5b94] * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) CompoundPotential now combines ConstantPotential and ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [cf4905] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added concatenateArguments to Extractors. Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [8203ce8] * src/FunctionApproximation/Extractors.cpp (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (added) * src/Potentials/Specifics/ConstantPotential.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (added) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) Added ConstantPotential to fit a non-zero offset in potential energy. ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [060e1e] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) Created AllPotentialHeaders.hpp from specific potentials headers in ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [154e88] * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (modified) * src/Potentials/CompoundPotential.cpp (added) * src/Potentials/CompoundPotential.hpp (added) * src/Potentials/Makefile.am (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (added) * src/Potentials/unittests/CompoundPotentialUnitTest.hpp (added) * src/Potentials/unittests/Makefile.am (modified) Added CompoundPotential as container for multiple FunctionModels. - ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [2bde72] * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) FIX: Removed CodePattern/Assert include from various PairPotential ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [3536a5f] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) FIX: Tiny fix to FitPotentialAction with static_casts. Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [fdd23a] * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialRegistry.hpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) EmpiricalPotential now inherits/combines FunctionModel, ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [a953c4] * configure.ac (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) Using priorizing of jobs. - we now require JobMarket 1.1.4. - ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [5f0c60] * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/SerializablePotential.hpp (modified) FIX: SerializablePotential::stream_from(), several fixes. - ... Mon, 08 Jul 2013 14:22:00 GMT Frederik Heber [bbc422] * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) FIX: Renamed arguments in PairPotential_Angle to make proper sense. ... Mon, 08 Jul 2013 14:22:00 GMT Frederik Heber [e352cb] * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) FIX: PairPotential_Harmonic did wrongly use to ..StrictOrdering in ... Mon, 08 Jul 2013 14:22:00 GMT Frederik Heber [bb1f3f] * src/FunctionApproximation/Extractors.cpp (modified) FIX: Removed doubly present inclusions from Extractors. - these are ... Mon, 08 Jul 2013 14:22:00 GMT Frederik Heber [4b8ab7] * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) FIX: Histogram did not use the pair-wise operator<<(). - his ... Mon, 08 Jul 2013 14:22:00 GMT Frederik Heber [172b6d] * src/builder_init.cpp (modified) FIX: Disclaimer of molecuilder on command-line shows new copyright, too. Wed, 12 Jun 2013 10:11:59 GMT Frederik Heber [5aaa43] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.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/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (modified) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/parseKeySetFile.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/Parameters/Validators/Specific/PotentialTypeValidator.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/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/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) * tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at (modified) * tests/regression/Graph/DestroyAdjacency/testsuite-graph-destroy-adjacency.at (modified) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) * tests/regression/testsuite.at (modified) FIX: Fixed new copyright line since start of 2013 in CodeChecks test. ... Mon, 06 May 2013 21:33:49 GMT Frederik Heber [87d6bd] * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Fragmentation/Mask.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/Parameters/Validators/DiscreteValidator.hpp (modified) * src/Parameters/Validators/RangeValidator.hpp (modified) * src/Parameters/Validators/RangeValidator_impl.hpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/UIElements/Dialog.hpp (modified) FIX: Fixing several clang errors such that we may safely use the ... Fri, 03 May 2013 11:58:26 GMT Frederik Heber [661d2d] * src/Fragmentation/Summation/Makefile.am (modified) FIX: Replaced BOOST_LDFLAGS by flags specific to boost serialization ... Fri, 03 May 2013 11:58:26 GMT Frederik Heber [48d20d] * configure.ac (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (added) * src/Actions/FragmentationAction/FitPotentialAction.def (added) * src/Actions/FragmentationAction/FitPotentialAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/LevMartester.cpp (deleted) * src/Makefile.am (modified) * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/potentials.dox (modified) * src/documentation/install.dox (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/pre/angle_homology.dat (added) * tests/regression/Fragmentation/FitPotential/pre/length_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/testsuite.at (modified) Added new action FitPotentialAction to fit empirical potentials. - ... Fri, 03 May 2013 09:46:46 GMT Frederik Heber [57f14c] * src/FunctionApproximation/Extractors.cpp (modified) FIX: Extractors::_detail::convertElementcountsToTargets() complains ... Fri, 03 May 2013 09:46:46 GMT Frederik Heber [f7ce2b] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) FIX: HomologyGraph::operator<<() did print last comma, too. Fri, 03 May 2013 09:46:45 GMT Frederik Heber [24ac59] * configure.ac (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/Specific/PotentialTypeValidator.cpp (added) * src/Parameters/Validators/Specific/PotentialTypeValidator.hpp (added) * src/UIElements/Makefile.am (modified) Added PotentialTypeValidator. - checks that user has entered a type ... Fri, 03 May 2013 09:46:45 GMT Frederik Heber [931077] * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) Using PotentialTypes in PotentialFactory. - used for creating the ... Fri, 03 May 2013 09:46:45 GMT Frederik Heber [a86666] * src/Potentials/Makefile.am (modified) * src/Potentials/Specifics/PotentialTypes.cpp (added) * src/Potentials/Specifics/PotentialTypes.def (added) * src/Potentials/Specifics/PotentialTypes.hpp (added) * src/Potentials/Specifics/PotentialTypes.undef (added) Added PotentialTypes. Fri, 03 May 2013 09:46:45 GMT Frederik Heber [e2925fd] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Eigenhistogram.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Eigenvalues.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Energy.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Forces.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_LongRangeEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Times.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_VMGEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Eigenhistogram.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Eigenvalues.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Energy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Forces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Times.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentShortRangeResults.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Split long-range calculations into two parts to overcome ... Fri, 03 May 2013 09:46:45 GMT Frederik Heber [5281ff] * 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) REFACTOR: extracted initLookups() in FragmentationLongRangeResults ... Fri, 03 May 2013 09:44:43 GMT Frederik Heber [781408] * src/Fragmentation/Summation/IndexSet.hpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.hpp (modified) FIX: Added inline comparators for IndexSet::ptr, fixed ... Wed, 01 May 2013 07:53:28 GMT Frederik Heber [e4721d3] * src/Jobs/InterfaceVMGJob.cpp (modified) FIX: Average forces in InterfaceVMGJob only if there actually are ... Wed, 01 May 2013 07:53:28 GMT Frederik Heber [10f0cb] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) VERBOSE: Increased verbosity level for grid printing. - grid values ... Wed, 01 May 2013 07:53:26 GMT Frederik Heber [b6b21a] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added option DoPrintDebug to FragmentationAutomationAction. - this ... Wed, 01 May 2013 07:52:55 GMT Frederik Heber [6ff62c] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenhistogram.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenvalues.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Energy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Forces.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentResults.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added DoValenceOnly has new option to FragmentationAutomationAction. ... Thu, 18 Apr 2013 16:23:48 GMT Frederik Heber [53c579] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) Removed fragment as parameter from ... Thu, 18 Apr 2013 16:23:26 GMT Frederik Heber [4f04ab8] * configure.ac (modified) * m4/boost.m4 (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) Using boost::graph to obtain maximum matching for bond degree ... Wed, 17 Apr 2013 18:56:55 GMT Frederik Heber [326000] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) BondGraph::CorrectBondDegree() now allows for incrementing only on a ... Wed, 17 Apr 2013 18:56:54 GMT Frederik Heber [378fc6b] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_observable.hpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) Refactored CorrectBondDegree() and resetBondDegree() out of ... Wed, 17 Apr 2013 18:56:54 GMT Frederik Heber [4b62d3] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) GLMoleculeObject_bond sets width of cylinder according to BondDegree. Wed, 17 Apr 2013 18:56:54 GMT Frederik Heber [2d5137] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp (modified) GLMoleculeObject may set scale independently for each component. - ... Wed, 17 Apr 2013 18:56:54 GMT Frederik Heber [1f693d] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Bond/bond_observable.hpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) Wrapped Bond::BondDegree in getter. - This is preparatory for a new ... Wed, 17 Apr 2013 18:56:53 GMT Frederik Heber [88ada9] * src/Atom/atom_bondedparticle.cpp (modified) Enhanced BondedParticle::CorrectBondDegree() to first fill up ... Wed, 17 Apr 2013 18:56:52 GMT Frederik Heber [c8bbf2] * src/UIElements/Qt4/QtMainWindow.cpp (modified) FIX: Added update() after show() in QtMainWindow. Wed, 17 Apr 2013 18:56:52 GMT Frederik Heber [70db8f] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) FIX: Significantly simplified observer use in GLMoleculeObject_bond. ...