# # ChangeLog for src # # Generated by Trac 1.6 # May 24, 2025, 10:25:35 AM Wed, 13 Feb 2013 15:47:38 GMT Frederik Heber [7d82a5] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/World.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) Changed bond::ptr into boost::shared_ptr. Changes: - refactored ... Wed, 13 Feb 2013 14:29:35 GMT Frederik Heber [c8302f3] * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.hpp (modified) Removed molecule::RemoveBond(s) and ::removeAtom(). - this ... Thu, 17 Jan 2013 22:59:15 GMT Frederik Heber [88c8ec] * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/BondInfo.hpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BreadthFirstSearchAdd.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.hpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) REFACTOR: Replaced all "bond *" appearances by bond::ptr. - this is ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [a30b7f] * src/LevMartester.cpp (modified) Added check on L2 sum and Lmax norms of fitted Tersoff with respect ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [17b3598] * src/LevMartester.cpp (modified) Starting parameters for Tersoff minimization in LevMartester are now ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [d03292] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Implemented box constraints for FunctionModel, using a feature of ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [f48ad3] * src/LevMartester.cpp (modified) * src/Makefile.am (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) LevMartester now uses FunctionModel::setParameter() to set initial ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [eb1efe] * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp (modified) Extended LevMartester to fit a Tersoff potential to the first order ... Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber [bc55c9] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) Added NaN check to Tersoff's parameter_derivative(). Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber [56c5de4] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) Added an offset to the Tersoff potential. Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber [2e9486] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) FIX: Tersoff must sum potential over every of the arguments. Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber [ca8d82] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) FIX: Corrected parameter derivatives of ManyBodyPotential_Tersoff. ... Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber [f904d5] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) Added complete parameter derivatives to ManyBodyPotential_Tersoff. ... Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber [752dc7] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) FIX: Made R and S also fixed parameters, this is in accordance with ... Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber [990a62] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) FIX: Tersoff parameters lambda3, alpha, chi, and omega are now fixed. ... Wed, 19 Dec 2012 15:25:53 GMT Frederik Heber [ffc368] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (added) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp (added) ManyBodyPotential_Tersoff is now correctly implemented. - changed ... Wed, 19 Dec 2012 15:25:53 GMT Frederik Heber [e7579e] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) Changed ManyBodyPotential_Tersoff to also have parameters_t instead ... Wed, 19 Dec 2012 15:25:43 GMT Frederik Heber [76cbd0] * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (added) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.hpp (added) Added PairPotential_MorseUnitTest. - so far, added simple test on ... Wed, 19 Dec 2012 15:25:43 GMT Frederik Heber [b70b53] * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) FIX: Checked PairPotential_Morse::parameter_derivative with Maple. ... Wed, 19 Dec 2012 15:25:43 GMT Frederik Heber [155cc2] * src/LevMartester.cpp (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (added) * src/Potentials/Specifics/PairPotential_Morse.hpp (added) Added PairPotential_Morse with derivatives, used by LevMartester. - ... Wed, 19 Dec 2012 15:25:32 GMT Frederik Heber [9e903b] * src/FunctionApproximation/FunctionArgument.cpp (added) * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/FunctionApproximation/Makefile.am (modified) Added operator<<() to FunctionArgument. Wed, 19 Dec 2012 15:25:32 GMT Frederik Heber [371c8b] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) Added FunctionApproximation::checkParameterDerivatives(). - ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [63b9f7] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) REFACTOR: Split off prepareModel() and prepareOutput() from ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [76e63d] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) Extended FunctionApproximation::operator() to receive JacobianMode ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [3c1465] * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (added) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (added) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.hpp (added) * src/unittests/Makefile.am (modified) Added PairPotential_HarmonicUnitTest. - so far, we test the ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [5b5724] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) FunctionApproximation now uses levmar_der, i.e. additionally the ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [1dca9a] * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) Modified PairPotential_Harmonic to have an internal vector of ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [3ccea3] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) EmpiricalPotential and FunctionModel are now inherited virtually, ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [dac89b1] * src/LevMartester.cpp (modified) Using FunctionModel and setTrainingData in LevMartester. Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [65c42c] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) PairPotential_Harmonic now has additional offset parameter. - do we ... Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber [c62f96] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/LevMartester.cpp (modified) * src/Makefile.am (modified) LevMartester uses now FunctionApproximation. Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber [4f82f8] * src/Potentials/EmpiricalPotential.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) Rewrote EmpiricalPotentials and the specific implementations such ... Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber [66cfc7] * src/FunctionApproximation/FunctionApproximation.cpp (added) * src/FunctionApproximation/FunctionApproximation.hpp (added) * src/FunctionApproximation/FunctionArgument.hpp (added) * src/FunctionApproximation/FunctionModel.hpp (added) * src/FunctionApproximation/Makefile.am (added) * src/Makefile.am (modified) Added new class FunctionApproximation that encapsulates the LevMar ... Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber [dda3e8] * src/Potentials/helpers.hpp (modified) Added Helpers::isEqual() as equality operator taking numerical ... Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber [bf12d1] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/writeTable.hpp (modified) FIX: WriteTable might fail because of size_t difference. - ... Wed, 19 Dec 2012 15:25:03 GMT Frederik Heber [f06d52] * configure.ac (modified) * m4/ax_blas.m4 (added) * m4/ax_lapack.m4 (added) * src/LevMartester.cpp (added) * src/Makefile.am (modified) Added LevMartester that employs levmar package for non-linear ... Sun, 16 Dec 2012 19:47:28 GMT Frederik Heber [fe0355] * src/Fragmentation/Homology/HomologyGraph_getFromKeysetStub.cpp (moved) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Split HomologyGraph_getFromKeyset module off from ... Sun, 16 Dec 2012 19:47:28 GMT Frederik Heber [610c11] * src/Potentials/Makefile.am (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (added) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (added) Added Tersoff potential as first many-body potential. Sun, 16 Dec 2012 19:47:27 GMT Frederik Heber [6bb72a] * src/Makefile.am (modified) * src/Potentials/EmpiricalPotential.hpp (added) * src/Potentials/Makefile.am (added) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (added) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (added) * src/Potentials/helpers.hpp (added) Added general interface EmpiricalPotential and a first potential, the ... Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber [12098a] * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.def (modified) Refactoring: use vector instead of vector in ... Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber [29ea65] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (added) * src/Actions/ShapeAction/StretchShapeAction.def (added) * src/Actions/ShapeAction/StretchShapeAction.hpp (added) * src/UIElements/Views/Qt4/QtShapeController.cpp (modified) * tests/Python/AllActions/options.dat (modified) StretchShapeAction added Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber [3ce0f1] * src/Actions/ShapeAction/RotateShapeAction.cpp (modified) * src/Actions/ShapeAction/RotateShapeAction.def (modified) RotateShapeAction now handles center!=0 Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber [216dad] * src/UIElements/Views/Qt4/QtShapeController.cpp (modified) added shape edit actions to QtShapeController Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber [7e19060] * src/Actions/ShapeAction/CreateShapeAction.cpp (modified) * src/Actions/ShapeAction/RotateShapeAction.cpp (modified) use degrees as angle input in shape actions Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber [a2bbb1] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/RotateShapeAction.cpp (added) * src/Actions/ShapeAction/RotateShapeAction.def (added) * src/Actions/ShapeAction/RotateShapeAction.hpp (added) RotateShapeAction added Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber [0b5057] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/TranslateShapeAction.cpp (added) * src/Actions/ShapeAction/TranslateShapeAction.def (added) * src/Actions/ShapeAction/TranslateShapeAction.hpp (added) * tests/Python/AllActions/options.dat (modified) TranslateShapeAction added Fri, 14 Dec 2012 17:40:12 GMT Frederik Heber [467069] * src/Tesselation/tesselation.cpp (modified) "FIX": allow tesselation of points with negative coordinates Fri, 14 Dec 2012 17:40:12 GMT Frederik Heber [2defa9] * src/Shapes/ShapeFactory.cpp (modified) FIX: (ShapeFactory) wrong test for trivial rotations Fri, 14 Dec 2012 17:40:12 GMT Frederik Heber [13202c] * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/unittests/ShapeOpsUnitTest.cpp (modified) * src/Shapes/unittests/ShapeOpsUnitTest.hpp (modified) FIX: made Cuboid.isOnSurface() robust enough for transformations Fri, 14 Dec 2012 17:40:12 GMT Frederik Heber [148dde0] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: missing map.erase() in GLWorldScene::removeShape() Fri, 14 Dec 2012 17:39:52 GMT Frederik Heber [6d084a4] * src/Jobs/InterfaceVMGJob.cpp (modified) DEBUG: InterfaceVMGJob does not printGrids anymore. - output folder ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [91a565] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) DEBUG: Added some debugging output for constructed HomologyGraphs in ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [28e203] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) FIX: nodes_t and edges_t in HomologyGraph must be a map. - there ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [d058e6] * src/Fragmentation/Homology/HomologyContainer.hpp (modified) Exposed const begin,end of container in HomologyContainer to allow ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [79398d] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) Extended map in FragmentResults to a pair of ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [2dd305] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) Split FragmentResults functionality in cstor into cstor and ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [bfbd4a] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) Storing KeySet file with global ids now. - We now parse in key set ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [d1ba0d] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/moleculelist.cpp (modified) FIX: Forces-Factors are now written with global ids, ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [e71325] * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/AdaptivityMap.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) FIX: All functions in Fragmentation and related now use const string ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [17c03f] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/parseKeySetFile.cpp (added) * src/Fragmentation/Automation/parseKeySetFile.hpp (added) Extracted parseKeySetFile from FragmentationResults, ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [766767] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) appendToHomologyFile() now constructs the HomologyGraph and its ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [372c912] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (modified) Extended HomologyGraph to also be constructable from IndexSet ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [b8f0b25] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) Extended FragmentResults and FragmentationChargeDensity to contain ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [69e065] * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) Added getContributionForIndexSet() and ...Value...() to ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [07266b] * src/Fragmentation/Summation/SetValueMap.hpp (modified) Added SetValueMap::getConstValue() for getting const reference to ... Fri, 14 Dec 2012 17:39:40 GMT Frederik Heber [240c3e] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * tests/Python/AllActions/options.dat (modified) FragmentationAutomationAction now uses a file containing a serialized ... Fri, 14 Dec 2012 17:39:40 GMT Frederik Heber [37ce5d] * src/Makefile.am (modified) FIX: Switched SYSTEM and FILESYSTEM libs in LDADD in src/Makefile.am. Fri, 14 Dec 2012 17:39:31 GMT Frederik Heber [f24af7] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/molecule.cpp (modified) FIX: FillRegularGridAction is now usable with random-atom- ... Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber [55feea1] * src/molecule.cpp (modified) * src/molecule.hpp (modified) molecule::getBoundingShape() can now be given an additional boundary ... Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber [0e2e6c] * src/Filling/Inserter/RandomInserter.cpp (modified) DEBUG: Checked that RandomInserter does its job correctly (correct undo). Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber [35ec9c] * src/Filling/ClusterInterface.cpp (added) * src/Filling/ClusterInterface.hpp (modified) * src/Filling/Makefile.am (modified) Added output operator to ClusterInterface. Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber [5251af] * src/Thermostats/ThermoStatContainer.cpp (modified) FIX: ThermoStatContainer generated a default thermostat but did not ... Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber [4882d5] * 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) * src/Thermostats/ThermoStatContainer.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) Rewrote VerletIntegrationAction to diminish dependence on ... Fri, 14 Dec 2012 17:38:49 GMT Frederik Heber [8b886f] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (added) * src/Actions/MoleculeAction/ChangeBondAngleAction.def (added) * src/Actions/MoleculeAction/ChangeBondAngleAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/ChangeBondAngle/post/water.pdb (added) * tests/regression/Molecules/ChangeBondAngle/pre/water.pdb (added) * tests/regression/Molecules/ChangeBondAngle/testsuite-molecules-change-bond-angle.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added ChangeBondAngleAction that changes the bond angle while keeping ... Fri, 14 Dec 2012 14:30:23 GMT Frederik Heber [f63e41] * src/Actions/BondAction/BondAddAction.cpp (added) * src/Actions/BondAction/BondAddAction.def (added) * src/Actions/BondAction/BondAddAction.hpp (added) * src/Actions/BondAction/BondRemoveAction.cpp (added) * src/Actions/BondAction/BondRemoveAction.def (added) * src/Actions/BondAction/BondRemoveAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/regression/Bond/Add/post/test.pdb (added) * tests/regression/Bond/Add/pre/test.pdb (added) * tests/regression/Bond/Add/testsuite-bond-add.at (added) * tests/regression/Bond/Remove/post/test.pdb (added) * tests/regression/Bond/Remove/pre/test.pdb (added) * tests/regression/Bond/Remove/testsuite-bond-remove.at (added) * tests/regression/Bond/testsuite-bond.at (added) * tests/regression/Makefile.am (modified) * tests/regression/testsuite.at (modified) Added Actions to add and remove a bond in between two atoms. - ... Fri, 14 Dec 2012 14:30:22 GMT Frederik Heber [cb2465] * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/RemoveAction.hpp (modified) FIX: Changed Atom's AddAction and RemoveAction header inclusion ... Fri, 14 Dec 2012 14:29:54 GMT Frederik Heber [e85169] * src/Fragmentation/BondsPerShortestPath.cpp (modified) FIX: Prevented errors message occured due to clearing BondsPerSPList. ... Fri, 14 Dec 2012 14:29:45 GMT Frederik Heber [0cfc27] * LinearAlgebra/configure.ac (modified) * LinearAlgebra/src/unittests/Makefile.am (modified) * configure.ac (modified) * src/unittests/Makefile.am (modified) If no CPPUNIT is found, compilation of unit tests is disabled. - ... Fri, 14 Dec 2012 14:29:34 GMT Frederik Heber [7ace68] * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * tests/regression/Parser/Psi3/pre/testtwocon.psi (modified) * tests/regression/Parser/Psi3/pre/testuhf.psi (modified) Added multiplicity guesser for Psi3Parser's UHF. - TESTFIX: changed ... Fri, 14 Dec 2012 14:29:09 GMT Frederik Heber [14de8e1] * src/Makefile.am (modified) * src/PythonScripting.hpp (added) * src/builder_init.cpp (modified) Molecuilder parses and executes python script 'molecuilder.py' prior ... Fri, 14 Dec 2012 13:03:36 GMT Frederik Heber [7ef5b9a] * src/UIElements/Dialog.hpp (modified) * src/documentation/constructs/actions.dox (modified) DOCU: Extended documentation on how values from the user are ... Fri, 14 Dec 2012 13:03:12 GMT Frederik Heber [6ffc0b] * src/documentation/tests/regression-tests.dox (modified) * src/documentation/tests/unit-tests.dox (modified) DOCU: Enhanced documentation of tests with information from TRAC. Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber [3b75c2] * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) FIX: FormatParserStorage now first deletes the parser, that flushes ... Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber [fc41df] * src/Parser/TremoloParser.cpp (modified) FIX: TremoloParser::readAtomDataLine now uses const ref word and ... Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber [05e2ed] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo/pre/bio.data (added) * tests/regression/Parser/Tremolo/pre/bio.potentials (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-improper.at (added) * tests/regression/Parser/testsuite-parser.at (modified) FIX: TremoloParser did not load/save imprData or torsion correctly. ... Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber [67ab71] * src/Parser/TremoloParser.cpp (modified) * tests/regression/Parser/Tremolo-Potentials/post/test.data (modified) * tests/regression/Parser/Tremolo/post/test.data (modified) * tests/regression/Parser/Tremolo/post/test_xyz.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save.at (modified) FIX: default's resSeq in TremoloParser written inconsistently. - ... Fri, 14 Dec 2012 13:02:49 GMT Frederik Heber [a86cda] * src/Parser/TremoloParser.cpp (modified) FIX: TremoloParser tripped over following tab in ATOMDATA line. - ... Fri, 14 Dec 2012 13:01:57 GMT Frederik Heber [1d02c2d] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) FIX: GLWorldView lacked molecule include. Fri, 14 Dec 2012 13:01:56 GMT Frederik Heber [8ce730] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) FIX: Issue related to LOG_OBSERVER in ... Thu, 13 Dec 2012 10:12:51 GMT Frederik Heber [79ac03] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/AdaptivityMap.hpp (modified) * src/Fragmentation/AtomMask.hpp (added) * src/Fragmentation/Exporters/ExportGraph.cpp (added) * src/Fragmentation/Exporters/ExportGraph.hpp (added) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (added) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (added) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (added) * src/Fragmentation/Homology/FragmentEdge.hpp (added) * src/Fragmentation/Homology/FragmentNode.cpp (added) * src/Fragmentation/Homology/FragmentNode.hpp (added) * src/Fragmentation/Homology/HomologyContainer.cpp (added) * src/Fragmentation/Homology/HomologyContainer.hpp (added) * src/Fragmentation/Homology/HomologyGraph.cpp (added) * src/Fragmentation/Homology/HomologyGraph.hpp (added) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/Makefile.am (added) * src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (added) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Mask.hpp (added) * src/Fragmentation/MoleculeMask.hpp (added) * src/Fragmentation/SortIndex.cpp (added) * src/Fragmentation/SortIndex.hpp (added) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) * src/Graph/AdjacencyList.cpp (added) * src/Graph/AdjacencyList.hpp (added) * src/Graph/CheckAgainstAdjacencyFile.cpp (deleted) * src/Graph/CheckAgainstAdjacencyFile.hpp (deleted) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.hpp (modified) * src/Graph/ListOfLocalAtoms.hpp (added) * src/Graph/Makefile.am (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (added) * src/Graph/unittests/AdjacencyListUnitTest.hpp (added) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (deleted) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp (deleted) * src/Graph/unittests/Makefile.am (modified) * src/MoleculeLeafClass.cpp (modified) * src/MoleculeLeafClass.hpp (modified) * src/MoleculeListClass.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/Makefile.am (modified) * tests/CodeChecks/testsuite-header-dist.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order5.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order6.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order5.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order6.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order5.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order6.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order1.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order2.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order3.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order4.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order5.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order6.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) Merge branch 'Fragmentation_Homology' into Candidate_v1.3.7 ... Thu, 13 Dec 2012 10:05:42 GMT Frederik Heber [a576eb] * src/Fragmentation/SetValues/Fragment.cpp (modified) * src/Fragmentation/SetValues/Fragment.hpp (modified) * src/Fragmentation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/SetValues/unittests/FragmentUnitTest.hpp (modified) * src/Fragmentation/SetValues/unittests/Makefile.am (modified) Added serialization capability to Fragment. - also added unit test ... Thu, 13 Dec 2012 09:32:50 GMT Frederik Heber [12a24c] * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) Added serialization to HomologyContainer and completed ... Thu, 13 Dec 2012 09:32:50 GMT Frederik Heber [67db80] * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.hpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/FragmentNode.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) Added serialization capabilities to FragmentEdge, FragmentNode, and ... Mon, 10 Dec 2012 10:11:00 GMT Frederik Heber [db6f7d] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * tests/JobMarket/pre/heptan.xyz (added) * tests/JobMarket/testsuite-jobmarket-molecuilderrun.at (modified) FIX: We must not assert but check whether full molecule is loaded in ... Mon, 10 Dec 2012 10:11:00 GMT Frederik Heber [cd2591] * 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/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added interpolation-degree as parameter to ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [67fec1] * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Jobs/VMGDataFused.hpp (modified) * src/Jobs/VMGDataMap.hpp (modified) * src/Jobs/VMGData_printKeyNames.hpp (modified) Changed VMGDataMap to contain entries for electron, nuclei, and total ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [82cbe4] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) Writing additional VMGEnergy table to file. Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [a82602] * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) InterfaceVMGJob now also calculates nuclei interaction energy. - ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [5a5196] * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) FIX: Now we OrthogonalSumPerLevel potential * charge per fragment. ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [d4f31f] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) FIX: FragmentResults now sums up long-range correction only for level ...