# # ChangeLog for / # # Generated by Trac 1.6 # Jun 9, 2025, 2:26:18 AM Mon, 08 Apr 2013 11:56:18 GMT Frederik Heber [830b3e] * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) VERBOSE: Changed Parser's verbosity level for stating "Saving changes." Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [7cdf58] * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) ExportGraph_ToFiles now uses one-by-one procedure to store fragments. ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [c39675] * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) Added saturate() to SaturatedFragment. - basically, this is ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [6cabaac] * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) Extended ExportGraph to spill our molecular fragments one by one. - ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [7d5fcd] * src/Fragmentation/Exporters/SaturatedFragment.cpp (added) * src/Fragmentation/Exporters/SaturatedFragment.hpp (added) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (added) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.hpp (added) * src/Fragmentation/Makefile.am (modified) Added SaturatedFragment as a wrapper to KeySet with saturation hydrogens. Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [c3df23] * src/Fragmentation/Exporters/HydrogenPool.cpp (added) * src/Fragmentation/Exporters/HydrogenPool.hpp (added) * src/Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.cpp (added) * src/Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.hpp (added) * src/Fragmentation/Exporters/unittests/Makefile.am (added) * src/Fragmentation/Makefile.am (modified) * src/unittests/Makefile.am (modified) Added HydrogenPool for controlling a set of saturation hydrogens. Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [3b0d2a] * src/cleanUp.cpp (modified) Added more timing output to cleanUp(). - final printTiming() is now ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [8652a30] * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Fragmentation/Makefile.am (modified) Moved some functions from ExportGraph_ToFiles into ExportGraph. - ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [22b786] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.def (modified) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (added) * src/Actions/GraphAction/UpdateMoleculesAction.def (added) * src/Actions/GraphAction/UpdateMoleculesAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) Made SubgraphDissection a MakroAction and added ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [560cbf] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (added) * src/Actions/GraphAction/DestroyAdjacencyAction.def (added) * src/Actions/GraphAction/DestroyAdjacencyAction.hpp (added) * src/Actions/Makefile.am (modified) * tests/regression/Graph/DestroyAdjacency/pre/ethane.pdb (added) * tests/regression/Graph/DestroyAdjacency/testsuite-graph-destroy-adjacency.at (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added a DestroyAdjacencyAction with undo/redo. - also added ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [055ad7] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.def (modified) * tests/regression/Graph/CreateAdjacency/post/ethane-half.pdb (added) * tests/regression/Graph/CreateAdjacency/post/ethane.pdb (added) * tests/regression/Graph/CreateAdjacency/pre/ethane.xyz (added) * tests/regression/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added Undo/Redo functionality to CreateAdjacencyAction. - also ... Mon, 08 Apr 2013 11:44:05 GMT Frederik Heber [f2fda6] * configure.ac (modified) Set version to 1.3.13. - MoleCuilder library is now 11:4:1. - ... Fri, 22 Mar 2013 00:04:17 GMT Frederik Heber [ddeed2] * configure.ac (modified) * src/cleanUp.cpp (modified) Using enhanced precision of CodePatterns' Chronos. - we now require ... Fri, 22 Mar 2013 00:04:17 GMT Frederik Heber [d948b4] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) atom_bondedparticle::addBond() returns no longer const bond::ptr. - ... Fri, 22 Mar 2013 00:04:17 GMT Frederik Heber [31021ab] * LinearAlgebra/configure.ac (modified) * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (modified) * LinearAlgebra/src/unittests/VectorSetUnitTest.cpp (modified) * LinearAlgebra/src/unittests/VectorSetUnitTest.hpp (modified) * src/Box.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) Optimized Bondgraph detection. - VectorSet::minDistance() now ... Fri, 22 Mar 2013 00:04:17 GMT Frederik Heber [cf1183] * src/LinkedCell/LinkedCell_Controller.cpp (modified) FIX: LinkedCell_Controller::updateModels() tried toString()'ing NULL. Fri, 22 Mar 2013 00:04:16 GMT Frederik Heber [4f54b3] * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) FIX: AllAtomsInsideVolumeAction stored state with additional ... Fri, 22 Mar 2013 00:03:38 GMT Frederik Heber [5589e7e] * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (added) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def (added) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/StoreSaturatedFragment/post/BondFragment0.xyz (added) * tests/regression/Fragmentation/StoreSaturatedFragment/pre/C6-0.Sheet.Aligned.xyz (added) * tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added StoreSaturatedFragmentAction to save a set of atoms satured ... Mon, 18 Mar 2013 14:46:12 GMT Frederik Heber [d5b90b] * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * tests/regression/Parser/Xyz/post/HugeCoordinates.xyz (added) * tests/regression/Parser/Xyz/pre/HugeCoordinates.xyz (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) FIX: XyzParser had lacking precision beyond coordinates of 100000. ... Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [15463a] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) Extended LinkedCell_Controller::getBestModel() to take box into ... Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [335011] * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) VERBOSE: Trimmed down verbosity when creating a bond graph and on ... Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [3b0cfc] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) FIX: Coloring of bond halves was wrong way around. Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [fae816] * data/molecules/water.pdb (modified) FIX: Water molecule in data/molecules had wrong bond angle. Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [03abd0] * src/World.cpp (modified) FIX: World::getLinkedCell() does not allow distance less than 1. - ... Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [1f5e97] * src/Parser/PdbParser.cpp (modified) FIX: PdbParser::saveLine() did not restrict some id values. - ... Mon, 18 Mar 2013 13:31:46 GMT Frederik Heber [105b72] * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.hpp (modified) FIX: PdbParser skipped when coordinate exceeded 9999.999. - the ... Sun, 17 Mar 2013 18:27:37 GMT Frederik Heber [e9bdef] * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0001.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0003.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0007.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0008.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0013.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0018.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0027.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0028.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0030.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0033.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0035.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0007.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0008.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0013.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0027.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0028.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0030.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat (modified) TESTFIX: Analysis' DipoleAngularCorrelation() and BinData() suffered ... Mon, 11 Mar 2013 22:31:46 GMT Frederik Heber [8c9049] * src/documentation/constructs/qt-gui.dox (modified) * src/documentation/constructs/shaperegistry.dox (modified) DOCU: Updates for qt-gui and shaperegistry documentation. Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [5c3ad5] * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) Modified SaturationPotential to allow fitting to e.g. HCC as well. ... Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [64bdfd] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) Changed Extractor's combineArguments() to neglect same arguments. - ... Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [035c0d] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) Removed typedef charges_t from FunctionModel, using ... Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [da2d5c] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.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) Removed parameter charges from getFragmentSpecificExtractor(). Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [3d2559] * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/SerializablePotential.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) Added virtual stream_to/from functions to SerializablePotential. - ... Wed, 27 Feb 2013 12:43:09 GMT Frederik Heber [dbcc47] * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) Arguments for PairPotential_Angle were used in wrong order. Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [863456] * src/Fragmentation/Fragmentation.cpp (modified) Small changes to printAtomMask(). Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [5a4955] * src/Fragmentation/Fragmentation.cpp (modified) We remove all single-index fragments in FragmentMolecule(). - this ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [276ac6] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) FIX: ExportGraph_ToFiles needs to know about hydrogen treatment to ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [a82127] * src/Potentials/Specifics/SaturationPotential.cpp (modified) FIX: SaturationPotential takes both angles in each triple. - ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [4ff79c] * src/LevMartester.cpp (modified) LevMartester casts FunctionModel to SerializablePotential if possible ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [77552d] * src/LevMartester.cpp (modified) FIX: LevMartester gives which distance in written table refers to ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [46fcc0] * src/LevMartester.cpp (modified) LevMartester has new option fragment such that fragment to use as ... Wed, 27 Feb 2013 12:42:36 GMT Frederik Heber [39a07a] * src/Fragmentation/Homology/HomologyContainer.hpp (modified) HomologyContainer now gives iterator on its keys, i.e. stored ... Wed, 27 Feb 2013 12:42:36 GMT Frederik Heber [9291d04] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.def (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/HydrogenSaturation_enum.hpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * tests/Python/AllActions/options.dat (modified) Split saturation with hydrogen of treatment of hydrogen. - now ... Wed, 27 Feb 2013 12:42:36 GMT Frederik Heber [c7c615] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FIX: FragmentationAction gave wrong number of molecules. Wed, 27 Feb 2013 12:40:25 GMT Frederik Heber [1edc87] * configure.ac (modified) Set version to 1.3.12. - MoleCuilder library is now 11:3:1. - ... Wed, 27 Feb 2013 12:39:33 GMT Frederik Heber [c16cce] * src/LevMartester.cpp (modified) Training fragments are sorted by error to fit value into a map. - ... Wed, 27 Feb 2013 12:39:33 GMT Frederik Heber [3e236e] * src/LevMartester.cpp (modified) LevMartester now fits potentials given on the command-line. - ... Wed, 27 Feb 2013 12:39:33 GMT Frederik Heber [d76ce74] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (added) * src/Potentials/PotentialFactory.hpp (added) Added PotentialFactory for creating potentials. Wed, 27 Feb 2013 12:39:15 GMT Frederik Heber [05f437] * src/LevMartester.cpp (modified) LevMartester now contains three generalized fits to Angle, Morse, and ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [e36ba2] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) FunctionModel extended by triplefunction setter, does nothing by ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [0dad5f] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) SaturationPotential now has an internal triplefunction. - ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [775dd1a] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/helpers.hpp (modified) Triplefunction for Saturation and Tersoff potential have to be given ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [d52819] * src/FunctionApproximation/FunctionModel.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/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) Extracted initial parameter setting per specific potential to ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [7b019a] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.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/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) Extended FunctionModel by getFragmentSpecificExtractor() definition. ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [69fcba] * src/FunctionApproximation/Extractors.cpp (modified) FIX: Extractor's convertTargetsToArguments() did not set argument_t's ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [9897ee9] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added combineArguments to Extractors. - this is required for ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [df350c] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added reorderArgumentsByParticleTypes() to Extractors. - this is ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [caa00e9] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added gatherAllDistancesFromFragment() to Extractors. - ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [dbf8c8] * src/LevMartester.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/SaturationPotential.cpp (modified) FIX: Now default parameters are present for every potential and used ... Wed, 27 Feb 2013 12:36:17 GMT Frederik Heber [b760bc3] * src/Potentials/Makefile.am (modified) * src/Potentials/ParticleTypeCheckers.cpp (added) * src/Potentials/ParticleTypeCheckers.hpp (added) * 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/SaturationPotential.cpp (modified) Added ParticleTypeChecker functions in own namespace and added checks ... Wed, 27 Feb 2013 11:45:14 GMT Frederik Heber [93e908] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) Added SaturationPotential::symmetrizeTypes() to get types for both ... Wed, 27 Feb 2013 11:44:01 GMT Frederik Heber [55fe788] * 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/unittests/ManyBodyPotential_TersoffUnitTest.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) All specific Potentials now assert that arguments have charges ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [b3eabc] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) SaturationPotential now requires symmetric distances. Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [b10ada] * src/LevMartester.cpp (modified) Initial parameters in LevMartester randomized for Morse and Angle. ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [0496af] * src/LevMartester.cpp (modified) LevMartester uses SerializationPotential::operator>>() to print ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [ed2551] * src/LevMartester.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) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.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) All Pair_.. and ManyBodyPotentials are now also derived from ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [6efcae] * src/LevMartester.cpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Exceptions.hpp (added) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialRegistry.hpp (modified) * src/Potentials/SerializablePotential.cpp (added) * src/Potentials/SerializablePotential.hpp (added) * 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) * src/Potentials/Specifics/SaturationPotential.hpp (modified) * src/Potentials/unittests/Makefile.am (added) * src/Potentials/unittests/SerializablePotentialUnitTest.cpp (added) * src/Potentials/unittests/SerializablePotentialUnitTest.hpp (added) * src/Potentials/unittests/stubs/SerializablePotentialMock.cpp (added) * src/Potentials/unittests/stubs/SerializablePotentialMock.hpp (added) * src/unittests/Makefile.am (modified) SerializablePotential is new type to be stored in PotentialRegistry. ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [67cd3a] * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialRegistry.cpp (added) * src/Potentials/PotentialRegistry.hpp (added) * 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) * src/Potentials/Specifics/SaturationPotential.hpp (modified) Added a PotentialRegistry for EmpiricalPotentials. - added virtual ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [201199] * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/potentials.dox (added) DOCU: Added documentation explaining purpose of potentials. Mon, 25 Feb 2013 17:29:08 GMT Frederik Heber [1f3b2a] * src/Parser/Exceptions.hpp (modified) FIX: double inclusion prevention of Parser/exceptions corrected. Mon, 25 Feb 2013 17:28:58 GMT Frederik Heber [691be4] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionArgument.cpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) FunctionArgument now contains charges, too, and rewrote Extractors ... Mon, 25 Feb 2013 17:28:58 GMT Frederik Heber [d94e7e] * src/LevMartester.cpp (modified) SaturationPotential test part in LevMartester checks whether graphs ... Mon, 25 Feb 2013 17:28:58 GMT Frederik Heber [edac7c] * src/LevMartester.cpp (modified) DEBUG: LevMartester now looks for the oxygen atom in water as ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber [dd8094] * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/LevMartester.cpp (modified) Added getTrainingOutputAverage() used to initialize all_energy_offset ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber [2ba2ed] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) FIX: SaturationPotential's parameter derivatives seem to be working ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber [b17e0f] * src/LevMartester.cpp (modified) Using getFirstGraphwithTimesSpecificElement() in main() of ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber [e920d3d] * src/Fragmentation/Homology/FragmentNode.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/LevMartester.cpp (modified) Added getFirstGraphwithTimesSpecificElement(). - this allows to ... Sun, 24 Feb 2013 13:00:40 GMT Frederik Heber [6cfb355] * configure.ac (modified) Set version to 1.3.11. - MoleCuilder library is now 11:2:1. - ... Sun, 24 Feb 2013 13:00:40 GMT Frederik Heber [c29c0a] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * tests/regression/Filling/RegularGrid/post/solved_double_sles.data (modified) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid-with-surface.at (modified) FIX: triangleintersectionlist suffered numerical instabilities. - ... Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [0cd225] * src/documentation/install.dox (modified) DOCU: Updates optional enable targets and required and optional ... Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [dd966f] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) DOCUFIX: Extra $ in documentation of ManyBodyPotential_Tersoff. Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [eee1b7] * src/documentation/constructs/actions.dox (modified) * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/parameters.dox (added) * src/documentation/constructs/qt-gui.dox (modified) * src/documentation/constructs/queries.dox (added) * src/documentation/constructs/shaperegistry.dox (added) * src/documentation/constructs/shapes.dox (modified) * src/documentation/constructs/validators.dox (added) DOCU: Documentation on ShapeRegistry, QtUI changes, validators, and ... Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [c91572] * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) DOCUFIX: Replaced \text by \mathrm in some formulas. Sun, 24 Feb 2013 12:59:18 GMT Frederik Heber [d760bb] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/UniqueFragments.hpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) REFACTOR: PowerSetGenerator now creates all orders in one go, not ... Sun, 24 Feb 2013 12:59:18 GMT Frederik Heber [b6b5b8] * src/Graph/AdjacencyList.cpp (modified) FIX: Removed Assert of parsable file in AdjacencyList cstor. Sun, 24 Feb 2013 12:59:18 GMT Frederik Heber [37e910] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) FIX: Qt3D changed cylinder offset to barimetric center. - this ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [04cc7e] * src/FunctionApproximation/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/FunctionApproximation/writeDistanceEnergyTable.hpp (added) * src/LevMartester.cpp (modified) Added pretty printer for distance-energy tables. - added ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [52e7da] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) * src/LevMartester.cpp (modified) Angle training now also uses TrainingData. Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [ac868ee] * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (added) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (added) * src/FunctionApproximation/unittests/Makefile.am (modified) Added unit test for functions in Extractors namespace. Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [49f163] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/LevMartester.cpp (modified) Added gatherAllSymmetricDistanceArguments(). - using it for ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [63e786] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Refactored realignElementTargets() out of gatherDistancesOfTuples(). Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [c211f7] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Refactored convertElementcountsToTargets() out of ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [bc6705] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Refactored getElementCounts out of gatherDistancesOfTuples(). Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [301dbf] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/LevMartester.cpp (modified) Refactored gatherDistanceOfTuples(). - it is now able to work on ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [4a77be7] * src/Fragmentation/SetValues/Fragment.hpp (modified) Added charge_t to Fragment. Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [69ab84] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/LevMartester.cpp (modified) FunctionApproximation's cstor now accepts TrainingData instance directly. Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [68172a] * src/FunctionApproximation/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (added) * src/FunctionApproximation/TrainingData.hpp (added) * src/LevMartester.cpp (modified) Shifted class TrainingData into its own module. Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [f68c68] * src/LevMartester.cpp (modified) Tersoff now also uses TrainingData class. - shifted calculation of ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [8aa597] * src/FunctionApproximation/Extractors.cpp (added) * src/FunctionApproximation/Extractors.hpp (added) * src/FunctionApproximation/Makefile.am (modified) * src/LevMartester.cpp (modified) Extracted namespace Extractors into own module. - placed ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [355af8] * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/FunctionApproximation/unittests/FunctionArgumentUnitTest.cpp (added) * src/FunctionApproximation/unittests/FunctionArgumentUnitTest.hpp (added) * src/FunctionApproximation/unittests/Makefile.am (added) * src/unittests/Makefile.am (modified) Argument_t now has two Comparators on indices or distance. - added ...