# # ChangeLog for src # # Generated by Trac 1.6 # May 24, 2025, 2:36:51 PM 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 ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [4ec18b] * src/LevMartester.cpp (modified) Added class TrainingData encapsulating the training input and output ... Sun, 24 Feb 2013 12:58:06 GMT Frederik Heber [8ea8c8] * src/LevMartester.cpp (modified) DEBUG: Adapted graph getting to Butane sampling. Sun, 24 Feb 2013 12:58:06 GMT Frederik Heber [9340ee] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) Added PairPotential_Angle training to LevMartester. Sun, 24 Feb 2013 12:57:42 GMT Frederik Heber [94f567] * src/Potentials/Specifics/SaturationPotential.cpp (modified) Added check if result of SaturationPotential::parameter_derivative is ... Sun, 24 Feb 2013 12:57:42 GMT Frederik Heber [1f06896] * src/LevMartester.cpp (modified) DEBUG: Added msg about L2 contribution. Sun, 24 Feb 2013 12:57:42 GMT Frederik Heber [19fa3b] * src/LevMartester.cpp (modified) FIX: Removing average energy from order1-fit to Saturation potential. Sun, 24 Feb 2013 12:57:42 GMT Frederik Heber [40fff1] * src/LevMartester.cpp (modified) Performing fit got CH4 now with SaturatonPotential instead of Tersoff. Sun, 24 Feb 2013 12:57:26 GMT Frederik Heber [4ffbb7] * src/Potentials/Makefile.am (modified) * src/Potentials/Specifics/SaturationPotential.cpp (added) * src/Potentials/Specifics/SaturationPotential.hpp (added) Added SaturatonPotential that combines a Morse and a Angle potential. Sun, 24 Feb 2013 12:57:26 GMT Frederik Heber [086070] * 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) Moved all setParameters() from header files into module. - also ... Sun, 24 Feb 2013 12:57:26 GMT Frederik Heber [c92c0d] * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (added) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.hpp (added) Added unit test for PairPotential_Angle. - also corrected ... Sun, 24 Feb 2013 12:57:26 GMT Frederik Heber [a63187] * src/Potentials/Makefile.am (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (added) * src/Potentials/Specifics/PairPotential_Angle.hpp (added) Added PairPotential_Angle. Sun, 24 Feb 2013 12:57:26 GMT Frederik Heber [51c502] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) FIX: GLMoleculeObject_molecule::update() did not use ObserverLog ... Sat, 23 Feb 2013 16:24:27 GMT Frederik Heber [69b30a] * src/LevMartester.cpp (modified) FIX: boost::iarchive includes needs to go before MemDebug in ... Sat, 16 Feb 2013 11:32:44 GMT Frederik Heber [ef918c] * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) DISTFIX: typo in header files. Fri, 15 Feb 2013 17:09:58 GMT Frederik Heber [1f1f80] * src/Jobs/Grid/SamplingGrid.cpp (modified) FIX: SamplingGrid::get..GridPoint() checks for begin, end bounds. - ... Fri, 15 Feb 2013 17:09:58 GMT Frederik Heber [313f83] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) SamplingGrid::operator*=() can now deal with incongruent windows. - ... Fri, 15 Feb 2013 17:09:58 GMT Frederik Heber [fb3485] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) Refactored copy routine out of AddOntoWindow(). - this is ... Fri, 15 Feb 2013 17:09:57 GMT Frederik Heber [c0e8fb] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) Added SamplingGrid::isCongruent(). - also added unit test function. Fri, 15 Feb 2013 17:09:57 GMT Frederik Heber [56b04c] * src/Jobs/Grid/SamplingGrid.cpp (modified) FIX: SamplingGrid::getNearestLowerGridPoint(), and ::get..Upper..() ... Fri, 15 Feb 2013 17:09:57 GMT Frederik Heber [620517] * src/Jobs/Grid/Makefile.am (modified) * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGrid_inline.hpp (added) FIX: SamplingGrid::getWindowGridPoints() was broken. - or at least ... Fri, 15 Feb 2013 17:07:49 GMT Frederik Heber [b123a5] * src/Jobs/InterfaceVMGDebugGridJob.cpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (added) * src/Jobs/WindowGrid_converter.hpp (added) Shifted functions to add window onto grid into own namespace. - ... Fri, 15 Feb 2013 17:07:31 GMT Frederik Heber [8f3cdd] * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) Adapted VMGJob and its Interface to new non-zero window use. - we ... Fri, 15 Feb 2013 09:52:02 GMT Frederik Heber [64bafe0] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) SamplingGrid's Window start and end are now always set on a grid ... Fri, 15 Feb 2013 09:51:49 GMT Frederik Heber [c6355f] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) FIX: New non-zero window operations of SamplingGrid are now fully ... Fri, 15 Feb 2013 09:51:49 GMT Frederik Heber [de6dfb] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) Extending AddOntoWindow() by prefactor, can deal with differently ... Fri, 15 Feb 2013 09:51:49 GMT Frederik Heber [e2404f] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) New SamplingGrid::setDomainSize() and ::setWindowSize() helper functions. Fri, 15 Feb 2013 09:51:48 GMT Frederik Heber [1a00bb] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) Rewrote parts of SampingGrid such that a window of non-zero entries ... Fri, 15 Feb 2013 09:51:39 GMT Frederik Heber [98f8fe] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) SamplingGrid must have power of 2 grid size. - all number ... Thu, 14 Feb 2013 13:29:24 GMT Frederik Heber [3d9a8d] * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.cpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/MPQCJob_binding.hpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) SamplingGrid has no more size parameter but an end array. - this ... Thu, 14 Feb 2013 12:26:12 GMT Frederik Heber [e089fb] * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) Moved particle arrays into a new struct in VMGJob. - also the docu ... Thu, 14 Feb 2013 12:26:12 GMT Frederik Heber [1b01e9] * src/Jobs/MPQCJob_binding.hpp (added) * src/Jobs/Makefile.am (modified) * src/Server.cpp (modified) * src/poolworker.cpp (modified) FIX: Server missed forced binding to MPQCJob. - present was only to ... Thu, 14 Feb 2013 12:26:01 GMT Frederik Heber [6752dc] * src/documentation/install.dox (modified) DOCU: Extended installation explanations extensively. Thu, 14 Feb 2013 12:25:52 GMT Frederik Heber [0a7834] * src/documentation/install.dox (modified) DOCU: Updates optional enable targets and required and optional ... Thu, 14 Feb 2013 12:25:42 GMT Frederik Heber [d0faa8] * src/documentation/tests/regression-tests.dox (modified) DOCU: Added note on failing regression test only on installcheck. Wed, 13 Feb 2013 16:38:23 GMT Frederik Heber [312c0d] * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (added) FIX: HomologyContainerUnitTest does not require libMolecuilderUI ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [4d4ef8] * src/Jobs/MPQCCommandJob_binding.hpp (added) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob_binding.hpp (added) * src/Jobs/VMGJob_binding.hpp (added) * src/Makefile.am (modified) * src/Server.cpp (modified) * src/poolworker.cpp (modified) FIX: Enforce binding to libMolecuilderJobs for Server and PoolWorker. ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [cf1d82] * src/Parameters/Parameter.hpp (modified) * src/Parameters/ParameterInterface.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value.hpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) Parameter now contains Value, not inherits. - added several ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [6440c6] * src/Parameters/Makefile.am (modified) * src/Parameters/Parameter.hpp (modified) * src/Parameters/ParameterAsString.hpp (deleted) * src/Parameters/ParameterInterface.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value.hpp (modified) * src/Parameters/ValueInterface.hpp (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_Parameters.hpp (modified) * src/Parser/Makefile.am (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/ParameterStorage.hpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) Reworked inheritance graph of Parameter and Value. - Value now ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [b11f5e] * src/Parameters/Parameter.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value.hpp (modified) * src/Parameters/ValueAsString.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * src/Parameters/Value_string.cpp (modified) * src/Parameters/Value_string.hpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) FIX: Value::setAsString(), ::getAsString take const ref. - arg ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [9e6722] * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value_impl.hpp (modified) FIX: Made Parameter functions inline. Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [2665d3] * src/Parameters/Makefile.am (modified) * src/Parameters/Value.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * src/Parameters/Value_string.cpp (added) * src/Parameters/Value_string.hpp (added) * src/Parser/Parameters/unittests/Makefile.am (modified) String specializations of Value placed into own module. Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [50eff3] * src/Parameters/Value_impl.hpp (modified) FIX: Value::getValidRange() and ::getValidValues() were broken. - ... Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [4e904b] * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/molecule.cpp (modified) Removed atom::IsInShape(). - this makes libMolecuilderAtom not ... Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [a2f5e5] * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/Psi3Parser.hpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) FIX: Cleaned up includes in Psi3Parser_Parameters. Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [42f2f0] * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) FIX: MpqcParser_Parameter now simply uses Parameter instead ... Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [58fccca] * src/Parser/XyzParser.cpp (modified) FIX: XyzParser::load() stumbled if no empty line between timesteps. ... Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [b4b364] * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) FIX: Parameter unit tests all lacked CodePatterns lib. 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()