# # ChangeLog for src # # Generated by Trac 1.6 # May 24, 2025, 9:56:07 PM 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() 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. ...