# # ChangeLog for src/Potentials/Specifics # # Generated by Trac 1.4.4 # Apr 11, 2025, 3:28:19 PM Thu, 02 Mar 2017 07:14:22 GMT Frederik Heber [4ecb2d] * LinearAlgebra/doc/am_doxygen_include.am (deleted) * LinearAlgebra/m4 (deleted) * Makefile.am (modified) * ThirdParty/LinearAlgebra/.gitignore (moved) * ThirdParty/LinearAlgebra/AUTHORS (moved) * ThirdParty/LinearAlgebra/COPYING (moved) * ThirdParty/LinearAlgebra/ChangeLog (moved) * ThirdParty/LinearAlgebra/INSTALL (moved) * ThirdParty/LinearAlgebra/LinearAlgebra-debug.pc.in (moved) * ThirdParty/LinearAlgebra/LinearAlgebra.pc.in (moved) * ThirdParty/LinearAlgebra/Makefile.am (moved) * ThirdParty/LinearAlgebra/NEWS (moved) * ThirdParty/LinearAlgebra/README (moved) * ThirdParty/LinearAlgebra/bootstrap (moved) * ThirdParty/LinearAlgebra/build-aux/README (moved) * ThirdParty/LinearAlgebra/configure.ac (moved) * ThirdParty/LinearAlgebra/doc/Doxyfile (moved) * ThirdParty/LinearAlgebra/doc/Makefile.am (moved) * ThirdParty/LinearAlgebra/doc/am_doxygen_include.am (added) * ThirdParty/LinearAlgebra/libLinearAlgebra_config.h.in (moved) * ThirdParty/LinearAlgebra/m4 (added) * ThirdParty/LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Line.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Line.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinePoint.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Makefile.am (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Plane.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Plane.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Space.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Space.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Vector.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Vector.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorContent.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorInterface.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/defs.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/fast_functions.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/leastsquaremin.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/vector_ops.hpp (moved) * ThirdParty/LinearAlgebra/src/documentation/Makefile.am (moved) * ThirdParty/LinearAlgebra/src/documentation/groups.dox (moved) * ThirdParty/LinearAlgebra/src/documentation/lines.dox (moved) * ThirdParty/LinearAlgebra/src/documentation/mainpage.dox (moved) * ThirdParty/LinearAlgebra/src/unittests/LineUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/LineUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/Makefile.am (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/PlaneUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/PlaneUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/RealSpaceMatrixUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/RealSpaceMatrixUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/TestRunnerMain.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/UnitTestMain.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorContentUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorSetUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorSetUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/Makefile.am (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/atlocal.in (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-date_in_dox.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-header-dist.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-project-disclaimer.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite.at (moved) * configure.ac (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved LinearAlgebra sub-package into ThirdParty folder. - needed to ... Fri, 11 Nov 2016 14:25:36 GMT Frederik Heber [1155ba] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Converted filterArguments... into faster filter, renamed other to ... Fri, 11 Nov 2016 14:25:36 GMT Frederik Heber [9c793c] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.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) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) All ..Potentials now return BindingModel instead of HomologyGraph, ... Fri, 11 Nov 2016 14:25:35 GMT Frederik Heber [884d8c] * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.hpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (modified) FIX: FourBodyPotential_Improper does not need to override ... Fri, 11 Nov 2016 14:25:30 GMT Frederik Heber [2124aa] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Extractors::reorderArgumentsByParticleTypes() rewritten to scan for ... Fri, 04 Nov 2016 09:37:51 GMT Frederik Heber [e60558] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) Extractors require additionally the binding graph of the fragment ... Fri, 04 Nov 2016 09:37:50 GMT Frederik Heber [67044a] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) Extractors require additional binding model which EmpiricalPotentials ... Fri, 04 Nov 2016 09:37:50 GMT Frederik Heber [d5ca1a] * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.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) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) Added HomologyGraph describing binding model to every EmpiricalPotential. Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [7d320c] * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) MEMFIX: Static coordinator instances of specificv potentials need to ... Thu, 21 Aug 2014 06:43:46 GMT Frederik Heber [748fc7] * src/Actions/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/builder_init.cpp (modified) * src/unittests/Makefile.am (modified) libMolecuilder is now a shared library. - linking error ... Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [e9e86f] * src/Actions/unittests/Makefile.am (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) FIX: UnitTestMain placed into convenience libUnitTest. - removed ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [e1fe7e] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.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) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp (modified) * src/Potentials/helpers.hpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FunctionModel now uses list_of_arguments to split sequence of subsets ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [16227a] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.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) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) Removed FunctionModel::getSpecificExtractor() that is not needed ... Fri, 27 Jun 2014 11:43:27 GMT Frederik Heber [0932c2] * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (modified) * src/documentation/constructs/potentials.dox (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) FIX: RandomNumberEngine_Encapsulation::clone() did not set the seed ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [a2a2f7] * src/Actions/ActionSequence.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Box.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) Huge warning fix. - fixed unused variables. - fixed set but unused ... Sun, 06 Oct 2013 08:45:08 GMT Frederik Heber [94453f1] * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.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) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) Added getCoordinator() to EmpiricalPotential interface. - ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [ff90e3] * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/PotentialTypes.def (modified) Renamed potential token harmonic to harmonic_bond. Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [791a12] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (added) * src/Potentials/Specifics/FourBodyPotential_Improper.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (added) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) * tests/regression/Fragmentation/FitPotential/pre/improper_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added improper potential based on torsion potential with flipped ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [a74a96] * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (modified) Made function_theta of FourBodyPotential_Torsion virtual. - also ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [e2037e] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (added) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (added) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) * tests/regression/Fragmentation/FitPotential/pre/torsion_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added FourBodyPotential_Torsion. - also added regression test to ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [484e2a] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (moved) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (moved) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp (moved) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.hpp (moved) Renamed PairPotential_Angle -> ThreeBodyPotential_Angle and also ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [1413f4] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (added) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp (added) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.hpp (added) * tests/regression/Fragmentation/FitPotential/pre/lj_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added LennardJones pair potential. - this is for later fitting ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [51e0e3] * configure.ac (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) Added two filter functions to Extractors. - renamed ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [0f5d38] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/helpers.hpp (modified) Added getSpecificFilter() and getSpecificArgumentCount() to ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [f0025d] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Renamed getFragmentSpecificExtractor() -> getSpecificExtractor(). Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [a82d33] * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) FIX: Default cstor of specific potentials did not allocate parameter ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [713888] * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/SerializablePotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Made PotentialFactory friend of all specific potentials and added ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [acc9b1] * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PotentialTypes.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) FIX: Added new copyright lines to files in src/Potentials, too. Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [b15ae7] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) Removed energy_offset from ManyBodyPotential_Tersoff. Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [1e242a] * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Removed energy_offset from PairPotential_Angle. - regression test ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [065a16] * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) Removed energy_offset from PairPotential_Harmonic. Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [919c8a] * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Removed energy_offset from PairPotential_Morse. - regression test ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [1e565c] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/SaturationPotential.cpp (deleted) * src/Potentials/Specifics/SaturationPotential.hpp (deleted) Removed SaturationPotential. - SaturationPotential can be seen as a ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [7e5b94] * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) CompoundPotential now combines ConstantPotential and ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [8203ce8] * src/FunctionApproximation/Extractors.cpp (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (added) * src/Potentials/Specifics/ConstantPotential.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (added) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) Added ConstantPotential to fit a non-zero offset in potential energy. ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [2bde72] * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) FIX: Removed CodePattern/Assert include from various PairPotential ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [fdd23a] * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialRegistry.hpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) EmpiricalPotential now inherits/combines FunctionModel, ... Mon, 08 Jul 2013 14:22:00 GMT Frederik Heber [bbc422] * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) FIX: Renamed arguments in PairPotential_Angle to make proper sense. ... Mon, 08 Jul 2013 14:22:00 GMT Frederik Heber [e352cb] * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) FIX: PairPotential_Harmonic did wrongly use to ..StrictOrdering in ... Fri, 03 May 2013 09:46:45 GMT Frederik Heber [a86666] * src/Potentials/Makefile.am (modified) * src/Potentials/Specifics/PotentialTypes.cpp (added) * src/Potentials/Specifics/PotentialTypes.def (added) * src/Potentials/Specifics/PotentialTypes.hpp (added) * src/Potentials/Specifics/PotentialTypes.undef (added) Added PotentialTypes. 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 [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 [a82127] * src/Potentials/Specifics/SaturationPotential.cpp (modified) FIX: SaturationPotential takes both angles in each triple. - ... 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 [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 [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 17:28:58 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 17:28:57 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 ... 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 12:58:06 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 12:57:26 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. 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 15:25:31 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 [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 [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 ... 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 ...