# # ChangeLog for src/LevMartester.cpp # # Generated by Trac 1.4.4 # Mar 26, 2025, 3:19:16 PM Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber <heber@…> [77552d] * src/LevMartester.cpp (modified) FIX: LevMartester gives which distance in written table refers to ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber <heber@…> [46fcc0] * src/LevMartester.cpp (modified) LevMartester has new option fragment such that fragment to use as ... Wed, 27 Feb 2013 12:39:33 GMT Frederik Heber <heber@…> [c16cce] * src/LevMartester.cpp (modified) Training fragments are sorted by error to fit value into a map. - ... Wed, 27 Feb 2013 12:39:33 GMT Frederik Heber <heber@…> [3e236e] * src/LevMartester.cpp (modified) LevMartester now fits potentials given on the command-line. - ... Wed, 27 Feb 2013 12:39:15 GMT Frederik Heber <heber@…> [05f437] * src/LevMartester.cpp (modified) LevMartester now contains three generalized fits to Angle, Morse, and ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber <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 <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 <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 <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 11:45:14 GMT Frederik Heber <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 ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber <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 <heber@…> [b10ada] * src/LevMartester.cpp (modified) Initial parameters in LevMartester randomized for Morse and Angle. ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber <heber@…> [0496af] * src/LevMartester.cpp (modified) LevMartester uses SerializationPotential::operator>>() to print ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber <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 <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 17:28:58 GMT Frederik Heber <heber@…> [691be4] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionArgument.cpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) FunctionArgument now contains charges, too, and rewrote Extractors ... Mon, 25 Feb 2013 17:28:58 GMT Frederik Heber <heber@…> [d94e7e] * src/LevMartester.cpp (modified) SaturationPotential test part in LevMartester checks whether graphs ... Mon, 25 Feb 2013 17:28:58 GMT Frederik Heber <heber@…> [edac7c] * src/LevMartester.cpp (modified) DEBUG: LevMartester now looks for the oxygen atom in water as ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber <heber@…> [dd8094] * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/LevMartester.cpp (modified) Added getTrainingOutputAverage() used to initialize all_energy_offset ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber <heber@…> [2ba2ed] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) FIX: SaturationPotential's parameter derivatives seem to be working ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber <heber@…> [b17e0f] * src/LevMartester.cpp (modified) Using getFirstGraphwithTimesSpecificElement() in main() of ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber <heber@…> [e920d3d] * src/Fragmentation/Homology/FragmentNode.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/LevMartester.cpp (modified) Added getFirstGraphwithTimesSpecificElement(). - this allows to ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber <heber@…> [04cc7e] * src/FunctionApproximation/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/FunctionApproximation/writeDistanceEnergyTable.hpp (added) * src/LevMartester.cpp (modified) Added pretty printer for distance-energy tables. - added ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber <heber@…> [52e7da] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) * src/LevMartester.cpp (modified) Angle training now also uses TrainingData. Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber <heber@…> [49f163] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/LevMartester.cpp (modified) Added gatherAllSymmetricDistanceArguments(). - using it for ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber <heber@…> [301dbf] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/LevMartester.cpp (modified) Refactored gatherDistanceOfTuples(). - it is now able to work on ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber <heber@…> [69ab84] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/LevMartester.cpp (modified) FunctionApproximation's cstor now accepts TrainingData instance directly. Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber <heber@…> [68172a] * src/FunctionApproximation/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (added) * src/FunctionApproximation/TrainingData.hpp (added) * src/LevMartester.cpp (modified) Shifted class TrainingData into its own module. Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber <heber@…> [f68c68] * src/LevMartester.cpp (modified) Tersoff now also uses TrainingData class. - shifted calculation of ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber <heber@…> [8aa597] * src/FunctionApproximation/Extractors.cpp (added) * src/FunctionApproximation/Extractors.hpp (added) * src/FunctionApproximation/Makefile.am (modified) * src/LevMartester.cpp (modified) Extracted namespace Extractors into own module. - placed ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber <heber@…> [4ec18b] * src/LevMartester.cpp (modified) Added class TrainingData encapsulating the training input and output ... Sun, 24 Feb 2013 12:58:06 GMT Frederik Heber <heber@…> [8ea8c8] * src/LevMartester.cpp (modified) DEBUG: Adapted graph getting to Butane sampling. Sun, 24 Feb 2013 12:58:06 GMT Frederik Heber <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 <heber@…> [1f06896] * src/LevMartester.cpp (modified) DEBUG: Added msg about L2 contribution. Sun, 24 Feb 2013 12:57:42 GMT Frederik Heber <heber@…> [19fa3b] * src/LevMartester.cpp (modified) FIX: Removing average energy from order1-fit to Saturation potential. Sun, 24 Feb 2013 12:57:42 GMT Frederik Heber <heber@…> [40fff1] * src/LevMartester.cpp (modified) Performing fit got CH4 now with SaturatonPotential instead of Tersoff. Sat, 23 Feb 2013 16:24:27 GMT Frederik Heber <heber@…> [69b30a] * src/LevMartester.cpp (modified) FIX: boost::iarchive includes needs to go before MemDebug in ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber <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 <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 <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 <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 <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 15:25:43 GMT Frederik Heber <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 <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 <heber@…> [dac89b1] * src/LevMartester.cpp (modified) Using FunctionModel and setTrainingData in LevMartester. Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber <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 <heber@…> [c62f96] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/LevMartester.cpp (modified) * src/Makefile.am (modified) LevMartester uses now FunctionApproximation. Wed, 19 Dec 2012 15:25:03 GMT Frederik Heber <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 ...