# # ChangeLog for src # # Generated by Trac 1.4.4 # Jan 16, 2025, 1:28:29 PM Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [7b019a] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) Extended FunctionModel by getFragmentSpecificExtractor() definition. ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [69fcba] * src/FunctionApproximation/Extractors.cpp (modified) FIX: Extractor's convertTargetsToArguments() did not set argument_t's ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [9897ee9] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added combineArguments to Extractors. - this is required for ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [df350c] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added reorderArgumentsByParticleTypes() to Extractors. - this is ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [caa00e9] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added gatherAllDistancesFromFragment() to Extractors. - ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [dbf8c8] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) FIX: Now default parameters are present for every potential and used ... Wed, 27 Feb 2013 12:36:17 GMT Frederik Heber [b760bc3] * src/Potentials/Makefile.am (modified) * src/Potentials/ParticleTypeCheckers.cpp (added) * src/Potentials/ParticleTypeCheckers.hpp (added) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) Added ParticleTypeChecker functions in own namespace and added checks ... Wed, 27 Feb 2013 11:45:14 GMT Frederik Heber [93e908] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) Added SaturationPotential::symmetrizeTypes() to get types for both ... Wed, 27 Feb 2013 11:44:01 GMT Frederik Heber [55fe788] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) All specific Potentials now assert that arguments have charges ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [b3eabc] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) SaturationPotential now requires symmetric distances. Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [b10ada] * src/LevMartester.cpp (modified) Initial parameters in LevMartester randomized for Morse and Angle. ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [0496af] * src/LevMartester.cpp (modified) LevMartester uses SerializationPotential::operator>>() to print ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [ed2551] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) All Pair_.. and ManyBodyPotentials are now also derived from ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [6efcae] * src/LevMartester.cpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Exceptions.hpp (added) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialRegistry.hpp (modified) * src/Potentials/SerializablePotential.cpp (added) * src/Potentials/SerializablePotential.hpp (added) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) * src/Potentials/unittests/Makefile.am (added) * src/Potentials/unittests/SerializablePotentialUnitTest.cpp (added) * src/Potentials/unittests/SerializablePotentialUnitTest.hpp (added) * src/Potentials/unittests/stubs/SerializablePotentialMock.cpp (added) * src/Potentials/unittests/stubs/SerializablePotentialMock.hpp (added) * src/unittests/Makefile.am (modified) SerializablePotential is new type to be stored in PotentialRegistry. ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [67cd3a] * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialRegistry.cpp (added) * src/Potentials/PotentialRegistry.hpp (added) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) Added a PotentialRegistry for EmpiricalPotentials. - added virtual ... Mon, 25 Feb 2013 17:29:09 GMT Frederik Heber [201199] * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/potentials.dox (added) DOCU: Added documentation explaining purpose of potentials. Mon, 25 Feb 2013 17:29:08 GMT Frederik Heber [1f3b2a] * src/Parser/Exceptions.hpp (modified) FIX: double inclusion prevention of Parser/exceptions corrected. Mon, 25 Feb 2013 17:28:58 GMT Frederik Heber [691be4] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionArgument.cpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) FunctionArgument now contains charges, too, and rewrote Extractors ... Mon, 25 Feb 2013 17:28:58 GMT Frederik Heber [d94e7e] * src/LevMartester.cpp (modified) SaturationPotential test part in LevMartester checks whether graphs ... Mon, 25 Feb 2013 17:28:58 GMT Frederik Heber [edac7c] * src/LevMartester.cpp (modified) DEBUG: LevMartester now looks for the oxygen atom in water as ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber [dd8094] * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/LevMartester.cpp (modified) Added getTrainingOutputAverage() used to initialize all_energy_offset ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber [2ba2ed] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) FIX: SaturationPotential's parameter derivatives seem to be working ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber [b17e0f] * src/LevMartester.cpp (modified) Using getFirstGraphwithTimesSpecificElement() in main() of ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber [e920d3d] * src/Fragmentation/Homology/FragmentNode.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/LevMartester.cpp (modified) Added getFirstGraphwithTimesSpecificElement(). - this allows to ... Sun, 24 Feb 2013 13:00:40 GMT Frederik Heber [c29c0a] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * tests/regression/Filling/RegularGrid/post/solved_double_sles.data (modified) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid-with-surface.at (modified) FIX: triangleintersectionlist suffered numerical instabilities. - ... Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [0cd225] * src/documentation/install.dox (modified) DOCU: Updates optional enable targets and required and optional ... Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [dd966f] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) DOCUFIX: Extra $ in documentation of ManyBodyPotential_Tersoff. Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [eee1b7] * src/documentation/constructs/actions.dox (modified) * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/parameters.dox (added) * src/documentation/constructs/qt-gui.dox (modified) * src/documentation/constructs/queries.dox (added) * src/documentation/constructs/shaperegistry.dox (added) * src/documentation/constructs/shapes.dox (modified) * src/documentation/constructs/validators.dox (added) DOCU: Documentation on ShapeRegistry, QtUI changes, validators, and ... Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [c91572] * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) DOCUFIX: Replaced \text by \mathrm in some formulas. Sun, 24 Feb 2013 12:59:18 GMT Frederik Heber [d760bb] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/UniqueFragments.hpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) REFACTOR: PowerSetGenerator now creates all orders in one go, not ... Sun, 24 Feb 2013 12:59:18 GMT Frederik Heber [b6b5b8] * src/Graph/AdjacencyList.cpp (modified) FIX: Removed Assert of parsable file in AdjacencyList cstor. Sun, 24 Feb 2013 12:59:18 GMT Frederik Heber [37e910] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) FIX: Qt3D changed cylinder offset to barimetric center. - this ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [04cc7e] * src/FunctionApproximation/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/FunctionApproximation/writeDistanceEnergyTable.hpp (added) * src/LevMartester.cpp (modified) Added pretty printer for distance-energy tables. - added ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [52e7da] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) * src/LevMartester.cpp (modified) Angle training now also uses TrainingData. Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [ac868ee] * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (added) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (added) * src/FunctionApproximation/unittests/Makefile.am (modified) Added unit test for functions in Extractors namespace. Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [49f163] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/LevMartester.cpp (modified) Added gatherAllSymmetricDistanceArguments(). - using it for ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [63e786] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Refactored realignElementTargets() out of gatherDistancesOfTuples(). Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [c211f7] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Refactored convertElementcountsToTargets() out of ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [bc6705] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Refactored getElementCounts out of gatherDistancesOfTuples(). Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [301dbf] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/LevMartester.cpp (modified) Refactored gatherDistanceOfTuples(). - it is now able to work on ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [4a77be7] * src/Fragmentation/SetValues/Fragment.hpp (modified) Added charge_t to Fragment. Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [69ab84] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/LevMartester.cpp (modified) FunctionApproximation's cstor now accepts TrainingData instance directly. Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [68172a] * src/FunctionApproximation/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (added) * src/FunctionApproximation/TrainingData.hpp (added) * src/LevMartester.cpp (modified) Shifted class TrainingData into its own module. Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [f68c68] * src/LevMartester.cpp (modified) Tersoff now also uses TrainingData class. - shifted calculation of ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [8aa597] * src/FunctionApproximation/Extractors.cpp (added) * src/FunctionApproximation/Extractors.hpp (added) * src/FunctionApproximation/Makefile.am (modified) * src/LevMartester.cpp (modified) Extracted namespace Extractors into own module. - placed ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [355af8] * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/FunctionApproximation/unittests/FunctionArgumentUnitTest.cpp (added) * src/FunctionApproximation/unittests/FunctionArgumentUnitTest.hpp (added) * src/FunctionApproximation/unittests/Makefile.am (added) * src/unittests/Makefile.am (modified) Argument_t now has two Comparators on indices or distance. - added ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [4ec18b] * src/LevMartester.cpp (modified) Added class TrainingData encapsulating the training input and output ... Sun, 24 Feb 2013 12:58:06 GMT Frederik Heber [8ea8c8] * src/LevMartester.cpp (modified) DEBUG: Adapted graph getting to Butane sampling. Sun, 24 Feb 2013 12:58:06 GMT Frederik Heber [9340ee] * src/LevMartester.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) Added PairPotential_Angle training to LevMartester. Sun, 24 Feb 2013 12:57:42 GMT Frederik Heber [94f567] * src/Potentials/Specifics/SaturationPotential.cpp (modified) Added check if result of SaturationPotential::parameter_derivative is ... Sun, 24 Feb 2013 12:57:42 GMT Frederik Heber [1f06896] * src/LevMartester.cpp (modified) DEBUG: Added msg about L2 contribution. Sun, 24 Feb 2013 12:57:42 GMT Frederik Heber [19fa3b] * src/LevMartester.cpp (modified) FIX: Removing average energy from order1-fit to Saturation potential. Sun, 24 Feb 2013 12:57:42 GMT Frederik Heber [40fff1] * src/LevMartester.cpp (modified) Performing fit got CH4 now with SaturatonPotential instead of Tersoff. Sun, 24 Feb 2013 12:57:26 GMT Frederik Heber [4ffbb7] * src/Potentials/Makefile.am (modified) * src/Potentials/Specifics/SaturationPotential.cpp (added) * src/Potentials/Specifics/SaturationPotential.hpp (added) Added SaturatonPotential that combines a Morse and a Angle potential. Sun, 24 Feb 2013 12:57:26 GMT Frederik Heber [086070] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Moved all setParameters() from header files into module. - also ... Sun, 24 Feb 2013 12:57:26 GMT Frederik Heber [c92c0d] * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (added) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.hpp (added) Added unit test for PairPotential_Angle. - also corrected ... Sun, 24 Feb 2013 12:57:26 GMT Frederik Heber [a63187] * src/Potentials/Makefile.am (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (added) * src/Potentials/Specifics/PairPotential_Angle.hpp (added) Added PairPotential_Angle. Sun, 24 Feb 2013 12:57:26 GMT Frederik Heber [51c502] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) FIX: GLMoleculeObject_molecule::update() did not use ObserverLog ... Sat, 23 Feb 2013 16:24:27 GMT Frederik Heber [69b30a] * src/LevMartester.cpp (modified) FIX: boost::iarchive includes needs to go before MemDebug in ... Sat, 16 Feb 2013 11:32:44 GMT Frederik Heber [ef918c] * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) DISTFIX: typo in header files. Fri, 15 Feb 2013 17:09:58 GMT Frederik Heber [1f1f80] * src/Jobs/Grid/SamplingGrid.cpp (modified) FIX: SamplingGrid::get..GridPoint() checks for begin, end bounds. - ... Fri, 15 Feb 2013 17:09:58 GMT Frederik Heber [313f83] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) SamplingGrid::operator*=() can now deal with incongruent windows. - ... Fri, 15 Feb 2013 17:09:58 GMT Frederik Heber [fb3485] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) Refactored copy routine out of AddOntoWindow(). - this is ... Fri, 15 Feb 2013 17:09:57 GMT Frederik Heber [c0e8fb] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) Added SamplingGrid::isCongruent(). - also added unit test function. Fri, 15 Feb 2013 17:09:57 GMT Frederik Heber [56b04c] * src/Jobs/Grid/SamplingGrid.cpp (modified) FIX: SamplingGrid::getNearestLowerGridPoint(), and ::get..Upper..() ... Fri, 15 Feb 2013 17:09:57 GMT Frederik Heber [620517] * src/Jobs/Grid/Makefile.am (modified) * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGrid_inline.hpp (added) FIX: SamplingGrid::getWindowGridPoints() was broken. - or at least ... Fri, 15 Feb 2013 17:07:49 GMT Frederik Heber [b123a5] * src/Jobs/InterfaceVMGDebugGridJob.cpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (added) * src/Jobs/WindowGrid_converter.hpp (added) Shifted functions to add window onto grid into own namespace. - ... Fri, 15 Feb 2013 17:07:31 GMT Frederik Heber [8f3cdd] * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) Adapted VMGJob and its Interface to new non-zero window use. - we ... Fri, 15 Feb 2013 09:52:02 GMT Frederik Heber [64bafe0] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) SamplingGrid's Window start and end are now always set on a grid ... Fri, 15 Feb 2013 09:51:49 GMT Frederik Heber [c6355f] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) FIX: New non-zero window operations of SamplingGrid are now fully ... Fri, 15 Feb 2013 09:51:49 GMT Frederik Heber [de6dfb] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) Extending AddOntoWindow() by prefactor, can deal with differently ... Fri, 15 Feb 2013 09:51:49 GMT Frederik Heber [e2404f] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) New SamplingGrid::setDomainSize() and ::setWindowSize() helper functions. Fri, 15 Feb 2013 09:51:48 GMT Frederik Heber [1a00bb] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) Rewrote parts of SampingGrid such that a window of non-zero entries ... Fri, 15 Feb 2013 09:51:39 GMT Frederik Heber [98f8fe] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) SamplingGrid must have power of 2 grid size. - all number ... Thu, 14 Feb 2013 13:29:24 GMT Frederik Heber [3d9a8d] * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.cpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/MPQCJob_binding.hpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) SamplingGrid has no more size parameter but an end array. - this ... Thu, 14 Feb 2013 12:26:12 GMT Frederik Heber [e089fb] * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) Moved particle arrays into a new struct in VMGJob. - also the docu ... Thu, 14 Feb 2013 12:26:12 GMT Frederik Heber [1b01e9] * src/Jobs/MPQCJob_binding.hpp (added) * src/Jobs/Makefile.am (modified) * src/Server.cpp (modified) * src/poolworker.cpp (modified) FIX: Server missed forced binding to MPQCJob. - present was only to ... Thu, 14 Feb 2013 12:26:01 GMT Frederik Heber [6752dc] * src/documentation/install.dox (modified) DOCU: Extended installation explanations extensively. Thu, 14 Feb 2013 12:25:52 GMT Frederik Heber [0a7834] * src/documentation/install.dox (modified) DOCU: Updates optional enable targets and required and optional ... Thu, 14 Feb 2013 12:25:42 GMT Frederik Heber [d0faa8] * src/documentation/tests/regression-tests.dox (modified) DOCU: Added note on failing regression test only on installcheck. Wed, 13 Feb 2013 16:38:23 GMT Frederik Heber [312c0d] * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (added) FIX: HomologyContainerUnitTest does not require libMolecuilderUI ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [4d4ef8] * src/Jobs/MPQCCommandJob_binding.hpp (added) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob_binding.hpp (added) * src/Jobs/VMGJob_binding.hpp (added) * src/Makefile.am (modified) * src/Server.cpp (modified) * src/poolworker.cpp (modified) FIX: Enforce binding to libMolecuilderJobs for Server and PoolWorker. ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [cf1d82] * src/Parameters/Parameter.hpp (modified) * src/Parameters/ParameterInterface.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value.hpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) Parameter now contains Value, not inherits. - added several ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [6440c6] * src/Parameters/Makefile.am (modified) * src/Parameters/Parameter.hpp (modified) * src/Parameters/ParameterAsString.hpp (deleted) * src/Parameters/ParameterInterface.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value.hpp (modified) * src/Parameters/ValueInterface.hpp (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_Parameters.hpp (modified) * src/Parser/Makefile.am (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/ParameterStorage.hpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) Reworked inheritance graph of Parameter and Value. - Value now ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [b11f5e] * src/Parameters/Parameter.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value.hpp (modified) * src/Parameters/ValueAsString.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * src/Parameters/Value_string.cpp (modified) * src/Parameters/Value_string.hpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) FIX: Value::setAsString(), ::getAsString take const ref. - arg ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [9e6722] * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value_impl.hpp (modified) FIX: Made Parameter functions inline. Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [2665d3] * src/Parameters/Makefile.am (modified) * src/Parameters/Value.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * src/Parameters/Value_string.cpp (added) * src/Parameters/Value_string.hpp (added) * src/Parser/Parameters/unittests/Makefile.am (modified) String specializations of Value placed into own module. Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [50eff3] * src/Parameters/Value_impl.hpp (modified) FIX: Value::getValidRange() and ::getValidValues() were broken. - ... Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [4e904b] * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/molecule.cpp (modified) Removed atom::IsInShape(). - this makes libMolecuilderAtom not ... Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [a2f5e5] * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/Psi3Parser.hpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) FIX: Cleaned up includes in Psi3Parser_Parameters. Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [42f2f0] * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) FIX: MpqcParser_Parameter now simply uses Parameter instead ... Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [58fccca] * src/Parser/XyzParser.cpp (modified) FIX: XyzParser::load() stumbled if no empty line between timesteps. ... Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [b4b364] * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) FIX: Parameter unit tests all lacked CodePatterns lib. Wed, 13 Feb 2013 15:47:38 GMT Frederik Heber [7d82a5] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/World.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) Changed bond::ptr into boost::shared_ptr. Changes: - refactored ... Wed, 13 Feb 2013 14:29:35 GMT Frederik Heber [c8302f3] * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.hpp (modified) Removed molecule::RemoveBond(s) and ::removeAtom(). - this ... Thu, 17 Jan 2013 22:59:15 GMT Frederik Heber [88c8ec] * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/BondInfo.hpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BreadthFirstSearchAdd.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.hpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) REFACTOR: Replaced all "bond *" appearances by bond::ptr. - this is ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [a30b7f] * src/LevMartester.cpp (modified) Added check on L2 sum and Lmax norms of fitted Tersoff with respect ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [17b3598] * src/LevMartester.cpp (modified) Starting parameters for Tersoff minimization in LevMartester are now ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [d03292] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Implemented box constraints for FunctionModel, using a feature of ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [f48ad3] * src/LevMartester.cpp (modified) * src/Makefile.am (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) LevMartester now uses FunctionModel::setParameter() to set initial ...