# # ChangeLog for src # # Generated by Trac 1.6 # May 24, 2025, 9:46:23 AM Thu, 02 Mar 2017 07:25:41 GMT Frederik Heber [99689b] * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) FIX: Missing JobMarket_LDFLAGS in executables and unit tests. Thu, 02 Mar 2017 07:17:26 GMT Frederik Heber [53ef0d4] * src/Actions/unittests/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: Missing CodePatterns_LDFLAGS or AM_LDFLAGS or missing boost ... 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 [f5dbea] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) VERBOSE: Verbosity fix 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 14:25:36 GMT Frederik Heber [bc069f] * src/Potentials/BindingModel.cpp (added) * src/Potentials/BindingModel.hpp (added) * src/Potentials/Makefile.am (modified) Added BindingModel which extends HomologyGraph for an ordered set of ... Fri, 11 Nov 2016 14:25:36 GMT Frederik Heber [824bba] * src/Fragmentation/Homology/FragmentNode.hpp (modified) FIX: FragmentNode lacked a header file from boost/serialization. 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 14:25:35 GMT Frederik Heber [c738f1] * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) FIX: SaturatedFragment::getEdges(). - SaturatedFragment now keeps ... 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 11:47:34 GMT Frederik Heber [228340] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) Extractors::gatherAllSymmetricDistances..() additionaly gets edge set ... Fri, 04 Nov 2016 09:37:52 GMT Frederik Heber [814b8c] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) AnalyseFragmentResults stores edge per fragment in value_t of ... Fri, 04 Nov 2016 09:37:52 GMT Frederik Heber [2ae400] * src/FunctionApproximation/FunctionArgument.cpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) Added bonded flag to argument_t. Fri, 04 Nov 2016 09:37:51 GMT Frederik Heber [ea63cb] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (modified) Edges per Fragment passed on to FragmentationShortRangeResults. - ... Fri, 04 Nov 2016 09:37:51 GMT Frederik Heber [9445081] * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) FragmentJobQueue additionally stores the bond graph as an edge set ... Fri, 04 Nov 2016 09:37:51 GMT Frederik Heber [041a79] * src/Fragmentation/EdgesPerFragment.hpp (added) * src/Fragmentation/Makefile.am (modified) Added definition for a set of edges in namespace FragmentEdges. 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. Fri, 04 Nov 2016 09:37:50 GMT Frederik Heber [c5e75f3] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/SerializablePotential.hpp (modified) * src/documentation/constructs/potentials.dox (modified) ParticleType_t is now an unsigned int. - this allows direct use of ... Fri, 04 Nov 2016 09:37:50 GMT Frederik Heber [c7aac9] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) FIX: TrainingData used charges instead of atomic numbers to recognize ... Fri, 04 Nov 2016 09:37:50 GMT Frederik Heber [e47ac7] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) REFACTOR: Removed many unused functions from Extractor namespace. - ... Fri, 04 Nov 2016 09:37:49 GMT Frederik Heber [6829d2] * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (modified) * tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) MPQCData additionally stores the atomic number per nuclei. - in ... Fri, 04 Nov 2016 09:37:49 GMT Frederik Heber [95304c] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) REFACTOR: Extracted registerPotentialIfNotPresent out of ... Fri, 04 Nov 2016 09:37:48 GMT Frederik Heber [f946b2] * src/Atom/atom_atominfo.cpp (modified) FIX: AtomInfo::CopyStepOnStep() did require present of velocity and ... Fri, 04 Nov 2016 09:37:48 GMT Frederik Heber [2d1280] * doc/userguide/userguide.xml (modified) * src/Actions/BondAction/BondSetDegreeAction.cpp (added) * src/Actions/BondAction/BondSetDegreeAction.def (added) * src/Actions/BondAction/BondSetDegreeAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Bond/SetDegree/post/test.pdb (added) * tests/regression/Bond/SetDegree/post/test_degree1.pdb (added) * tests/regression/Bond/SetDegree/post/test_degree2.pdb (added) * tests/regression/Bond/SetDegree/post/test_multiple.pdb (added) * tests/regression/Bond/SetDegree/post/test_multiple_degree1.pdb (added) * tests/regression/Bond/SetDegree/post/test_multiple_degree2.pdb (added) * tests/regression/Bond/SetDegree/pre/.pdb (added) * tests/regression/Bond/SetDegree/pre/test.pdb (added) * tests/regression/Bond/SetDegree/pre/test_multiple.pdb (added) * tests/regression/Bond/SetDegree/pre/test_multiple_fail.pdb (added) * tests/regression/Bond/SetDegree/testsuite-bond-set-degree.at (added) * tests/regression/Bond/SetDegree/testsuite-bond-set-degree_multiple.at (added) * tests/regression/Bond/testsuite-bond.at (modified) * tests/regression/Makefile.am (modified) Added BondSetDegreeAction for manipulating bond degrees. Fri, 04 Nov 2016 09:37:48 GMT Frederik Heber [3400bb] * src/Potentials/PotentialTrainer.cpp (modified) MEMFIX: PotentialTrainer::operator() had potential memory leak. Thu, 20 Oct 2016 20:54:58 GMT Frederik Heber [d24750] * src/Potentials/RegistryDeserializer_impl.hpp (modified) FIX: RegistryDeserializer stumbled over comments. Thu, 20 Oct 2016 20:54:48 GMT Frederik Heber [72e40d0] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.cpp (added) * src/Actions/WorldAction/StepWorldTimeAction.def (added) * src/Actions/WorldAction/StepWorldTimeAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/testsuite-options.at (modified) * tests/regression/WorldTime/SetWorldTime/testsuite-worldtime-set-world-time.at (moved) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (added) * tests/regression/WorldTime/testsuite-worldtime.at (added) * tests/regression/testsuite.at (modified) Added single action to step backward and forward through time. - ... Thu, 20 Oct 2016 20:54:23 GMT Frederik Heber [a1c8fa] * 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/Fragmentation.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) FIX: BondedParticleInfo::MaxOrder and ::AdapativeOrder are now stored ... Thu, 20 Oct 2016 20:54:23 GMT Frederik Heber [064b34] * src/Actions/WorldAction/OutputAction.cpp (modified) FIX: OutputAction gives a more helpful error message on fail. Thu, 20 Oct 2016 20:54:23 GMT Frederik Heber [180b5f] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FragmentationAction does not give error on adjacencyfile when not ... Tue, 20 Sep 2016 09:02:32 GMT Frederik Heber [b85145] * src/Tesselation/tesselation.cpp (modified) FIX: Tesselation::GetCircleOfSetOfPoints() did not check for ... Tue, 20 Sep 2016 09:02:32 GMT Frederik Heber [67645e] * src/Tesselation/tesselation.cpp (modified) WARNINGFIX: unused variable in NDEBUG case in Tesselation::operator(). Tue, 20 Sep 2016 09:02:32 GMT Frederik Heber [d00441] * src/Filling/Cluster.cpp (modified) WARNINGFIX: Cluster::insert() unused variable in NDEBUG case. Mon, 19 Sep 2016 18:12:01 GMT Frederik Heber [72b467] * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) ParseFragmentResultsAction warns when parsing container with grids ... Sun, 18 Sep 2016 19:52:09 GMT Frederik Heber [25f5b66] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) WARNINGFIX: Commented-out unused ... Sun, 18 Sep 2016 19:52:09 GMT Frederik Heber [42715d] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillVolumeAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified) WARNINGFIX: Removed AtomVector typedef in some Fill..Actions. Sun, 18 Sep 2016 19:52:09 GMT Frederik Heber [bcf351] * src/Potentials/Particles/ParticleRegistry.hpp (modified) MEMFIX: ParticleRegistry did not cleanup on dstor. Sun, 18 Sep 2016 19:52:03 GMT Frederik Heber [34709f] * src/Fragmentation/Exporters/unittests/Makefile.am (modified) DISTFIX: SphericalPointDistribution_assistant.hpp missing in Makefile.am. Wed, 14 Sep 2016 18:43:53 GMT Frederik Heber [3fb9ab] * src/Parser/MpqcParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * tests/regression/Atoms/Add/post/test.in (modified) * tests/regression/Atoms/Remove/post/test.in (modified) * tests/regression/Parser/Mpqc/post/doublewater.in (modified) * tests/regression/Parser/Mpqc/post/empty.in (modified) * tests/regression/Parser/Mpqc/post/test.in (modified) * tests/regression/Parser/Mpqc/post/testCLHF.in (modified) * tests/regression/Parser/Mpqc/post/testCLKS.in (modified) * tests/regression/Parser/Mpqc/post/testMBPT2.in (modified) * tests/regression/Parser/Mpqc/post/testMBPT2_R12.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n_ascend_ids.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n_mixed_ids.in (modified) * tests/regression/Parser/Mpqc/pre/testCLKS.in (modified) * tests/regression/Parser/Mpqc/pre/testMBPT2.in (modified) * tests/regression/Parser/Mpqc/pre/testMBPT2_R12.in (modified) * tests/regression/Parser/Mpqc/pre/water.in (modified) * tests/regression/Parser/SetParameters/Mpqc/post/testCLHF.in (modified) * tests/regression/Parser/SetParameters/Mpqc/pre/testCLHF.in (modified) FIX: Preventing MPQC from using old temp files for restart. - ... Wed, 14 Sep 2016 18:43:53 GMT Frederik Heber [703369] * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) FIX: FragmentationAutomation limited nfc to 20 and grid to 10 ... Wed, 14 Sep 2016 18:43:53 GMT Frederik Heber [291ad9] * src/Fragmentation/Summation/SetValues/FragmentForces.cpp (modified) * src/Fragmentation/Summation/SetValues/FragmentForces.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentForcesUnitTest.cpp (added) * src/Fragmentation/Summation/SetValues/unittests/FragmentForcesUnitTest.hpp (added) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) Added operator+=() to FragmentForces and unit test. - FIX: ... Wed, 14 Sep 2016 18:43:46 GMT Frederik Heber [82034f1] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) Added currently inactive alternative NN contribution calculation from ... Wed, 14 Sep 2016 18:43:46 GMT Frederik Heber [964c63] * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) Need to check given max-meshwidth for not being too large w.r.t delta. Wed, 14 Sep 2016 18:43:46 GMT Frederik Heber [dd9b90] * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/unittests/ExportGraph_ToJobsUnitTest.cpp (modified) FIX: Fragment grid may also become smaller than specified level. - ... Wed, 14 Sep 2016 18:43:46 GMT Frederik Heber [eaef9b] * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) Modying nfc by power of 2 for each additional level in fragment grid. Wed, 14 Sep 2016 18:43:46 GMT Frederik Heber [4c648a] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) UNBREAKS: No longer downsample all grids but enforce a coarser global ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [45f4b6b] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) FragmentationLongRangeResults requires additional zeroinstance in ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [ebadb4] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp (modified) FragmentationChargeDensity requires additional zeroinstance in cstor. Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [b5134a] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp (modified) Split operations in FragmentationChargeDensity into cstor and ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [409a05] * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) ..SumUpPerLevel are now functors that allow to set the zero instance ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [da098d2] * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) * src/Fragmentation/Summation/ZeroInstanceInitializer.hpp (added) ..Summators and AllLevel..Summators pass through ZeroInstance, added ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [3d444a] * src/Fragmentation/Summation/OrthogonalSummation_impl.hpp (modified) * src/Fragmentation/Summation/Summation_impl.hpp (modified) (Orthogonal)Summation's Sum() can be further simplified now. Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [ff7ac6] * src/Fragmentation/Summation/OrthogonalSummation.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummation_impl.hpp (modified) * src/Fragmentation/Summation/Summation.hpp (modified) * src/Fragmentation/Summation/Summation_impl.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) BREAKS: Summation and OrthogonalSummation both now allow to set a ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [f856ec] * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) Histogram uses copy instead of superposeOtherHistogram() when ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [760fa22] * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) FragmentationLongRangeResults::operator() does not need to calculate ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [52a789] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) AnalyseFragmentationResultsAction now uses downsampled charge grids ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [11edf0] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/GridDownsampler.cpp (added) * src/Fragmentation/Summation/Containers/GridDownsampler.hpp (added) * src/Fragmentation/Summation/Containers/Makefile.am (modified) Added GridDownsampler as static functor. - extracted function from ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [4a3df8] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * tests/Python/AllActions/options.dat (modified) Fragmentation.. and ..AutomationAction accept a desired maximum mesh- ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [2ebfd7] * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) MPQCData::assignWithDownsampledGrid() uses downsample(). - in order ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [ec1aae] * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) FIX: MPQCData now correctly checks sampled_grid to be cubic. Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [160ad7] * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Fragmentation/Exporters/unittests/ExportGraph_ToJobsUnitTest.cpp (added) * src/Fragmentation/Exporters/unittests/ExportGraph_ToJobsUnitTest.hpp (added) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) ExportGraph_ToJobs::operator() now calculates a specific level for ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [b839fb] * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) Extracted getDomainGrid from ExportGraph_ToJobs as static fct. Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [57fda0] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) SamplingGrid::operator*=(), ::superposeOtherGrids() and ::integral() ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [6a5eb2] * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) SamplingGrid::downsample() uses padWithZerosForEvenNumberedSamples(). ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [d56e21] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (modified) Added padWithZerosForEvenNumberedSamples(), required by downsample(). ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [91e7658] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (modified) SamplingGridUnitTest checks downsample on window. - FIX: ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [06653a] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (modified) SamplingGrid has downsample() function. - we need this when small ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [cb30d9] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (modified) Extended SamplingGridProperties::isCompatible() to allow more finely ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [ca4b372] * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) Added getSurplusLevel() to SamplingGridProperties. - FIX: ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [336da8] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) WindowGrid_converter's refactored a bit with ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [c1948c] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (modified) Added getDiscreteWindowIndices() and getDiscreteWindowLengthPerAxis() ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [c6da5e] * src/Jobs/InterfaceVMGJob.cpp (modified) FIX: InterfaceVMGJob used box_end as end point, not as length of ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [978234] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties_inline.hpp (modified) FIX: Made getGridPointsPerAxis() not use pow() in every call. Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [e51f2c] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Potentials/PartialNucleiChargeFitter.cpp (modified) Renamed SamplingGrid::getDiscreteWindowIndices() -> ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [5b1e5e] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties_inline.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) FIX: Replaced 3 by NDIM in SamplingGrid which avoids some confusion ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [028790] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) Moved getNearestLowerGridPoint and ..Higher:: from SamplingGrid to ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [c6ddcb] * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.hpp (modified) Added getRoughBoundingBox to SaturatedFragment. Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [c24071] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToAtomFragments.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToAtomFragments.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) ExportGraph::operator() now returns bool. - FragmentationAction ... Wed, 14 Sep 2016 13:36:04 GMT Frederik Heber [3dadd5] * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (modified) Revert "Removing SphericalPointDistribution::getSimplePolygon() to ... Wed, 14 Sep 2016 13:36:04 GMT Frederik Heber [1af2ae] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) FIX: SphericalPointDistribution::findBestMatching() does not assert ... Wed, 14 Sep 2016 07:02:33 GMT Frederik Heber [fe90ab] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) recurseMatching() now takes connections into account. - ... Wed, 14 Sep 2016 07:02:33 GMT Frederik Heber [36bd59] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) FIX: Need to check whether old and newcenter are not linear dependent. Wed, 14 Sep 2016 07:02:31 GMT Frederik Heber [2ccdf4] * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest_assistant.hpp (modified) Fixing getConnectionTest() due to ambiguous tesselation. - with N=8 ... Mon, 12 Sep 2016 23:58:11 GMT Frederik Heber [2d8c4e] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) Removed all IsZero() checking and special cases for the triangle idea. Mon, 12 Sep 2016 23:48:37 GMT Frederik Heber [6393ff] * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution_getConnections.cpp (added) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest_assistant.hpp (added) * src/Fragmentation/Makefile.am (modified) Added getConnections() to SphericalPointDistribution. - we use ... Mon, 12 Sep 2016 23:48:37 GMT Frederik Heber [3678eb] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Added calculation of center of minimum distance by bisection. - ... Mon, 12 Sep 2016 23:48:36 GMT Frederik Heber [0983e6] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) Refactoring SphericalPointDistribution to combine point list and ... Mon, 12 Sep 2016 23:48:36 GMT Frederik Heber [653cea] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) SphericalPointDistribution is now working with bond degree weights. ... Mon, 12 Sep 2016 23:48:36 GMT Frederik Heber [450adf] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Extracted joinPoints() function to make it accessible to tests. - ... Mon, 12 Sep 2016 23:48:36 GMT Frederik Heber [2199c2] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) Extended SphericalPointDistribution::Polygon_t to WeightedPolygon_t. ... Mon, 12 Sep 2016 23:48:34 GMT Frederik Heber [b67d89] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Using the idea of three points giving a triangle to find rotation ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [158ecb] * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) Extended SphericalPointDistributionUnitTest to two and three matching ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [b3c052] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Dropped quaternion rotation for simple arbitrary rotation axis and ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [8e4471] * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) Added "arbitrary" rotation for matchSphericalPointDistributionsTest_2(). Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [92bc5c] * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Adding QuaternionTest for SphericalPointDistributionUnitTest, fixed ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [f9d85f] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) Implemented rotations via boost::quaternions. Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [8d38e6] * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Added more unit test functions up to N=8 to ...