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CHANGE_LOG
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CHANGE_LOG
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*Important changes with respect to the 1.0 version:
- A bug in the copy constructor of GeomParameter was removed
- The running canvas option is back non-MPI enebaled versions: you can observe running simulations
- XML examples were added
2015-03-11 Marc de Kamps <scsmdk@campus-10-41-141-40.wireless.leeds.ac.uk>
modified: python/xml/duffin.xml
2015-03-10 Marc de Kamps <scsmdk@locals-mbp-3.lan>
Committer: Marc de Kamps <scsmdk@locals-mbp-3.lan> modified: apps/BasicDemos/miind.cpp modified: libs/MPILib/include/report/handler/RootCanvasMPI.hpp modified: python/simulation.py modified: python/xml/duffin.xml modified: python/xml/omurtag.xml modified: python/xml/twopop.xml modified: python/xml/wilsoncowan.xml
2015-03-06 Marc de Kamps <scsmdk@campus-10-41-142-95.wireless.leeds.ac.uk>
new file: apps/PerformanceGeom/QifCorrelated.cpp
modified: apps/BasicDemos/miind.cpp modified: apps/PerformanceGeom/CMakeLists.txt modified: apps/PerformanceGeom/LifOneCanvas.cpp modified: apps/PerformanceGeom/QifJumpPoisson.cpp modified: python/algorithms.py
2015-03-01 Marc de Kamps <scsmdk@locals-mbp-3.lan>
modified: libs/MPILib/include/report/handler/RootCanvasMPI.hpp modified: libs/MPILib/include/report/handler/RootReportHandler.hpp
modified: libs/MPILib/include/report/handler/RootCanvasMPI.hpp
modified: libs/MPILib/include/report/handler/RootCanvasNoMPI.hpp
modified: libs/GeomLib/MasterFactory.hpp modified: libs/GeomLib/MasterParameter.hpp modified: libs/MPILib/include/report/handler/RootCanvasMPI.hpp modified: libs/MPILib/include/report/handler/RootReportHandler.hpp modified: libs/MPILib/src/report/handler/RootCanvasNoMPI.cpp
renamed: libs/MPILib/include/report/handler/RootCanvasNoMPi.hpp -> libs/MPILib/include/report/handler/RootCanvasNoMPI.hpp modified: libs/MPILib/include/report/handler/RootReportHandler.hpp modified: libs/MPILib/src/report/handler/RootCanvasNoMPI.cpp
modified: apps/UnitGeomLib/CurrentCompensationParameterTest.cpp modified: apps/UnitGeomLib/GeomInputConvertorTest.cpp modified: libs/MPILib/src/report/handler/RootCanvasNoMPI.cpp
new file: libs/MPILib/include/report/handler/RootCanvasNoMPi.hpp
new file: libs/MPILib/include/report/handler/CanvasParameter.hpp
new file: libs/MPILib/src/report/handler/CanvasParameter.cpp new file: libs/MPILib/src/report/handler/RootCanvasNoMPI.cpp apps/UnitMPILib/DelayAlgorithm_test.cpp libs/MPILib/include/report/handler/CanvasParameter.hpp libs/MPILib/include/report/handler/RootCanvasNoMPi.hpp
modified: CHANGE_LOG new file: apps/PerformanceGeom/LifOneCanvas.cpp new file: apps/PerformanceGeom/LifTwoCanvas.cpp
new file: python/xml/duffin.xml renamed: python/miind.xml -> python/xml/miind.xml renamed: python/omurtag.xml -> python/xml/omurtag.xml new file: python/xml/twopop.xml new file: python/xml/wilsoncowan.xml
new file: libs/MPILib/include/report/handler/RootCanvasMPI.hpp
2015-02-28 Marc de Kamps <scsmdk@locals-mbp-3.lan>
modified: apps/PerformanceGeom/CMakeLists.txt modified: apps/PerformanceGeom/LifOne.cpp modified: apps/PerformanceGeom/LifTwo.cpp modified: apps/PerformanceGeom/QifJumpPoisson.cpp modified: apps/PerformanceGeom/TwoPopulationDefinitions.hpp modified: libs/GeomLib/CurrentCompensationParameter.hpp modified: libs/GeomLib/NumericalMasterEquation.cpp modified: libs/MPILib/src/report/handler/RootReportHandler.cpp
2015-02-25 Marc de Kamps <scsmdk@campus-10-41-137-195.wireless.leeds.ac.uk>
modified: apps/BasicDemos/miind.cpp modified: apps/PerformanceGeom/CMakeLists.txt modified: apps/PerformanceGeom/LifOne.py modified: apps/UnitGeomLib/GeomAlgorithmTest.cpp modified: apps/UnitGeomLib/MuSigmaScalarProductTest.cpp modified: apps/UnitGeomLib/QifOdeSystemTest.cpp modified: libs/GeomLib/GeomAlgorithmCode.hpp modified: libs/MPILib/CMakeLists.txt modified: libs/MPILib/include/SimulationRunParameter.hpp modified: libs/MPILib/include/algorithm/DelayAlgorithm.hpp modified: libs/MPILib/include/algorithm/DelayAlgorithmCode.hpp modified: libs/MPILib/include/report/handler/RootReportHandler.hpp modified: libs/MPILib/src/SimulationRunParameter.cpp deleted: libs/MPILib/src/populist/zeroLeakEquations/ABConvertor.cpp modified: libs/MPILib/src/populist/zeroLeakEquations/LIFConvertor.cpp modified: libs/MPILib/src/report/handler/RootReportHandler.cpp modified: libs/MPILib/test/algorithm/CMakeLists.txt deleted: libs/MPILib/test/algorithm/DelayAlgorithm_test.cpp modified: libs/MPILib/test/algorithm/RateAlgorithm_test.cpp deleted: libs/MPILib/test/populist/zeroLeakEquations/ABConvertor_test.cpp deleted: libs/MPILib/test/populist/zeroLeakEquations/ABQStruct_test.cpp deleted: libs/MPILib/test/populist/zeroLeakEquations/ABScalarProduct_test.cpp deleted: libs/MPILib/test/populist/zeroLeakEquations/OneDMZeroLeakEquation_test.cpp modified: libs/MPILib/test/report/handler/RootReportHandler_test.cpp modified: libs/UtilLib/CMakeLists.txt deleted: libs/UtilLib/DinA.cpp deleted: libs/UtilLib/DinA.h deleted: libs/UtilLib/Page.cpp deleted: libs/UtilLib/Page.h deleted: libs/UtilLib/Util.cpp modified: libs/UtilLib/UtilLib.h
2015-02-02 Marc de Kamps <scsmdk@campus-10-41-142-228.wireless.leeds.ac.uk>
new file: apps/UnitMPILib/UnitMPILib.cpp
new file: apps/PerformanceGeom/QifJumpPoisson.cpp deleted: apps/UnitMPILib/UnitMPILIb.cpp
modified: libs/GeomLib/GeomInputConvertor.cpp
Committer: Marc de Kamps <scsmdk@campus-10-41-142-228.wireless.leeds.ac.uk> Changes to be committed: modified: apps/PerformanceGeom/CMakeLists.txt modified: doc/Mainpage.hpp modified: doc/examples.hpp modified: doc/xml_example.hpp modified: libs/GeomLib/GeomInputConvertor.cpp modified: libs/GeomLib/GeomInputConvertor.hpp modified: libs/GeomLib/GeomParameter.cpp modified: libs/GeomLib/GeomParameter.hpp modified: libs/GeomLib/QifOdeSystem.hpp modified: libs/GeomLib/SpikingQifNeuralDynamics.hpp
2015-01-25 Marc de Kamps <scsmdk@locals-mbp-3.lan>
Committer: Marc de Kamps <scsmdk@locals-mbp-3.lan> modified: python/algorithms.py
modified: doc/Mainpage.hpp modified: doc/xml_example.hpp modified: libs/GeomLib/BinEstimator.hpp modified: libs/GeomLib/CurrentCompensationParameter.hpp modified: libs/GeomLib/GeomParameter.hpp modified: libs/GeomLib/LifNeuralDynamics.hpp modified: libs/GeomLib/OdeParameter.hpp modified: libs/GeomLib/QifParameter.hpp new file: libs/MPILib/include/algorithm/RateFunctor.hpp new file: libs/MPILib/include/algorithm/RateFunctorCode.hpp modified: libs/MPILib/include/populist/PopulationAlgorithm.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/AbstractZeroLeakEquations.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/NumericalZeroLeakEquations.hpp
new file: python/omurtag.xml
new file: doc/xml_example.hpp new file: images/xml_alg.png new file: images/xml_io.png new file: images/xml_nodes.png new file: images/xml_simpar.png new file: images/xml_top.png
new file: apps/UnitMPILib/CMakeLists.txt new file: apps/UnitMPILib/RateFunctorTest.cpp new file: apps/UnitMPILib/UnitMPILIb.cpp
Committer: Marc de Kamps <scsmdk@locals-mbp-3.lan> Changes to be committed: modified: apps/BasicDemos/miind.cpp modified: apps/BasicDemos/population-example.cpp modified: apps/CMakeLists.txt modified: doc/Doxyfile.cmake modified: doc/cpp_example.hpp modified: doc/examples.hpp modified: doc/installation.hpp modified: libs/GeomLib/AbstractNeuralDynamics.hpp modified: libs/GeomLib/AbstractOdeSystem.hpp modified: libs/GeomLib/OdeParameter.hpp modified: libs/GeomLib/QifOdeSystem.hpp modified: libs/GeomLib/QifParameter.hpp modified: libs/GeomLib/SpikingLifNeuralDynamics.hpp modified: libs/GeomLib/SpikingQifNeuralDynamics.hpp modified: libs/MPILib/include/MPINode.hpp modified: libs/MPILib/include/algorithm/RateAlgorithm.hpp modified: python/algorithms.py modified: python/connections.py modified: python/include.py modified: python/miind.py modified: python/miind.xml
2015-01-21 Marc de Kamps <scsmdk@campus-10-41-141-173.wireless.leeds.ac.uk>
Committer: Marc de Kamps <scsmdk@campus-10-41-141-173.wireless.leeds.ac.uk> On branch integration Your branch is ahead of 'origin/integration' by 2 commits.
Changes to be committed:
new file: images/dense.png
new file: images/dense.svg
new file: images/rate.png
new file: images/rate.svg
new file: images/spikeraster.png
Committer: Marc de Kamps <scsmdk@campus-10-41-141-173.wireless.leeds.ac.uk> Changes to be committed: new file: apps/PerformanceGeom/LifOne.py new file: apps/PerformanceGeom/density_count.dat new file: apps/PerformanceGeom/om_counts.dat new file: doc/cpp_example.hpp new file: doc/examples.hpp
Committer: Marc de Kamps <scsmdk@campus-10-41-141-173.wireless.leeds.ac.uk> On branch integration Your branch is up-to-date with 'origin/integration'. Changes to be committed: new file: apps/BasicDemos/miind.cpp modified: apps/BasicDemos/population-example.cpp modified: apps/PerformanceGeom/LifOne.cpp modified: doc/Doxyfile.cmake modified: doc/Mainpage.hpp modified: doc/customdoxygen.css modified: libs/MPILib/include/MPINetwork.hpp modified: libs/MPILib/include/populist/ProbabilityQueue.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/LIFZeroLeakEquations.hpp deleted: libs/MPILib/include/populist/zeroLeakEquations/OneDMZeroLeakEquations.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/SingleInputZeroLeakEquations.hpp modified: libs/MPILib/src/populist/ZeroLeakBuilder.cpp deleted: libs/MPILib/src/populist/zeroLeakEquations/OneDMZeroLeakEquations.cpp modified: python/algorithms.py modified: python/miind.py new file: python/miind.xml new file: python/simulation.py
2015-01-17 Marc de Kamps <scsmdk@Locals-MacBook-Pro-3.local>
modified: apps/BasicDemos/CMakeLists.txt modified: apps/PerformanceGeom/LifTwo.cpp modified: libs/GeomLib/GeomParameter.cpp modified: libs/GeomLib/GeomParameter.hpp new file: python/algorithms.py new file: python/connections.py new file: python/include.py new file: python/miind.py new file: python/nodes.py
2015-01-08 Marc de Kamps <scsmdk@locals-mbp-3.lan>
modified: libs/GeomLib/GeomAlgorithmCode.hpp
modified: apps/BasicDemos/CMakeLists.txt modified: apps/BasicDemos/population-example.cpp modified: apps/PerformanceGeom/CMakeLists.txt modified: apps/PerformanceGeom/CreateTwoPopulationNetwork.hpp modified: apps/PerformanceGeom/CreateTwoPopulationNetworkCode.hpp modified: apps/PerformanceGeom/LifOne.cpp modified: apps/PerformanceGeom/LifTwo.cpp modified: apps/PerformanceGeom/TwoPopulationDefinitions.hpp modified: apps/UnitGeomLib/BinEstimatorTest.cpp modified: apps/UnitGeomLib/CMakeLists.txt modified: apps/UnitGeomLib/GeomInputConvertorTest.cpp modified: apps/UnitGeomLib/GeomParameterTest.cpp modified: apps/UnitGeomLib/LeakingOdeSystemTest.cpp modified: apps/UnitGeomLib/LifNeuralDynamicsTest.cpp modified: apps/UnitGeomLib/MuSigmaScalarProductTest.cpp modified: apps/UnitGeomLib/NeuronParameterTest.cpp modified: apps/largeNetwork/GenerateHexagonalNetwork.hpp modified: apps/largeNetwork/LargeNetwork.cpp modified: doc/Doxyfile.cmake modified: doc/MPILibDoc.hpp modified: doc/Mainpage.hpp modified: doc/doxygen.css modified: libs/GeomLib/AbstractMasterEquation.hpp modified: libs/GeomLib/CMakeLists.txt modified: libs/GeomLib/GeomAlgorithm.hpp modified: libs/GeomLib/GeomInputConvertor.cpp modified: libs/GeomLib/GeomInputConvertor.hpp modified: libs/GeomLib/MuSigmaScalarProduct.cpp modified: libs/GeomLib/MuSigmaScalarProduct.hpp renamed: libs/GeomLib/OrnsteinUhlenbeckParameter.hpp -> libs/GeomLib/NeuronParameter.hpp modified: libs/GeomLib/NumericalMasterEquation.cpp modified: libs/GeomLib/NumericalMasterEquation.h modified: libs/GeomLib/OdeParameter.cpp modified: libs/GeomLib/OdeParameter.hpp modified: libs/MPILib/CMakeLists.txt renamed: libs/MPILib/include/populist/OrnsteinUhlenbeckConnection.hpp -> libs/MPILib/include/DelayedConnection.hpp modified: libs/MPILib/include/algorithm/WilsonCowanAlgorithm.hpp modified: libs/MPILib/include/populist/PopulationAlgorithm.hpp modified: libs/MPILib/include/populist/PopulationAlgorithmCode.hpp modified: libs/MPILib/include/populist/PopulationGridController.hpp modified: libs/MPILib/include/populist/PopulationGridControllerCode.hpp modified: libs/MPILib/include/populist/rateComputation/AbstractRateComputation.hpp modified: libs/MPILib/include/populist/rateComputation/IntegralRateComputation.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/ABConvertor.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/ABScalarProduct.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/AbstractZeroLeakEquations.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/ConnectionSquaredProduct.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/InputConvertor.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/LIFConvertor.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/LIFZeroLeakEquations.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/MuSigmaScalarProduct.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/NumericalZeroLeakEquations.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/OldLifZeroLeakEquations.hpp modified: libs/MPILib/include/populist/zeroLeakEquations/OneDMZeroLeakEquations.hpp modified: libs/MPILib/src/populist/zeroLeakEquations/InputConvertor.cpp modified: libs/MPILib/src/populist/zeroLeakEquations/LIFZeroLeakEquations.cpp modified: libs/MPILib/src/populist/zeroLeakEquations/MuSigmaScalarProduct.cpp modified: libs/MPILib/src/populist/zeroLeakEquations/NumericalZeroLeakEquations.cpp modified: libs/MPILib/test/populist/OrnsteinUhlenbeckConnection_test.cpp
2014-12-28 Marc de Kamps <scsmdk@locals-mbp-3.lan>
new file: apps/UnitGeomLib/GeomAlgorithmTest.cpp
new file: apps/PerformanceGeom/CMakeLists.txt new file: apps/PerformanceGeom/CreateTwoPopulationNetwork.hpp new file: apps/PerformanceGeom/CreateTwoPopulationNetworkCode.hpp new file: apps/PerformanceGeom/LifOne.cpp new file: apps/PerformanceGeom/LifTwo.cpp new file: apps/PerformanceGeom/TwoPopulationDefinitions.hpp
modified: apps/CMakeLists.txt modified: libs/GeomLib/GeomInputConvertor.cpp modified: libs/GeomLib/GeomParameter.hpp modified: libs/GeomLib/NumericalMasterEquation.cpp
2014-12-23 Marc de Kamps <scsmdk@locals-mbp-3.lan>
modified: libs/MPILib/src/populist/ProbabilityQueue.cpp
new file: libs/GeomLib/AbstractMasterEquation.hpp
new file: libs/GeomLib/MasterFactory.cpp new file: libs/GeomLib/MasterFactory.hpp
new file: apps/UnitGeomLib/NumericalMasterEquationTest.cpp
modified: apps/BasicDemos/population-example.cpp modified: apps/UnitGeomLib/CMakeLists.txt modified: apps/UnitGeomLib/GeomParameterTest.cpp modified: libs/GeomLib/BasicDefinitions.hpp modified: libs/GeomLib/BinEstimator.hpp modified: libs/GeomLib/CMakeLists.txt modified: libs/GeomLib/CNZLCache.cpp modified: libs/GeomLib/GeomAlgorithm.hpp modified: libs/GeomLib/GeomAlgorithmCode.hpp modified: libs/GeomLib/GeomInputConvertor.hpp modified: libs/GeomLib/GeomLib.hpp modified: libs/GeomLib/GeomParameter.cpp modified: libs/GeomLib/GeomParameter.hpp modified: libs/GeomLib/NumericalMasterEquation.cpp modified: libs/GeomLib/NumericalMasterEquation.h modified: libs/MPILib/include/MPINetworkCode.hpp modified: libs/MPILib/include/algorithm/AlgorithmInterface.hpp modified: libs/MPILib/include/populist/PopulationAlgorithm.hpp
2014-12-14 Marc de Kamps <scsmdk@locals-mbp-3.lan>
modified: libs/GeomLib/GeomParameter.hpp
new file: UnitGeomLib/QifOdeSystemTest.cpp
new file: apps/BasicDemos/population-example.cpp
new file: apps/UnitGeomLib/BinEstimatorTest.cpp
new file: apps/UnitGeomLib/GeomInputConvertorTest.cpp
new file: libs/GeomLib/LifParameter.hpp new file: libs/GeomLib/MasterParameter.hpp
new file: libs/GeomLib/QifOdeSystem.cpp new file: libs/GeomLib/QifOdeSystem.hpp new file: libs/GeomLib/QifParameter.hpp
new file: libs/GeomLib/NumericalMasterEquation.cpp new file: libs/GeomLib/NumericalMasterEquation.h
new file: libs/GeomLib/MatrixMasterEquation.cpp new file: libs/GeomLib/MatrixMasterEquation.h
new file: libs/GeomLib/CurrentParameter.hpp new file: libs/GeomLib/DiffusionParameter.hpp modified: libs/GeomLib/GeomInputConvertor.hpp modified: libs/GeomLib/GeomParameter.hpp
new file: libs/GeomLib/SpikingLifNeuralDynamics.cpp new file: libs/GeomLib/SpikingLifNeuralDynamics.hpp new file: libs/GeomLib/SpikingNeuralDynamics.cpp new file: libs/GeomLib/SpikingNeuralDynamics.hpp new file: libs/GeomLib/SpikingOdeSystem.cpp new file: libs/GeomLib/SpikingOdeSystem.hpp new file: libs/GeomLib/SpikingQifNeuralDynamics.cpp new file: libs/GeomLib/SpikingQifNeuralDynamics.hpp
new file: libs/GeomLib/GeomAlgorithm.hpp new file: libs/GeomLib/GeomAlgorithmCode.hpp
new file: libs/GeomLib/BinEstimator.cpp new file: libs/GeomLib/BinEstimator.hpp new file: libs/GeomLib/CNZLCache.cpp new file: libs/GeomLib/CNZLCache.hpp
new file: UnitGeomLib/GeomParameterTest.cpp
modified: apps/BasicDemos/CMakeLists.txt modified: apps/UnitGeomLib/CMakeLists.txt modified: apps/UnitGeomLib/LifNeuralDynamicsTest.cpp modified: libs/GeomLib/AbstractNeuralDynamics.hpp modified: libs/GeomLib/AbstractOdeSystem.cpp modified: libs/GeomLib/AbstractOdeSystem.hpp modified: libs/GeomLib/BasicDefinitions.hpp modified: libs/GeomLib/CMakeLists.txt modified: libs/GeomLib/CurrentCompensationParameter.hpp modified: libs/GeomLib/GeomInputConvertor.cpp modified: libs/GeomLib/GeomInputConvertor.hpp modified: libs/GeomLib/GeomLib.hpp new file: libs/GeomLib/GeomParameter.cpp new file: libs/GeomLib/GeomParameter.hpp modified: libs/GeomLib/InputParameterSet.hpp modified: libs/MPILib/include/MPINetwork.hpp modified: libs/MPILib/include/populist/ProbabilityQueue.hpp modified: libs/MPILib/src/populist/ProbabilityQueue.cpp
2014-11-28 Marc de Kamps <scsmdk@locals-mbp-3.lan>
new file: libs/GeomLib/CMakeLists.txt
modified: apps/UnitGeomLib/CMakeLists.txt modified: apps/UnitGeomLib/LeakingOdeSystemTest.cpp modified: apps/UnitGeomLib/LifNeuralDynamicsTest.cpp modified: apps/UnitGeomLib/NeuronParameterTest.cpp modified: libs/CMakeLists.txt modified: libs/GeomLib/AbstractOdeSystem.cpp renamed: libs/GeomLib/AbstractOdeSystem.h -> libs/GeomLib/AbstractOdeSystem.hpp modified: libs/GeomLib/GeomInputConvertor.hpp modified: libs/GeomLib/GeomLib.hpp modified: libs/GeomLib/LeakingOdeSystem.hpp modified: libs/GeomLib/MuSigmaScalarProduct.hpp modified: libs/GeomLib/OrnsteinUhlenbeckParameter.hpp
modified: apps/UnitGeomLib/CurrentCompensationParameterTest.cpp modified: apps/UnitGeomLib/InitialDensityParameterTest.cpp modified: apps/UnitGeomLib/LeakingOdeSystemTest.cpp modified: apps/UnitGeomLib/LifNeuralDynamicsTest.cpp modified: apps/UnitGeomLib/MuSigmaScalarProductTest.cpp modified: apps/UnitGeomLib/NeuronParameterTest.cpp modified: apps/UnitGeomLib/OdeParameterTest.cpp new file: libs/GeomLib/GeomLib.hpp
new file: libs/GeomLib/BasicDefinitions.hpp new file: libs/GeomLib/CurrentCompensationParameter.hpp new file: libs/GeomLib/GeomInputConvertor.cpp new file: libs/GeomLib/GeomInputConvertor.hpp new file: libs/GeomLib/LifNeuralDynamics.cpp new file: libs/GeomLib/LifNeuralDynamics.hpp new file: libs/GeomLib/MuSigma.hpp new file: libs/GeomLib/OdeParameter.cpp new file: libs/GeomLib/OdeParameter.hpp
new file: libs/GeomLib/InitialDensityParameter.hpp
new file: apps/UnitGeomLib/CurrentCompensationParameterTest.cpp new file: apps/UnitGeomLib/InitialDensityParameterTest.cpp new file: apps/UnitGeomLib/LeakingOdeSystemTest.cpp new file: apps/UnitGeomLib/LifNeuralDynamicsTest.cpp new file: apps/UnitGeomLib/MuSigmaScalarProductTest.cpp new file: apps/UnitGeomLib/NeuronParameterTest.cpp new file: apps/UnitGeomLib/OdeParameterTest.cpp new file: libs/GeomLib/AbstractNeuralDynamics.cpp new file: libs/GeomLib/AbstractNeuralDynamics.hpp new file: libs/GeomLib/AbstractOdeSystem.cpp new file: libs/GeomLib/AbstractOdeSystem.h new file: libs/NumtoolsLib/Modulo.h
modified: CHANGE_LOG modified: apps/UnitGeomLib/CMakeLists.txt new file: libs/GeomLib/GeomLibException.hpp new file: libs/GeomLib/InputParameterSet.hpp new file: libs/GeomLib/LeakingOdeSystem.cpp new file: libs/GeomLib/LeakingOdeSystem.hpp new file: libs/GeomLib/MuSigmaScalarProduct.cpp new file: libs/GeomLib/MuSigmaScalarProduct.hpp new file: libs/GeomLib/OrnsteinUhlenbeckParameter.hpp modified: libs/MPILib/include/algorithm/AlgorithmInterface.hpp new file: libs/MPILib/include/populist/parameters/NeuronParameter.hpp modified: libs/MPILib/include/populist/parameters/OrnsteinUhlenbeckParameter.hpp modified: libs/MPILib/include/utilities/MPIProxy.hpp modified: libs/MPILib/src/populist/zeroLeakEquations/MuSigmaScalarProduct.cpp modified: libs/MPILib/test/utilities/MPIProxy_test.cpp modified: libs/NumtoolsLib/NumtoolsLib.h
apps/UnitGeomLib/CMakeLists.txt~
apps/UnitGeomLib/CurrentCompensationParameterTest.cpp
apps/UnitGeomLib/InitialDensityParameterTest.cpp
apps/UnitGeomLib/LeakingOdeSystemTest.cpp
apps/UnitGeomLib/LifNeuralDynamicsTest.cpp
apps/UnitGeomLib/MuSigmaScalarProductTest.cpp
apps/UnitGeomLib/NeuronParameterTest.cpp
apps/UnitGeomLib/OdeParameterTest.cpp
apps/UnitGeomLib/OdeParameterTest.cpp~
apps/largeNetwork/.gitignore
libs/GeomLib/AbstractNeuralDynamics.cpp
libs/GeomLib/AbstractNeuralDynamics.hpp
libs/GeomLib/AbstractOdeSystem.cpp
libs/GeomLib/AbstractOdeSystem.h
libs/GeomLib/BasicDefinitions.hpp
libs/GeomLib/CurrentCompensationParameter.hpp
libs/GeomLib/GeomInputConvertor.cpp
libs/GeomLib/GeomInputConvertor.hpp
libs/GeomLib/GeomLib.h
libs/GeomLib/InitialDensityParameter.hpp
libs/GeomLib/LifNeuralDynamics.cpp
libs/GeomLib/LifNeuralDynamics.hpp
libs/GeomLib/MuSigma.hpp
libs/GeomLib/OdeParameter.cpp
libs/GeomLib/OdeParameter.hpp
libs/NumtoolsLib/Modulo.h
2014-11-19 Marc de Kamps <scsmdk@campus-10-41-136-222.wireless.leeds.ac.uk>
new file: Interpolation.cpp
modified: MPILib/include/MPINetworkCode.hpp modified: MPILib/include/populist/rateComputation/AbstractRateComputation.hpp modified: MPILib/src/populist/rateComputation/AbstractRateComputation.cpp modified: MPILib/src/populist/zeroLeakEquations/LIFConvertor.cpp deleted: MPILib/src/populist/zeroLeakEquations/OldLifZeroLeakEquations.cpp modified: MPILib/test/MPINetwork_test.cpp modified: MPILib/test/MPINode_test.cpp modified: MPILib/test/NodeType_test.cpp modified: MPILib/test/populist/zeroLeakEquations/ABConvertor_test.cpp modified: NumtoolsLib/CMakeLists.txt modified: NumtoolsLib/GaussianDistribution.h deleted: NumtoolsLib/Interpolation.cpp deleted: NumtoolsLib/InterpolationTest.cpp
2014-11-12 de Kamps <scsmdk@login1.arc2.leeds.ac.uk>
modified: libs/MPILib/include/MPINetworkCode.hpp modified: libs/MPILib/include/NodeType.hpp modified: libs/MPILib/src/populist/zeroLeakEquations/InputConvertor.cpp
modified: apps/CMakeLists.txt modified: cmake-modules/FindRoot.cmake modified: libs/MPILib/include/MPINetworkCode.hpp modified: libs/MPILib/include/NodeType.hpp modified: libs/MPILib/src/populist/zeroLeakEquations/InputConvertor.cpp
modified: CMakeLists.txt modified: apps/CMakeLists.txt modified: cmake-modules/FindRoot.cmake modified: libs/MPILib/include/MPINetworkCode.hpp modified: libs/MPILib/include/NodeType.hpp modified: libs/MPILib/src/populist/zeroLeakEquations/InputConvertor.cpp
new file: apps/largeNetwork/CMakeLists.txt modified: apps/largeNetwork/GenerateHexagonalNetwork.cpp modified: apps/largeNetwork/LargeNetwork.cpp modified: CMakeLists.txt modified: apps/CMakeLists.txt modified: cmake-modules/FindRoot.cmake modified: libs/MPILib/include/MPINetworkCode.hpp modified: libs/MPILib/include/NodeType.hpp modified: libs/MPILib/src/populist/zeroLeakEquations/InputConvertor.cpp
new file: CHANGE_LOG new file: apps/BasicDemos/CMakeLists.txt new file: apps/BasicDemos/miind-mpi.cpp new file: apps/BasicDemos/two-population.cpp new file: apps/UnitGeomLib/CMakeLists.txt deleted: apps/UnitGeomLib/UnitGeom.cpp modified: CMakeLists.txt modified: apps/CMakeLists.txt modified: apps/largeNetwork/GenerateHexagonalNetwork.cpp modified: apps/largeNetwork/LargeNetwork.cpp modified: cmake-modules/FindRoot.cmake modified: libs/MPILib/include/MPINetworkCode.hpp modified: libs/MPILib/include/NodeType.hpp modified: libs/MPILib/src/populist/zeroLeakEquations/InputConvertor.cpp apps/largeNetwork/CMakeLists.txt
new file: apps/UnitGeomLib/UnitGeom.cpp new file: apps/UnitGeomLib/UnitGeomLib.cpp renamed: apps/LargeNetwork.cpp -> apps/largeNetwork/LargeNetwork.cpp deleted: apps/miind-mpi.cpp deleted: apps/two-population.cpp modified: CMakeLists.txt modified: apps/CMakeLists.txt modified: apps/largeNetwork/GenerateHexagonalNetwork.cpp modified: apps/largeNetwork/LargeNetwork.cpp modified: cmake-modules/FindRoot.cmake modified: libs/MPILib/include/MPINetworkCode.hpp modified: libs/MPILib/include/NodeType.hpp modified: libs/MPILib/src/populist/zeroLeakEquations/InputConvertor.cpp
CHANGE_LOG
apps/BasicDemos/
apps/UnitGeomLib/CMakeLists.txt
apps/largeNetwork/CMakeLists.txt
2014-07-22 Marc de Kamps <M.deKamps@leeds.ac.uk>
modified: miind_logo.png
modified: Mainpage.hpp modified: customdoxygen.css modified: footer.html modified: header.html modified: installation.hpp
2014-07-21 Marc de Kamps <m.dekamps@leeds.ac.uk>
new file: customdoxygen.css new file: footer.html modified: header.html
modified: Mainpage.hpp
new file: hbp.png
new file: miind_logo.png
2013-06-26 David Sichau <mailatsichau.eu>
fixed tests
2013-02-25 David-Matthias Sichau <mail@sichau.eu>
Added affiliation.
2013-02-13 David-Matthias Sichau <mail@sichau.eu>
Rewritten the main simulation loop section. Adding more details on the underlying mli parallelization.
2013-02-06 David-Matthias Sichau <mail@sichau.eu>
Rewritten section partly and added source code
Added figure about the two population network and more text about mpi added.
ignore more temporary tex files.
2013-01-29 Marc <marc@miind.(none)>
Trying to merge
new file: bib.bib
modified: pmiind.tex
2013-01-28 David-Matthias Sichau <mail@sichau.eu>
Written more about the parallelization.
2013-01-18 David-Matthias Sichau <mail@sichau.eu>
fixed double entry in bib
2013-01-11 Marc <marc@miind.(none)>
Adding bib file
frontiers bst file
2013-01-11 David-Matthias Sichau <mail@sichau.eu>
Added gitignore for the latex rubbish
Added the publication to the repository.
2013-01-10 David-Matthias Sichau <mail@sichau.eu>
added Barrier to method addNode to make sure that the order is always the same removed the type of the second Node at the method makeFirstInput to avoid any inconsitencies.
2013-01-09 David-Matthias Sichau <mail@sichau.eu>
removed wrong files. merged header files.
2013-01-08 Marc <marc@miind.(none)>
missing files
Christmas changes Mdk
2012-10-01 David-Matthias Sichau <mail@sichau.eu>
Fixed bug in the generation of the network.
2012-09-30 David-Matthias Sichau <mail@sichau.eu>
Added changes from cvs version.
Added changes from cvs version.
2012-08-13 David-Matthias Sichau <mail@sichau.eu>
fixed compiler warning of gcc4.7
2012-08-09 David-Matthias Sichau <mail@sichau.eu>
Documentation for adaption of old code added.
2012-08-08 David-Matthias Sichau <mail@sichau.eu>
fixed forgotten std::
fixed unused variable warnings
doc fix
fixed unused variable warnings
Removed unneded cmake modules
Removed not MPI related libraries.
2012-08-07 David-Matthias Sichau <mail@sichau.eu>
doc update
2012-08-06 David-Matthias Sichau <mail@sichau.eu>
fixed false include
fixed typo
doc update
Debug Levels changed, as they are not really important :)
The Log Level is defined at compile time.
This is done via a compile flag
Test and interfaces adapted to the new NodeType distribution
The nodeTypes of the precursors are now added during the call of makeFirstInputOfSecond, as the Distribution over the network is not possible with larger networks, as the messages cannot be differentiated anymore.
Loging changed
Log Messages added for MPI communication.
changed to typedef
get std::exceptions also.
Moved files out of library. Error with wrong NodeIds fixed.
try to fix linker error
try to fix linker error
try to fix linker error
Large network added to MPILib for benchmarks.
2012-08-02 David-Matthias Sichau <mail@sichau.eu>
New wrapper function added to avoid to always write out the access to the singleton instance.
Added Singleton class. The MPIProxy is now a singleton instance to avoid unnecessary creation and deletion.
removed unneeded constants
2012-07-31 David-Matthias Sichau <mail@sichau.eu>
Fixes for Delay ALgorithm
Added Delay Algorithm
doc update
doc update
doc update
NDEBUG is stetted if not debug build is chosen
Doc update
Revert "Revert "Doc update for rebinner""
This reverts commit 69d3e8b7838b2e14fa3f05b30dd76f4d7c53567d.
Merge branch 'templateNode' of ssh://miind.git.sourceforge.net/gitroot/miind/miind into templateNode
doc update
Revert "Doc update for rebinner"
Doc update for rebiller
2012-07-30 David-Matthias Sichau <mail@sichau.eu>
Merge branch 'newLogger' into templateNode
fix for wrong test oracle
Doc update for RateComputation
Merge branch 'newLogger' into templateNode
Doc for NonCirculantSolvers added
added different filenames for the different methods
fix for wrong test oracle
typo fixed
Changed the default logLevel to logINFO instead of logDEBUG4.
Merge branch 'newLogger' into templateNode
Doc for CirculantSolvers added
Log messages formated nicer.
Log message is set to a lower level if it is not a debug build. Instead of debug messages to std::cout they are printed to the log.
Printed error message to log instead of std::bout
removed unneeded tests.
Switched to new logger instead of LogStream
2012-07-27 David-Matthias Sichau <mail@sichau.eu>
Doc update
Test for CirculantMode added.
Formatting of the source code added C++11 features
2012-07-26 David-Matthias Sichau <mail@sichau.eu>
GCC does now compile without -fpermissive
added missed namespace
fixed missing includes
Added stub tests
Namespace for ZEROLEAKEQUATIONS classes added.
Namespace for rebinner classes added.
Namespace for RATECOMPUTATION classes added.
Namespace for NONCIRCULANTSOLVERS classes added.
Moved CiculantSolvers in own namespace
VArray moved to circulantSolvers
Moved Adaptive Hazard to zeroLeakEquations
Moved MuSigma classes into zeroLeakEquations
Mock test for rebiller move rebiller class into own folder replaced boost::shared_ptr with std::shared_ptr
Moved rateComputation related stuff in own folder.
Moved nonCiculantSolvers in own folder and added mock test
Moved circulantEquations into own folder added mock test.
Stub test added for ZeroLeakEquations
2012-07-25 David-Matthias Sichau <mail@sichau.eu>
fix replace auto_ptr with unique_ptr
Doc update for OldLifZeroLeakEquation C++11 features added.
fixes forgotten include dir
set c++11 flags also for non mph build
fixed missing pointer cast
Added -fpermissive flag for gcc in all build types
Compiler flags set for Release and Debug compilations.
Added better timing.
2012-07-24 David-Matthias Sichau <mail@sichau.eu>
Log test fix for brutus
Log test fix for brutus
Log test fix for brutus
Set gcc flag -fpermissive to remove error. This needs to be fixed.
Fix for gcc
Merge commit '350c538e3058f4784495a483b9a2470b988f1e35' into templateNode
Fix for gcc
Fix for gcc
fixed missing include for gcc
fixed forgotten throw() statement
fixed CaseSensitive inclued
Added messages about root during configuration.
fixed missing include for gcc
switched from queue to list, as the queue resulted in interoperability between gcc and clang
Removed unused-parameter warning in gcc
Fix for gcc as it assumes no throw in default destructor.
2012-07-23 David-Matthias Sichau <mail@sichau.eu>
Doc update Converted from boost::shared_ptr to std::shared_ptr Included stub tests
Test for LIFConvertor added.
- doc update - interface renaming to naming scheme
Fixed missing namespace declarator.
2012-07-20 David-Matthias Sichau <mail@sichau.eu>
Doc update.
Moved ZeroLeakEquations related classes into the Folder zeroLeakEquations/
Moved parameter classes of populib in namespace parameters.
Fixed illegal read
fixed wrong initialization of unsigned int.
fixed test, as they failed with MPI enabled. This was due to generation of the MPIProxy before the MPI environment was constructed.
2012-07-19 David-Matthias Sichau <mail@sichau.eu>
Fixed memory leak. Now the application does not contain any memory leaks :)
Memory leak in node fixed.
MPI test now have a fallback to normal test.
Fixed CircularDistribution such that it is possible to generate it at compile time.
Fixed memory leak, buy switching to static members and references instead of pointers.
memory leak fixed in the Circular Distribution. Now uses members instead of pointers.
Fixed memory leak caused by circular shared_ptr. Use weak_ptr instead to resolve this circular dependency.
Compiler Warnings fixed.
2012-07-18 David-Matthias Sichau <mail@sichau.eu>
Fixed memory leak in ValueHandlerHandler
Memtest works. Now the memory leaks need to be fixed.
Different testing implemented. Only test that need to have an MPI Environment are executed with MPI. All other test will be executed like normal unit test. This reduced the time of a test run significantly, as the MPI environment does not be generated. Additional for this test memory test can be executed. As the are very slow this feature is only enabled if wanted (therefore the flag ENABLE_MEMORY_TEST is introduced)
PopulistParameters moved into folder parameters Doc update test implemented.
OrnsteinUhlenbeckParameter moved into folder parameters Doc updated Test implemented
OneDMParameter refractored Doc update Test implemented
OneDMInputSetParameter moved into folder parameters Doc update
NumericalZeroLeakParameter moved to folder parameters Doc updated Test implemented
Moved InptParameterSet to folder parameters
Adapted include paths.
Moved AdaptionParameter to folder parameters Doc update Test generated for AdaptionParameter
Moved Parameters in own folder but not own namespace at the moment.
Test for PopulistSpecificParameters added
PopulistSpecificParameter adapted interface to naming scheme. Doc update C++11 features added.
Test for InitialDensityParameter added
Test for ABScalarProduct added. Doc update.
2012-07-17 David-Matthias Sichau <mail@sichau.eu>
removed todo, as this issue is already fixed.
Revert "removed todo, as this issue is already fixed."
This reverts commit c16c057070c4ededc41c0b67020e7b2b0a04f2ca.
removed todo, as this issue is already fixed.
Fixed inheritance from std lib
Logo added to doc
Added documentation about license and Installation.
Licence update.
Log class changed to shared_ptr. Added real setter and getter for the Log class.
2012-07-13 David-Matthias Sichau <mail@sichau.eu>
Added test for the log class.
Pictures for doxygen added.
Doc update
Log Class further improved. It now logs if the report level is changed. It also provides getter and setter for the reportingLevel
Log class simplified.
2012-07-12 David-Matthias Sichau <mail@sichau.eu>
time added to the log.
New Log class
More C++11 refractoring
More C++11 refractoring
first refractoring to c++11
doc update
Doc updates.
2012-07-11 David-Matthias Sichau <mail@sichau.eu>
Adapted interface to naming scheme Added override notation to population algorithm.
Splited the basic definitions in 3 files. One for types one for strings and one for numerical values.
Fixed bug which caused wrong naming of graphs. The bug was due to wrong default initialization.
doc update
Moved all MPI Code from MPINode to the MPIProxy
The main methods only contain the generation of the mpi environment.
Added test for the MPI Proxy
Code can be compiles without mpi and it works.
RootHighThroughputHandler depends on MPIProxy instead of boost mpi
Config file is copied in build dir instead of source dir.
2012-07-10 David-Matthias Sichau <mail@sichau.eu>
Adapted test
Added broadcast operation to MPIProxy and removed broadcast from MPINetwork
Depend only on MPIProxy
CircularDistribution depends on MPIProxy for all MPI stuff
Removed stupid bug, local variables generated instead change of attributes.
Simplified MPIProxy
Cmake changes
Added MPI Proxy Class to hide the mpi implementation.
Added Precompiler Statements to exclude mph code if needed.
Wrong tags corrected. The old version only worked of one node was on one process, otherwise it would have failed. Therefore now the nodeIds are used as tags instead of the ranks of the processes.
fixed test, as wait all is called from external.
2012-07-09 David-Matthias Sichau <mail@sichau.eu>
Added single executable for the two populist test.
Merge branch 'clang' into templateNode
Conflicts:
.gitignore
Fixed all clang errors.
Initialization done in own method.
mpiStatuses need to be static, otherwise a deadlock occurs.
2012-07-06 David-Matthias Sichau <mail@sichau.eu>
Added forgotten method. It now compiles and links.
Remove 2 linker errors and compile errors.
Compiles but still linking errors.
Added weight template to Rate Algorithm
Added more classes to MPILib
2012-07-05 David-Matthias Sichau <mail@sichau.eu>
Adapted lot of code to MPILib. This is not finished yet
Added source files to cmake
Added more classes to MPILib
Added more classes to MPILib
Added more classes to MPILib
Added more classes to MPILib
Added more classes to MPILib
Added gridcontroler
Added more classes from Populib to mpilib
Moved initialization to prepareEvolve
Added prepare Evolve method to the algorithm interface
Added prepareEvolve method which than can be used instead of the CollectExternalInput method.
2012-07-04 David-Matthias Sichau <mail@sichau.eu>
Added PopulationAlgorithm to MPILib
Adapted two-population to the new added classes.
Merge branch 'NodeTypesAdded' into templateNode
Doc update
Added a new method to the algorithm interface. One can overwrite either of them to get the desired behaviour.
Added test case for nodeType exchange
Added exchange of the NodeTypes to the MPINodes.
changed code such that clang does not throw a warning
2012-07-03 David-Matthias Sichau <mail@sichau.eu>
Interface adaptions.
Adapted Interfaces, to MPILib
2012-07-02 David-Matthias Sichau <mail@sichau.eu>
More files added from populist
More classes added from populib
More Classes added to MPILib
Added more Populist classes to mpi lib
More files added for population list
Moved populist related files in own namespace populist instead of algorithm.
2012-07-01 David-Matthias Sichau <mail@sichau.eu>
Does need changes.
2012-06-29 David Sichau <mail@sichau.eu>
Added PopulistSpecificParameters to MPILib
Added initialDensityparamters to mpilib
Added parameter to Basic Definitions
AbstractRateComputation added to MPILib
Added input paramter set to mpi lib
Added abstract Rebinner to MPILib
OrnsteinUhlenbeckParameters added to MPILib
2012-06-28 David Sichau <mail@sichau.eu>
Added Poplist parameter
Added two population test to cake but it does not compile at the moment.
Added first Algorithm needed for two population test
2012-06-27 David Sichau <mail@sichau.eu>
Coverage with full path but still does not work
Simplified cake adding of the sources.
Preparation for code coverage with clang
Code compiles with clang.
Moved todo messages to doxygen
Added test for RoothighThroughputHandler improved other tests.
switched to nullptr removed unneded parameter in constructor
The RootHighThroughputHandler now stores the gloabal node ids and retriev them for the generation of the graphs.
2012-06-26 David Sichau <mail@sichau.eu>
Fixed documentation, the node id do not work at the moment.
No warnings for MPILib with gcc
supressed warnings
fixed more gcc warnings
Removed compiler warnings
Added the local nodes to the root file.
Removed unneeded variables.
RootHighThroughputHandler is working. But he needs to get the number of nodes on a CPU.
Added the number of local nodes to the report.
2012-06-25 David Sichau <mail@sichau.eu>
Added Fatal Error if Clang is detected.
Removed duplicate of NodeType Attribute
2012-06-24 David Sichau <mail@sichau.eu>
Add ignore of eclipse settings
2012-06-22 David Sichau <mail@sichau.eu>
- doc update
Coverage fails with gccc 4.7 one need to wait for the lcov update. There is a patch available for lcov.
Code Coverage added, with a mac it does not work. Does it work on Linux??
- Doc update, no doxygen warnings anymore
excluded std files from doxygen
Added target make doc to Miind-mpi
moved implementation code into cpp file
Fixed test, as now the output files are named differently
The file renaming is automatically handled, one need only provide the prefix of the file name
Switched to generating of filenames with FileNameGenerator
- Doc update
Helper Class for Filenames generated.
2012-06-21 David Sichau <mail@sichau.eu>
Test the highthroughput handler unfortunally it does not work anymore.
- Doc update - renamed to consistent naming scheme
Added RootHighThroughputHandler to MPILib
-ValueHandlerHandler test added - Doc update
- Doc Update - Test for Inactive and Root-ReportHandler added.
- doc update of GraphKey - added test for GraphKey
- Added test for ReportType and ReportValue - Improved doc
- Added test for Report - Doc update for Report
2012-06-20 David Sichau <mail@sichau.eu>
WilsonCowanParamter c++11 features added Test for WilsonCowanParamter added.
Added helper class for a test algorithm
Test for WilsonCowanAlgorithm
fixed exceptions they are thrown again
Removed not anymore needed sleep algorithm
Improved the RateAlgorithm test
Changed interface of AlgorithmGrid.
Changed test from BOOST_REQUIRED to BOOST_CHECK, as this will print all erros and not only the first one. Added test for the AlgorithmGrid
2012-06-19 David Sichau <mail@sichau.eu>
Interface renaming
- Doc updates - Interface naming - Moved implementation code to cpp files
Improved Exception test, now it checks if a exception is catched at the correct position
Added test for IterationNumberException
Added test for logStream
Added test for the ProgressBar
Added Test for Timer and refractored Timer
Added test for time exception
Added test for NetworkState, refractored NetworkState
small unit test for NodeType
Added Test for SimulationRunParameter
renamed getter to start with get. Moved implementation into cpp file.
Improved MPINetwork test
Made cosmetic code changes
Added Dales Law to MiindMPI
2012-06-18 David Sichau <mail@sichau.eu>
Adapted include guards to new paths.
moved report and report handler in own namespaces.
Changed loop to c++11 foreach loop
Removed the infotuple from the root handler
2012-06-15 David Sichau <mail@sichau.eu>
removed time test
2012-06-14 David Sichau <mail@sichau.eu>
MPINode has a timer for the algorithm and mpi time.
working progress bar.
Added progressbar and removed unneded Time classes.
2012-06-13 David Sichau <mail@sichau.eu>
Added boost timers to application.
in class initialisation of MPINetwork
switched to std shared_ptr
Removed more code related to grapical output.
switched to std shared_ptr. Removed Stuff related to grapical updates.
Cleaned and documented the RootHandler Interface