heart/test/performance/Test1dMonodomainShannonCvodeBenchmarks.hpp

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*/

#ifndef TEST1DMONODOMAINSHANNONCVODEBENCHMARKS_HPP_
#define TEST1DMONODOMAINSHANNONCVODEBENCHMARKS_HPP_

#include <cxxtest/TestSuite.h>
#include <sstream>
#include <iostream>

#include "TetrahedralMesh.hpp"
#include "MonodomainProblem.hpp"
#include "RegularStimulus.hpp"
#include "Shannon2004.hpp"
#include "Shannon2004Cvode.hpp"
//#include "Shannon2004BackwardEulerOpt.hpp"
#include "AbstractCardiacCellFactory.hpp"
#include "HeartConfig.hpp"
#include "CvodeAdaptor.hpp"
#include "EulerIvpOdeSolver.hpp"
#include "Timer.hpp"

#include "PetscSetupAndFinalize.hpp"

/**
 * Cell Factory defining cells for 1d chain.
 *
 * This gives a shared default solver to all the cells, as standard.
 */
template <class CELL_MODEL>
class ShannonCardiacCellFactory : public AbstractCardiacCellFactory<1>
{
private:

    boost::shared_ptr<RegularStimulus> mpStimulus;

public:
    ShannonCardiacCellFactory()
    : AbstractCardiacCellFactory<1>(),
      mpStimulus(new RegularStimulus(-250000,5,2000,1))
      {
      }

    AbstractCardiacCell* CreateCardiacCellForTissueNode(Node<1>* pNode)
    {
        CELL_MODEL *p_cell;

        if (pNode->GetPoint()[0] == 0.0)
        {
            p_cell = new CELL_MODEL(this->mpSolver,
                                    mpStimulus);
        }
        else
        {
            p_cell = new CELL_MODEL(this->mpSolver,
                                    this->mpZeroStimulus);
        }

        return p_cell;
    }
};

#ifdef CHASTE_CVODE

/**
 *
 * Cell Factory defining Shannon cells for 1d chain.
 *
 * In this version each node has its own Cvode adaptor solver
 */
class ShannonCvodeAdaptorCellFactory : public AbstractCardiacCellFactory<1>
{
private:

    boost::shared_ptr<RegularStimulus> mpStimulus;

public:
    ShannonCvodeAdaptorCellFactory()
    : AbstractCardiacCellFactory<1>(),
      mpStimulus(new RegularStimulus(-250000,5,2000,1))
      {
      }

    AbstractCardiacCell* CreateCardiacCellForTissueNode(Node<1>* pNode)
    {
        AbstractCardiacCell* p_cell;

        /*
         * HOW_TO_TAG Cardiac/Problem definition
         * Use a CVODE adaptor solver in a tissue simulation
         */

        // Here we add a new Cvode Adaptor solver for every node.
        boost::shared_ptr<CvodeAdaptor> p_cvode_solver(new CvodeAdaptor());
        p_cvode_solver->SetMinimalReset(true);
        p_cvode_solver->SetTolerances(1e-4,1e-6);// NB These defaulted to different values in AbstractCvodeSystem.
        if (pNode->GetPoint()[0] == 0.0)
        {
            p_cell = new CellShannon2004FromCellML(p_cvode_solver,
                                                   mpStimulus);
        }
        else
        {
            p_cell = new CellShannon2004FromCellML(p_cvode_solver,
                                                   this->mpZeroStimulus);
        }

        return p_cell;
    }
};

/**
 *
 * Cell Factory defining Shannon cells for 1d chain.
 *
 * In this version each node has its own native Cvode solver
 */
class ShannonCvodeNativeCellFactory : public AbstractCardiacCellFactory<1>
{
private:

    boost::shared_ptr<RegularStimulus> mpStimulus;

public:
    ShannonCvodeNativeCellFactory()
    : AbstractCardiacCellFactory<1>(),
      mpStimulus(new RegularStimulus(-250000,5,2000,1))
      {
      }

    AbstractCvodeCell* CreateCardiacCellForTissueNode(Node<1>* pNode)
    {
        AbstractCvodeCell* p_cell;

        /*
         * HOW_TO_TAG Cardiac/Problem definition
         * Use a native CVODE cell in a tissue simulation
         */

        // Here we add a native Cvode cell (which includes its own solver) at every node.
        boost::shared_ptr<AbstractIvpOdeSolver> p_empty_solver;

        if (pNode->GetPoint()[0] == 0.0)
        {
            p_cell = new CellShannon2004FromCellMLCvode(p_empty_solver,
                                                        mpStimulus);
        }
        else
        {
            p_cell = new CellShannon2004FromCellMLCvode(p_empty_solver,
                                                        this->mpZeroStimulus);
        }
        // p_cell->SetMinimalReset(true); // This is now done by AbstractCardiacCellFactory for any AbstractCvodeCell.
        p_cell->SetTolerances(1e-4,1e-6); // NB These defaulted to different values in CvodeAdaptor.
        return p_cell;
    }
};
#endif // CHASTE_CVODE

/**
 * This class tests that a CVODE tissue simulation gets comparable results to those
 * of Forward and Backward Euler.
 *
 * At present FE and BE are more different than FE and CVODE.
 */
class Test1dMonodomainShannonCvodeBenchmarks : public CxxTest::TestSuite
{
private:
    bool CompareBenchmarkResults(const std::vector<double>& rReferenceTrace, const std::vector<double>& rTestTrace, double tol)
    {
        assert(rReferenceTrace.size()==rTestTrace.size());

        // See what the maximum difference in voltages recorded at final time at this node is
        unsigned last_time = rReferenceTrace.size() - 1u;
        double difference = fabs(rReferenceTrace[last_time] - rTestTrace[last_time]);

        // I was looping over all of the time trace here, but conduction velocity must
        // be slightly affected by the different solvers, giving rise to massive
        // (height of upstroke ~135mV) differences, so test at 'plateau' instead.

        // Return a false if it is too big.
        bool result = true;
        if (difference > tol)
        {
            std::cout << "\nDifference in recorded voltages = " << difference << std::endl << std::flush;
            result = false;
        }

        // Also return a false if the cell didn't get stimulated (assuming test only runs to plateau).
        if (rTestTrace[last_time] < 0)
        {
            std::cout << "Cell is not depolarized\n" << std::endl << std::flush;
            result = false;
        }

        return result;
    }

public:

    void TestWithDifferentCellsAndSolvers()
    {
        double duration = 25;
        HeartConfig::Instance()->SetSimulationDuration(duration); //ms
        HeartConfig::Instance()->SetMeshFileName("mesh/test/data/1D_0_to_1_100_elements");
        double pde_time_step = 0.1; //ms
        double printing_time_step = 0.1; //ms

        std::vector<double> fe_node_0;
        std::vector<double> fe_node_100;
        std::vector<double> times;

        {
            HeartConfig::Instance()->SetOutputDirectory("ShannonBenchmark/forward_euler");
            HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.0025,pde_time_step,printing_time_step);
            ShannonCardiacCellFactory<CellShannon2004FromCellML> cell_factory;
            MonodomainProblem<1> monodomain_problem( &cell_factory );

            monodomain_problem.Initialise();

            std::stringstream message;
            message << "1. Forward Euler for " << duration << " ms took";

            Timer::Reset();
            monodomain_problem.Solve();
            Timer::Print(message.str());

            Hdf5DataReader data_reader = monodomain_problem.GetDataReader();
            times = data_reader.GetUnlimitedDimensionValues();
            fe_node_0 = data_reader.GetVariableOverTime("V", 0);
            fe_node_100 = data_reader.GetVariableOverTime("V", 100);

        }

        /*
         * To test backward Euler you need to generate an extra Chaste variant of the model from the CellML.
         *
         * i.e. go to heart/src/odes/cellml/Shannon2004-conf.xml and add
         * <arg>--backward-euler</arg>
         *
         * then uncomment the //#include "Shannon2004BackwardEulerOpt.hpp" and the below block of code.
         *
         * Same idea for checking optimised models.
         */

//        {
//            HeartConfig::Instance()->SetOutputDirectory("ShannonBenchmark/backward_euler");
//            HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(pde_time_step,pde_time_step,printing_time_step);
//            ShannonCardiacCellFactory<CellShannon2004FromCellMLBackwardEulerOpt> cell_factory;
//            MonodomainProblem<1> monodomain_problem( &cell_factory );
//
//            monodomain_problem.Initialise();
//
//            std::stringstream message;
//            message << "2. Backward Euler for " << duration << " ms took";
//
//            Timer::Reset();
//            monodomain_problem.Solve();
//            Timer::Print(message.str());
//
//            Hdf5DataReader data_reader = monodomain_problem.GetDataReader();
//            std::vector<double> be_node_0 = data_reader.GetVariableOverTime("V", 0);
//            std::vector<double> be_node_100 = data_reader.GetVariableOverTime("V", 100);
//
//            TS_ASSERT(CompareBenchmarkResults(fe_node_0, be_node_0, 1.1));     // More than a milliVolt of difference with B.E.
//            TS_ASSERT(CompareBenchmarkResults(fe_node_100, be_node_100, 1.1)); // More than a milliVolt of difference with B.E.
//        }

#ifdef CHASTE_CVODE
        // First test a CVODE adaptor
        // The ODE system remains the same (std::vectors) and standard vectors are converted into N_Vectors
        // every time CVODE talks to the ODE system.
        {
            HeartConfig::Instance()->SetOutputDirectory("ShannonBenchmark/cvode_adaptor");
            HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(pde_time_step,pde_time_step,printing_time_step);
            ShannonCvodeAdaptorCellFactory cell_factory;
            MonodomainProblem<1> monodomain_problem( &cell_factory );

            monodomain_problem.Initialise();

            std::stringstream message;
            message << "2. CVODE adaptor for " << duration << " ms took";
            Timer::Reset();
            monodomain_problem.Solve();
            Timer::Print(message.str());

            Hdf5DataReader data_reader = monodomain_problem.GetDataReader();
            std::vector<double> cvode_node_0 = data_reader.GetVariableOverTime("V", 0);
            std::vector<double> cvode_node_100 = data_reader.GetVariableOverTime("V", 100);

            TS_ASSERT(CompareBenchmarkResults(fe_node_0, cvode_node_0, 0.4));     // Only 0.2 -- 0.4mV difference with CVODE
            TS_ASSERT(CompareBenchmarkResults(fe_node_100, cvode_node_100, 0.4)); // Only 0.2 -- 0.4mV difference with CVODE
        }


        // Now test a native CVODE cell
        // The ODE system uses N_Vectors, and interacts with CVODE optimally.
        // When Chaste needs to talk to the system, it converts to std::vector.
        {
            HeartConfig::Instance()->SetOutputDirectory("ShannonBenchmark/cvode_native");
            HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(pde_time_step,pde_time_step,printing_time_step);
            ShannonCvodeNativeCellFactory cell_factory;
            MonodomainProblem<1> monodomain_problem( &cell_factory );

            monodomain_problem.Initialise();

            std::stringstream message;
            message << "3. CVODE native for " << duration << " ms took";

            Timer::Reset();
            monodomain_problem.Solve();
            Timer::Print(message.str());

            Hdf5DataReader data_reader = monodomain_problem.GetDataReader();
            std::vector<double> cvode_node_0 = data_reader.GetVariableOverTime("V", 0);
            std::vector<double> cvode_node_100 = data_reader.GetVariableOverTime("V", 100);

            TS_ASSERT(CompareBenchmarkResults(fe_node_0, cvode_node_0, 0.4));     // Only 0.2 -- 0.4mV difference with CVODE
            TS_ASSERT(CompareBenchmarkResults(fe_node_100, cvode_node_100, 0.4)); // Only 0.2 -- 0.4mV difference with CVODE
        }
#endif // CHASTE_CVODE
    }
};

#endif /*TEST1DMONODOMAINSHANNONCVODEBENCHMARKS_HPP_*/