AbstractBackwardEulerCardiacCell.hpp

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#ifndef ABSTRACTBACKWARDEULERCARDIACCELL_HPP_
#define ABSTRACTBACKWARDEULERCARDIACCELL_HPP_

#include <cassert>
#include <cmath>

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include "ClassIsAbstract.hpp"

#include "AbstractCardiacCell.hpp"
#include "Exception.hpp"
#include "PetscTools.hpp"
#include "TimeStepper.hpp"

template<unsigned SIZE>
class AbstractBackwardEulerCardiacCell : public AbstractCardiacCell
{
    private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // This calls serialize on the base class.
        archive & boost::serialization::base_object<AbstractCardiacCell>(*this);
    }
public:

    AbstractBackwardEulerCardiacCell(
        unsigned numberOfStateVariables,
        unsigned voltageIndex,
        boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);

    virtual ~AbstractBackwardEulerCardiacCell();

    virtual void ComputeResidual(double time, const double rCurrentGuess[SIZE], double rResidual[SIZE])=0;

    virtual void ComputeJacobian(double time, const double rCurrentGuess[SIZE], double rJacobian[SIZE][SIZE])=0;

    OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0);

    void ComputeExceptVoltage(double tStart, double tEnd);

    void SolveAndUpdateState(double tStart, double tEnd);

private:
#define COVERAGE_IGNORE

    void EvaluateYDerivatives(double time, const std::vector<double> &rY, std::vector<double> &rDY)
    {
        NEVER_REACHED;
    }
#undef COVERAGE_IGNORE

protected:
    virtual void ComputeOneStepExceptVoltage(double tStart)=0;

    virtual void UpdateTransmembranePotential(double time)=0;
};


/*
 * NOTE: Explicit instantiation is not used for this class, because the SIZE
 * template parameter could take arbitrary values.
 */


template <unsigned SIZE>
AbstractBackwardEulerCardiacCell<SIZE>::AbstractBackwardEulerCardiacCell(
    unsigned numberOfStateVariables,
    unsigned voltageIndex,
    boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
        : AbstractCardiacCell(boost::shared_ptr<AbstractIvpOdeSolver>(),
                              numberOfStateVariables,
                              voltageIndex,
                              pIntracellularStimulus)
{}

template <unsigned SIZE>
AbstractBackwardEulerCardiacCell<SIZE>::~AbstractBackwardEulerCardiacCell()
{}

template <unsigned SIZE>
OdeSolution AbstractBackwardEulerCardiacCell<SIZE>::Compute(double tStart, double tEnd, double tSamp)
{
    // In this method, we iterate over timesteps, doing the following for each:
    //   - update V using a forward Euler step
    //   - call ComputeExceptVoltage(t) to update the remaining state variables
    //     using backward Euler

    // Check length of time interval
    if (tSamp < mDt)
    {
        tSamp = mDt;
    }
    double _n_steps = (tEnd - tStart) / tSamp;
    const unsigned n_steps = (unsigned) floor(_n_steps+0.5);
    assert(fabs(tStart+n_steps*tSamp - tEnd) < 1e-12);
    const unsigned n_small_steps = (unsigned) floor(tSamp/mDt+0.5);
    assert(fabs(mDt*n_small_steps - tSamp) < 1e-12);

    // Initialise solution store
    OdeSolution solutions;
    solutions.SetNumberOfTimeSteps(n_steps);
    solutions.rGetSolutions().push_back(rGetStateVariables());
    solutions.rGetTimes().push_back(tStart);
    solutions.SetOdeSystemInformation(this->mpSystemInfo);

    // Loop over time
    double curr_time = tStart;
    for (unsigned i=0; i<n_steps; i++)
    {
        for (unsigned j=0; j<n_small_steps; j++)
        {
            curr_time = tStart + i*tSamp + j*mDt;

            // Compute next value of V
            UpdateTransmembranePotential(curr_time);

            // Compute other state variables
            ComputeOneStepExceptVoltage(curr_time);

            // check gating variables are still in range
            VerifyStateVariables();
        }

        // Update solutions
        solutions.rGetSolutions().push_back(rGetStateVariables());
        solutions.rGetTimes().push_back(curr_time+mDt);
    }

    return solutions;
}

template <unsigned SIZE>
void AbstractBackwardEulerCardiacCell<SIZE>::ComputeExceptVoltage(double tStart, double tEnd)
{
    // This method iterates over timesteps, calling ComputeExceptVoltage(t) at
    // each one, to update all state variables except for V, using backward Euler.

    // Check length of time interval
    unsigned n_steps = (unsigned)((tEnd - tStart) / mDt + 0.5);
    assert(fabs(tStart + n_steps*mDt - tEnd) < 1e-12);

    // Loop over time
    double curr_time;
    for (unsigned i=0; i<n_steps; i++)
    {
        curr_time = tStart + i*mDt;

        // Compute other state variables
        ComputeOneStepExceptVoltage(curr_time);

#ifndef NDEBUG
        // Check gating variables are still in range
        VerifyStateVariables();
#endif // NDEBUG
    }
}

template<unsigned SIZE>
void AbstractBackwardEulerCardiacCell<SIZE>::SolveAndUpdateState(double tStart, double tEnd)
{
    TimeStepper stepper(tStart, tEnd, mDt);

    while(!stepper.IsTimeAtEnd())
    {
        double time = stepper.GetTime();

        // Compute next value of V
        UpdateTransmembranePotential(time);

        // Compute other state variables
        ComputeOneStepExceptVoltage(time);

        // check gating variables are still in range
        VerifyStateVariables();

        stepper.AdvanceOneTimeStep();
    }
}




template<>
class AbstractBackwardEulerCardiacCell<0u> : public AbstractCardiacCell
{
private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // This calls serialize on the base class.
        archive & boost::serialization::base_object<AbstractCardiacCell>(*this);
    }

public:
    AbstractBackwardEulerCardiacCell(unsigned numberOfStateVariables,
                                     unsigned voltageIndex,
                                     boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
        : AbstractCardiacCell(boost::shared_ptr<AbstractIvpOdeSolver>(),
                              numberOfStateVariables,
                              voltageIndex,
                              pIntracellularStimulus)
    {}

    virtual ~AbstractBackwardEulerCardiacCell()
    {}

    OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)
    {
        // In this method, we iterate over timesteps, doing the following for each:
        //   - update V using a forward Euler step
        //   - call ComputeExceptVoltage(t) to update the remaining state variables
        //     using backward Euler

        // Check length of time interval
        if (tSamp < mDt)
        {
            tSamp = mDt;
        }
        double _n_steps = (tEnd - tStart) / tSamp;
        const unsigned n_steps = (unsigned) floor(_n_steps+0.5);
        assert(fabs(tStart+n_steps*tSamp - tEnd) < 1e-12);
        const unsigned n_small_steps = (unsigned) floor(tSamp/mDt+0.5);
        assert(fabs(mDt*n_small_steps - tSamp) < 1e-12);

        // Initialise solution store
        OdeSolution solutions;
        solutions.SetNumberOfTimeSteps(n_steps);
        solutions.rGetSolutions().push_back(rGetStateVariables());
        solutions.rGetTimes().push_back(tStart);
        solutions.SetOdeSystemInformation(this->mpSystemInfo);

        // Loop over time
        double curr_time = tStart;
        for (unsigned i=0; i<n_steps; i++)
        {
            for (unsigned j=0; j<n_small_steps; j++)
            {
                curr_time = tStart + i*tSamp + j*mDt;

                // Compute next value of V
                UpdateTransmembranePotential(curr_time);

                // Compute other state variables
                ComputeOneStepExceptVoltage(curr_time);

                // check gating variables are still in range
                VerifyStateVariables();
            }

            // Update solutions
            solutions.rGetSolutions().push_back(rGetStateVariables());
            solutions.rGetTimes().push_back(curr_time+mDt);
        }

        return solutions;
    }

    void ComputeExceptVoltage(double tStart, double tEnd)
    {
        // This method iterates over timesteps, calling ComputeExceptVoltage(t) at
        // each one, to update all state variables except for V, using backward Euler.

        // Check length of time interval
        unsigned n_steps = (unsigned)((tEnd - tStart) / mDt + 0.5);
        assert(fabs(tStart + n_steps*mDt - tEnd) < 1e-12);

        // Loop over time
        double curr_time;
        for (unsigned i=0; i<n_steps; i++)
        {
            curr_time = tStart + i*mDt;

            // Compute other state variables
            ComputeOneStepExceptVoltage(curr_time);

#ifndef NDEBUG
            // Check gating variables are still in range
            VerifyStateVariables();
#endif // NDEBUG
        }
    }

    void SolveAndUpdateState(double tStart, double tEnd)
    {
        TimeStepper stepper(tStart, tEnd, mDt);

        while(!stepper.IsTimeAtEnd())
        {
            double time = stepper.GetTime();

            // Compute next value of V
            UpdateTransmembranePotential(time);

            // Compute other state variables
            ComputeOneStepExceptVoltage(time);

            // check gating variables are still in range
            VerifyStateVariables();

            stepper.AdvanceOneTimeStep();
        }
    }

private:
#define COVERAGE_IGNORE

    void EvaluateYDerivatives(double time, const std::vector<double> &rY, std::vector<double> &rDY)
    {
        NEVER_REACHED;
    }
#undef COVERAGE_IGNORE

protected:
    virtual void ComputeOneStepExceptVoltage(double tStart)=0;

    virtual void UpdateTransmembranePotential(double time)=0;
};


// Debugging
#ifndef NDEBUG
#include "OutputFileHandler.hpp"
#include <boost/foreach.hpp>
template<unsigned SIZE>
void DumpJacobianToFile(double time, const double rCurrentGuess[SIZE], double rJacobian[SIZE][SIZE],
                        const std::vector<double>& rY)
{
    OutputFileHandler handler("DumpJacs", false);
    out_stream p_file = handler.OpenOutputFile("J.txt", std::ios::app);
    (*p_file) << "At " << time << " " << SIZE << std::endl;
    (*p_file) << "rY";
    BOOST_FOREACH(double y, rY)
    {
        (*p_file) << " " << y;
    }
    (*p_file) << std::endl;
    (*p_file) << "rCurrentGuess";
    for (unsigned i=0; i<SIZE; i++)
    {
        (*p_file) << " " << rCurrentGuess[i];
    }
    (*p_file) << std::endl;
    (*p_file) << "rJacobian";
    for (unsigned i=0; i<SIZE; i++)
    {
        for (unsigned j=0; j<SIZE; j++)
        {
            (*p_file) << " " << rJacobian[i][j];
        }
    }
    (*p_file) << std::endl;
}
#endif



TEMPLATED_CLASS_IS_ABSTRACT_1_UNSIGNED(AbstractBackwardEulerCardiacCell)

#endif /*ABSTRACTBACKWARDEULERCARDIACCELL_HPP_*/