AbstractGeneralizedRushLarsenCardiacCell.cpp

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/*
Megan E. Marsh, Raymond J. Spiteri
Numerical Simulation Laboratory
University of Saskatchewan
December 2011
Partial support provided by research grants from the National
Science and Engineering Research Council (NSERC) of Canada
and the MITACS/Mprime Canadian Network of Centres of Excellence.
*/

#include "AbstractGeneralizedRushLarsenCardiacCell.hpp"
#include <cassert>
#include <cmath>
#include "Exception.hpp"
#include "OdeSolution.hpp"
#include "TimeStepper.hpp"

AbstractGeneralizedRushLarsenCardiacCell::AbstractGeneralizedRushLarsenCardiacCell(unsigned numberOfStateVariables,
                                                             unsigned voltageIndex,
                                                             boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
    : AbstractCardiacCell(boost::shared_ptr<AbstractIvpOdeSolver>(),
                          numberOfStateVariables,
                          voltageIndex,
                          pIntracellularStimulus),
      mHasAnalyticJacobian(false)
{
    mPartialF.resize(numberOfStateVariables);
    mEvalF.resize(numberOfStateVariables);
    mYInit.resize(numberOfStateVariables);
}

AbstractGeneralizedRushLarsenCardiacCell::~AbstractGeneralizedRushLarsenCardiacCell()
{}

OdeSolution AbstractGeneralizedRushLarsenCardiacCell::Compute(double tStart, double tEnd, double tSamp)
{
    // Check length of time interval
    if (tSamp < mDt)
    {
        tSamp = mDt;
    }
    const unsigned n_steps = (unsigned) floor((tEnd - tStart)/tSamp + 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 v_old, v_new;
    double& r_V = rGetStateVariables()[GetVoltageIndex()];
    for (unsigned i=0; i<n_steps; i++)
    {
        double curr_time = tStart;
        for (unsigned j=0; j<n_small_steps; j++)
        {
            curr_time = tStart + i*tSamp + j*mDt;
            v_old = r_V;
            UpdateTransmembranePotential(curr_time);
            v_new = r_V;
            r_V = v_old;
            ComputeOneStepExceptVoltage(curr_time);
            r_V = v_new;
            VerifyStateVariables();
        }

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

    return solutions;
}

void AbstractGeneralizedRushLarsenCardiacCell::ComputeExceptVoltage(double tStart, double tEnd)
{
    SetVoltageDerivativeToZero(true);
    TimeStepper stepper(tStart, tEnd, mDt);

    while (!stepper.IsTimeAtEnd())
    {
        ComputeOneStepExceptVoltage(stepper.GetTime());

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

        stepper.AdvanceOneTimeStep();
    }
    SetVoltageDerivativeToZero(false);
}

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

    double v_old, v_new;
    double& r_V = rGetStateVariables()[GetVoltageIndex()];
    while (!stepper.IsTimeAtEnd())
    {
        v_old = r_V;
        UpdateTransmembranePotential(stepper.GetTime());
        v_new = r_V;
        r_V = v_old;
        ComputeOneStepExceptVoltage(stepper.GetTime());
        r_V = v_new;
        VerifyStateVariables();

        stepper.AdvanceOneTimeStep();
    }
}

bool AbstractGeneralizedRushLarsenCardiacCell::HasAnalyticJacobian() const
{
    return mHasAnalyticJacobian;
}

void AbstractGeneralizedRushLarsenCardiacCell::ForceUseOfNumericalJacobian(bool useNumericalJacobian)
{
    if (!useNumericalJacobian)
    {
        EXCEPTION("Using analytic Jacobian terms for generalised Rush-Larsen is not yet supported.");
    }
//    if (!useNumericalJacobian && !mHasAnalyticJacobian)
//    {
//        EXCEPTION("Analytic Jacobian requested, but this ODE system doesn't have one. You can check this with HasAnalyticJacobian().");
//    }
    mUseAnalyticJacobian = !useNumericalJacobian;
}