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)
{
    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
    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;
           // EvaluateEquations(curr_time, dy);
            UpdateTransmembranePotential(curr_time);
            ComputeOneStepExceptVoltage(curr_time);
            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);

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

        stepper.AdvanceOneTimeStep();
    }
}