AbstractRushLarsenCardiacCell.cpp

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#include "AbstractRushLarsenCardiacCell.hpp"

#include <cassert>
#include <cmath>

#include "Exception.hpp"
#include "OdeSolution.hpp"
#include "TimeStepper.hpp"

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

AbstractRushLarsenCardiacCell::~AbstractRushLarsenCardiacCell()
{}

OdeSolution AbstractRushLarsenCardiacCell::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
    //   - do as in ComputeExceptVoltage(t) to update the remaining state variables
    //     using Rush Larsen method or forward Euler as appropriate

    // 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);

    std::vector<double> dy(mNumberOfStateVariables, 0);
    std::vector<double> alpha(mNumberOfStateVariables, 0);
    std::vector<double> beta(mNumberOfStateVariables, 0);

    // 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, alpha, beta);
            UpdateTransmembranePotential(dy);
            ComputeOneStepExceptVoltage(dy, alpha, beta);
            VerifyStateVariables();
        }

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

    return solutions;
}

void AbstractRushLarsenCardiacCell::ComputeExceptVoltage(double tStart, double tEnd)
{
    mSetVoltageDerivativeToZero = true;
    TimeStepper stepper(tStart, tEnd, mDt);

    std::vector<double> dy(mNumberOfStateVariables, 0);
    std::vector<double> alpha(mNumberOfStateVariables, 0);
    std::vector<double> beta(mNumberOfStateVariables, 0);

    while (!stepper.IsTimeAtEnd())
    {
        EvaluateEquations(stepper.GetTime(), dy, alpha, beta);
        ComputeOneStepExceptVoltage(dy, alpha, beta);

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

        stepper.AdvanceOneTimeStep();
    }
    mSetVoltageDerivativeToZero = false;
}

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

    std::vector<double> dy(mNumberOfStateVariables, 0);
    std::vector<double> alpha(mNumberOfStateVariables, 0);
    std::vector<double> beta(mNumberOfStateVariables, 0);

    while (!stepper.IsTimeAtEnd())
    {
        EvaluateEquations(stepper.GetTime(), dy, alpha, beta);
        UpdateTransmembranePotential(dy);
        ComputeOneStepExceptVoltage(dy, alpha, beta);
        VerifyStateVariables();

        stepper.AdvanceOneTimeStep();
    }
}

void AbstractRushLarsenCardiacCell::UpdateTransmembranePotential(const std::vector<double> &rDY)
{
    unsigned v_index = GetVoltageIndex();
    rGetStateVariables()[v_index] += mDt*rDY[v_index];
}