AbstractCardiacCellInterface.cpp

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#include "HeartConfig.hpp" // First for Boost 1.33/PETSc 2.2
#include "AbstractCardiacCellInterface.hpp"
#include "Exception.hpp"

#include "Citations.hpp"
static PetscBool CardiacCellChasteCite = PETSC_FALSE;
const char CardiacCellChasteCitation[] = "@article{cooper2015cce,\n"
" title = {{Cellular cardiac electrophysiology modelling with Chaste and CellML}},\n"
"  author = {Cooper, Jonathan and Spiteri, Raymond and Mirams, Gary R},\n"
"  year = {2015},\n"
"  journal = {Frontiers in Physiology},\n"
"  pages = {511},\n"
"  url = {http://journal.frontiersin.org/Journal/10.3389/fphys.2014.00511},\n"
"  volume = {5},\n"
"  doi = {10.3389/fphys.2014.00511},\n"
"}\n";

AbstractCardiacCellInterface::AbstractCardiacCellInterface(
            boost::shared_ptr<AbstractIvpOdeSolver> pOdeSolver,
            unsigned voltageIndex,
            boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
    : mVoltageIndex(voltageIndex),
      mpOdeSolver(pOdeSolver),
      mpIntracellularStimulus(pIntracellularStimulus),
      mSetVoltageDerivativeToZero(false),
      mIsUsedInTissue(false),
      mHasDefaultStimulusFromCellML(false),
      mFixedVoltage(DOUBLE_UNSET)
{
    // Record a reference for the calculations performed using this class,
    // can be extracted with the '-citations' flag as an argument to any executable.
    Citations::Register(CardiacCellChasteCitation, &CardiacCellChasteCite);
}


AbstractCardiacCellInterface::~AbstractCardiacCellInterface()
{
}


unsigned AbstractCardiacCellInterface::GetVoltageIndex()
{
    return mVoltageIndex;
}


void AbstractCardiacCellInterface::SetStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus)
{
    SetIntracellularStimulusFunction(pStimulus);
}


double AbstractCardiacCellInterface::GetStimulus(double time)
{
    return GetIntracellularStimulus(time);
}


void AbstractCardiacCellInterface::SetIntracellularStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus)
{
    mpIntracellularStimulus = pStimulus;
}


double AbstractCardiacCellInterface::GetIntracellularStimulus(double time)
{
    return mpIntracellularStimulus->GetStimulus(time);
}


double AbstractCardiacCellInterface::GetIntracellularAreaStimulus(double time)
{
    double stim;
    if (mIsUsedInTissue)
    {
        // Convert from uA/cm^3 to uA/cm^2 by dividing by Am
        stim = GetIntracellularStimulus(time) / HeartConfig::Instance()->GetSurfaceAreaToVolumeRatio();
    }
    else
    {
        stim = GetIntracellularStimulus(time);
    }
    return stim;
}

void AbstractCardiacCellInterface::SetUsedInTissueSimulation(bool tissue)
{
    mIsUsedInTissue = tissue;
}

boost::shared_ptr<RegularStimulus> AbstractCardiacCellInterface::UseCellMLDefaultStimulus()
{
    assert(!mHasDefaultStimulusFromCellML);
    EXCEPTION("This class has no default stimulus from CellML metadata.");
    return boost::shared_ptr<RegularStimulus>();
}

bool AbstractCardiacCellInterface::HasCellMLDefaultStimulus()
{
    return mHasDefaultStimulusFromCellML;
}

boost::shared_ptr<AbstractStimulusFunction> AbstractCardiacCellInterface::GetStimulusFunction()
{
    return mpIntracellularStimulus;
}

// Methods needed by boost serialization.
const boost::shared_ptr<AbstractStimulusFunction> AbstractCardiacCellInterface::GetStimulusFunction() const
{
    return mpIntracellularStimulus;
}

const boost::shared_ptr<AbstractIvpOdeSolver> AbstractCardiacCellInterface::GetSolver() const
{
    return mpOdeSolver;
}

void AbstractCardiacCellInterface::SetSolver(boost::shared_ptr<AbstractIvpOdeSolver> pSolver)
{
    mpOdeSolver = pSolver;
}

void AbstractCardiacCellInterface::SetVoltageDerivativeToZero(bool clamp)
{
    mSetVoltageDerivativeToZero = clamp;
    if (clamp)
    {
        mFixedVoltage = GetVoltage();
    }
}

void AbstractCardiacCellInterface::SetFixedVoltage(double voltage)
{
    mFixedVoltage = voltage;
}

double AbstractCardiacCellInterface::GetIntracellularCalciumConcentration()
{
    EXCEPTION("AbstractCardiacCellInterface::GetIntracellularCalciumConcentration() called. "
              "Either model has no [Ca_i] or method has not been implemented yet");
}