AbstractOdeBasedCellCycleModel.cpp

/*

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*/

#include "AbstractOdeBasedCellCycleModel.hpp"

AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel(double lastTime,
                                                               boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : CellCycleModelOdeHandler(lastTime, pOdeSolver),
      mDivideTime(lastTime)
{
    AbstractCellCycleModel::SetBirthTime(lastTime);
}

AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel()
{
}

AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel(const AbstractOdeBasedCellCycleModel& rModel)
    : AbstractCellCycleModel(rModel),
      CellCycleModelOdeHandler(rModel),
      mDivideTime(rModel.mDivideTime)
{
    /*
     * Initialize only those member variables defined in this class.
     *
     * The member variables mBirthTime, mReadyToDivide and mDimension
     * are initialized in the AbstractCellCycleModel constructor.
     */
}

void AbstractOdeBasedCellCycleModel::SetBirthTime(double birthTime)
{
    AbstractCellCycleModel::SetBirthTime(birthTime);
    mLastTime = birthTime;
    mDivideTime = birthTime;
}

bool AbstractOdeBasedCellCycleModel::ReadyToDivide()
{
    assert(mpCell != nullptr);

    if (!mReadyToDivide)
    {
        assert(mpOdeSystem != nullptr);

        double current_time = SimulationTime::Instance()->GetTime();

        if (current_time > mLastTime)
        {
            // Update whether a stopping event has occurred
            mReadyToDivide = SolveOdeToTime(current_time);

            // Check no concentrations have gone negative
            for (unsigned i=0; i<mpOdeSystem->GetNumberOfStateVariables(); i++)
            {
                if (mpOdeSystem->rGetStateVariables()[i] < -DBL_EPSILON)
                {
                    // LCOV_EXCL_START
                    EXCEPTION("A protein concentration " << i << " has gone negative (" <<
                              mpOdeSystem->rGetStateVariables()[i] << ")\n"
                              << "Chaste predicts that the CellCycleModel numerical method is probably unstable.");
                    // LCOV_EXCL_STOP
                }
            }
            if (mReadyToDivide)
            {
                mDivideTime = GetOdeStopTime();
            }
        }
    }
    return mReadyToDivide;
}

void AbstractOdeBasedCellCycleModel::ResetForDivision()
{
    assert(mReadyToDivide);
    AbstractCellCycleModel::ResetForDivision();
    mBirthTime = mDivideTime;
    mLastTime = mDivideTime;
    mDivideTime = DBL_MAX;
}

double AbstractOdeBasedCellCycleModel::GetOdeStopTime()
{
    double stop_time = DOUBLE_UNSET;
    if (mpOdeSolver->StoppingEventOccurred())
    {
        stop_time = mpOdeSolver->GetStoppingTime();
    }
    return stop_time;
}

void AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
    // No new parameters to output, so just call method on direct parent class
    AbstractCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
}