AbstractOdeBasedPhaseBasedCellCycleModel.cpp

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*/
 
#include "AbstractOdeBasedPhaseBasedCellCycleModel.hpp"
 
AbstractOdeBasedPhaseBasedCellCycleModel::AbstractOdeBasedPhaseBasedCellCycleModel(double lastTime,
                                                               boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : CellCycleModelOdeHandler(lastTime, pOdeSolver),
      mDivideTime(lastTime),
      mG2PhaseStartTime(DBL_MAX)
{
    AbstractPhaseBasedCellCycleModel::SetBirthTime(lastTime);
}
 
AbstractOdeBasedPhaseBasedCellCycleModel::~AbstractOdeBasedPhaseBasedCellCycleModel()
{
}
 
AbstractOdeBasedPhaseBasedCellCycleModel::AbstractOdeBasedPhaseBasedCellCycleModel(const AbstractOdeBasedPhaseBasedCellCycleModel& rModel)
    : AbstractPhaseBasedCellCycleModel(rModel),
      CellCycleModelOdeHandler(rModel),
      mDivideTime(rModel.mDivideTime),
      mG2PhaseStartTime(rModel.mG2PhaseStartTime)
{
    /*
     * Initialize only those member variables defined in this class.
     *
     * The member variables mCurrentCellCyclePhase, mG1Duration,
     * mMinimumGapDuration, mStemCellG1Duration, mTransitCellG1Duration,
     * mSDuration, mG2Duration and mMDuration are initialized in the
     * AbstractPhaseBasedCellCycleModel constructor.
     *
     * The member variables mBirthTime, mReadyToDivide and mDimension
     * are initialized in the AbstractCellCycleModel constructor.
     */
}
 
void AbstractOdeBasedPhaseBasedCellCycleModel::SetBirthTime(double birthTime)
{
    AbstractPhaseBasedCellCycleModel::SetBirthTime(birthTime);
    mLastTime = birthTime;
    mDivideTime = birthTime;
}
 
void AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase()
{
    assert(mpOdeSystem != nullptr);
 
    double current_time = SimulationTime::Instance()->GetTime();
 
    // Update the phase from M to G1 when necessary
    if (mCurrentCellCyclePhase == M_PHASE)
    {
        double m_duration = GetMDuration();
        if (GetAge() >= m_duration)
        {
            mCurrentCellCyclePhase = G_ONE_PHASE;
            mLastTime = m_duration + mBirthTime;
        }
        else
        {
            // Still dividing; don't run ODEs
            return;
        }
    }
 
    if (current_time > mLastTime)
    {
        if (!this->mFinishedRunningOdes)
        {
            // Update whether a stopping event has occurred
            this->mFinishedRunningOdes = 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 (this->mFinishedRunningOdes)
            {
                // Update durations of each phase
                mG1Duration = GetOdeStopTime() - mBirthTime - GetMDuration();
                mG2PhaseStartTime = GetOdeStopTime() + GetSDuration();
                mDivideTime = mG2PhaseStartTime + GetG2Duration();
 
                // Update phase
                if (current_time >= mG2PhaseStartTime)
                {
                    mCurrentCellCyclePhase = G_TWO_PHASE;
                }
                else
                {
                    mCurrentCellCyclePhase = S_PHASE;
                }
            }
        }
        else
        {
            // ODE model finished, just increasing time until division...
            if (current_time >= mG2PhaseStartTime)
            {
                mCurrentCellCyclePhase = G_TWO_PHASE;
            }
        }
    }
}
 
void AbstractOdeBasedPhaseBasedCellCycleModel::ResetForDivision()
{
    assert(this->mFinishedRunningOdes);
    AbstractPhaseBasedCellCycleModel::ResetForDivision();
    mBirthTime = mDivideTime;
    mLastTime = mDivideTime;
    this->mFinishedRunningOdes = false;
    mG1Duration = DBL_MAX;
    mDivideTime = DBL_MAX;
}
 
double AbstractOdeBasedPhaseBasedCellCycleModel::GetOdeStopTime()
{
    double stop_time = DOUBLE_UNSET;
    if (mpOdeSolver->StoppingEventOccurred())
    {
        stop_time = mpOdeSolver->GetStoppingTime();
    }
    return stop_time;
}
 
void AbstractOdeBasedPhaseBasedCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
    // No new parameters to output, so just call method on direct parent class
    AbstractPhaseBasedCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
}