AbstractTargetAreaModifier.cpp

/*

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*/

#include "AbstractTargetAreaModifier.hpp"

template<unsigned DIM>
AbstractTargetAreaModifier<DIM>::AbstractTargetAreaModifier()
    : AbstractCellBasedSimulationModifier<DIM>(),
      mReferenceTargetArea(1.0)
{
}

template<unsigned DIM>
AbstractTargetAreaModifier<DIM>::~AbstractTargetAreaModifier()
{
}

template<unsigned DIM>
void AbstractTargetAreaModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    UpdateTargetAreas(rCellPopulation);
}

template<unsigned DIM>
void AbstractTargetAreaModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
{
    if (dynamic_cast<VertexBasedCellPopulation<DIM>*>(&rCellPopulation) == NULL)
    {
        EXCEPTION("AbstractTargetAreaModifiers are to be used with a VertexBasedCellPopulation only");
    }

    /*
     * We must update CellData in SetupSolve(), otherwise it will not have been
     * fully initialised by the time we enter the main time loop.
     */
    UpdateTargetAreas(rCellPopulation);
}

template<unsigned DIM>
void AbstractTargetAreaModifier<DIM>::UpdateTargetAreas(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Assume that SetupSolve() has already been called, so we must be using a VertexBasedCellPopulation

    // Loop over the list of cells, rather than using the population iterator, so as to include dead cells
    for (std::list<CellPtr>::iterator cell_iter = rCellPopulation.rGetCells().begin();
         cell_iter != rCellPopulation.rGetCells().end();
         ++cell_iter)
    {
        UpdateTargetAreaOfCell(*cell_iter);
    }
}

template<unsigned DIM>
double AbstractTargetAreaModifier<DIM>::GetReferenceTargetArea()
{
    return mReferenceTargetArea;
}

template<unsigned DIM>
void AbstractTargetAreaModifier<DIM>::SetReferenceTargetArea(double referenceTargetArea)
{
    assert(referenceTargetArea >= 0.0);
    mReferenceTargetArea = referenceTargetArea;
}

template<unsigned DIM>
void AbstractTargetAreaModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<ReferenceTargetArea>" << mReferenceTargetArea << "</ReferenceTargetArea>\n";

    // Next, call method on direct parent class
    AbstractCellBasedSimulationModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}

// Explicit instantiation
template class AbstractTargetAreaModifier<1>;
template class AbstractTargetAreaModifier<2>;
template class AbstractTargetAreaModifier<3>;