AveragedSourcePde.cpp

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#include "AveragedSourcePde.hpp"
#include "ApoptoticCellProperty.hpp"
#include "PetscTools.hpp"

template<unsigned DIM>
AveragedSourcePde<DIM>::AveragedSourcePde(AbstractCellPopulation<DIM>& rCellPopulation, double coefficient)
    : mrCellPopulation(rCellPopulation),
      mCoefficient(coefficient)
{
}

template<unsigned DIM>
const AbstractCellPopulation<DIM>& AveragedSourcePde<DIM>::rGetCellPopulation() const
{
    return mrCellPopulation;
}

template<unsigned DIM>
double AveragedSourcePde<DIM>::GetCoefficient() const
{
    return mCoefficient;
}

template<unsigned DIM>
void AveragedSourcePde<DIM>::SetupSourceTerms(TetrahedralMesh<DIM,DIM>& rCoarseMesh, std::map< CellPtr, unsigned >* pCellPdeElementMap) // must be called before solve
{
    // Allocate memory
    mCellDensityOnCoarseElements.resize(rCoarseMesh.GetNumElements());
    for (unsigned elem_index=0; elem_index<mCellDensityOnCoarseElements.size(); elem_index++)
    {
        mCellDensityOnCoarseElements[elem_index] = 0.0;
    }

    // Loop over cells, find which coarse element it is in, and add 1 to mSourceTermOnCoarseElements[elem_index]
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = mrCellPopulation.Begin();
         cell_iter != mrCellPopulation.End();
         ++cell_iter)
    {
        unsigned elem_index = 0;
        const ChastePoint<DIM>& r_position_of_cell = mrCellPopulation.GetLocationOfCellCentre(*cell_iter);

        if (pCellPdeElementMap != NULL)
        {
            elem_index = (*pCellPdeElementMap)[*cell_iter];
        }
        else
        {
            elem_index = rCoarseMesh.GetContainingElementIndex(r_position_of_cell);
        }

        // Update element map if cell has moved
        bool cell_is_apoptotic = cell_iter->template HasCellProperty<ApoptoticCellProperty>();

        if (!cell_is_apoptotic)
        {
            mCellDensityOnCoarseElements[elem_index] += 1.0;
        }
    }

    // Then divide each entry of mSourceTermOnCoarseElements by the element's area
    c_matrix<double, DIM, DIM> jacobian;
    double det;
    for (unsigned elem_index=0; elem_index<mCellDensityOnCoarseElements.size(); elem_index++)
    {
        rCoarseMesh.GetElement(elem_index)->CalculateJacobian(jacobian, det);
        mCellDensityOnCoarseElements[elem_index] /= rCoarseMesh.GetElement(elem_index)->GetVolume(det);
    }
}

template<unsigned DIM>
double AveragedSourcePde<DIM>::ComputeConstantInUSourceTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement)
{
    return 0.0;
}

template<unsigned DIM>
double AveragedSourcePde<DIM>::ComputeLinearInUCoeffInSourceTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement) // now takes in element
{
    assert(!mCellDensityOnCoarseElements.empty());
    return mCoefficient * mCellDensityOnCoarseElements[pElement->GetIndex()];
}

template<unsigned DIM>
c_matrix<double,DIM,DIM> AveragedSourcePde<DIM>::ComputeDiffusionTerm(const ChastePoint<DIM>& rX)
{
    return identity_matrix<double>(DIM);
}

template<unsigned DIM>
double AveragedSourcePde<DIM>::GetUptakeRateForElement(unsigned elementIndex)
{
    return this->mCellDensityOnCoarseElements[elementIndex];
}

// Explicit instantiation

template class AveragedSourcePde<1>;
template class AveragedSourcePde<2>;
template class AveragedSourcePde<3>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(AveragedSourcePde)