VolumeDependentAveragedSourcePde.cpp

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#include "VolumeDependentAveragedSourcePde.hpp"
#include "ApoptoticCellProperty.hpp"

template<unsigned DIM>
VolumeDependentAveragedSourcePde<DIM>::VolumeDependentAveragedSourcePde(AbstractCellPopulation<DIM>& rCellPopulation, double coefficient)
    : AveragedSourcePde<DIM>(rCellPopulation, coefficient)
{
    assert(dynamic_cast<NodeBasedCellPopulation<DIM>*>(&(this->mrCellPopulation)));
    mpStaticCastCellPopulation = static_cast<NodeBasedCellPopulation<DIM>*>(&(this->mrCellPopulation));
}

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

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

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

        unsigned node_index = this->mrCellPopulation.GetLocationIndexUsingCell(*cell_iter);

        // Uptake normalised to 1 for unit cell
        double radius = mpStaticCastCellPopulation->rGetMesh().GetCellRadius(node_index);
        double cell_weight = radius*radius;

        bool cell_is_apoptotic = cell_iter->template HasCellProperty<ApoptoticCellProperty>();
        if (!cell_is_apoptotic)
        {
            this->mCellDensityOnCoarseElements[elem_index] += cell_weight;
        }
    }

    // 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<this->mCellDensityOnCoarseElements.size(); elem_index++)
    {
        rCoarseMesh.GetElement(elem_index)->CalculateJacobian(jacobian, det);
        this->mCellDensityOnCoarseElements[elem_index] /= rCoarseMesh.GetElement(elem_index)->GetVolume(det);
    }
}

// Explicit instantiation

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

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