AveragedSourceParabolicPde.cpp

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#include "AveragedSourceParabolicPde.hpp"
#include "ApoptoticCellProperty.hpp"
 
template<unsigned DIM>
AveragedSourceParabolicPde<DIM>::AveragedSourceParabolicPde(AbstractCellPopulation<DIM,DIM>& rCellPopulation,
                                                            double constantSourceCoefficient, 
                                                            double linearSourceCoefficient, 
                                                            double diffusionCoefficient,
                                                            double duDtCoefficient,
                                                            bool scaleByCellVolume)
    : mrCellPopulation(rCellPopulation),
      mConstantSourceCoefficient(constantSourceCoefficient),
      mLinearSourceCoefficient(linearSourceCoefficient),
      mDiffusionCoefficient(diffusionCoefficient),
      mDuDtCoefficient(duDtCoefficient),
      mScaleByCellVolume(scaleByCellVolume)
{
}
AveragedSourceParabolicPde<DIM>::AveragedSourceParabolicPde(AbstractCellPopulation<DIM,DIM>& rCellPopulation, {…}
 
template<unsigned DIM>
const AbstractCellPopulation<DIM,DIM>& AveragedSourceParabolicPde<DIM>::rGetCellPopulation() const
{
    return mrCellPopulation;
}
const AbstractCellPopulation<DIM,DIM>& AveragedSourceParabolicPde<DIM>::rGetCellPopulation() const {…}
 
template<unsigned DIM>
double AveragedSourceParabolicPde<DIM>::GetConstantCoefficient() const
{
    return mConstantSourceCoefficient;
}
double AveragedSourceParabolicPde<DIM>::GetConstantCoefficient() const {…}
 
template<unsigned DIM>
double AveragedSourceParabolicPde<DIM>::GetLinearCoefficient() const
{
    return mLinearSourceCoefficient;
}
double AveragedSourceParabolicPde<DIM>::GetLinearCoefficient() const {…}
 
template<unsigned DIM>
double AveragedSourceParabolicPde<DIM>::GetDiffusionCoefficient() const
{
    return mDiffusionCoefficient;
}
double AveragedSourceParabolicPde<DIM>::GetDiffusionCoefficient() const {…}
 
template<unsigned DIM>
double AveragedSourceParabolicPde<DIM>::GetDuDtCoefficient() const
{
    return mDuDtCoefficient;
}
double AveragedSourceParabolicPde<DIM>::GetDuDtCoefficient() const {…}
 
template<unsigned DIM>
bool AveragedSourceParabolicPde<DIM>::GetScaleByCellVolume() const
{
    return mScaleByCellVolume;
}
bool AveragedSourceParabolicPde<DIM>::GetScaleByCellVolume() const {…}
 
template<unsigned DIM>
void AveragedSourceParabolicPde<DIM>::SetupSourceTerms(TetrahedralMesh<DIM,DIM>& rCoarseMesh, std::map<CellPtr, unsigned>* pCellPdeElementMap) // must be called before solve
{
    // Allocate memory
    mCellDensityOnCoarseElements.resize(rCoarseMesh.GetNumElements());
    for (double & mCellDensityOnCoarseElement : mCellDensityOnCoarseElements)
    {
        mCellDensityOnCoarseElement = 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 != nullptr)
        {
            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)
        {
            double cell_weight = 1.0;
 
            if (mScaleByCellVolume)
            {   
                // If scaling by cell volume then use volume her instead of cell count 
                cell_weight = mrCellPopulation.GetVolumeOfCell(*cell_iter);
 
                if (cell_weight <1e-6)
                {
                    EXCEPTION("The volume of one of the cells is " << cell_weight << 
                              " and you are scaling by cell volume. Either turn scaling off or use"  
                              " a cell model with non zero areas (i.e. a Bounded Voronoi Tesselation model).");
                }
            }
 
            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<mCellDensityOnCoarseElements.size(); elem_index++)
    {
        rCoarseMesh.GetElement(elem_index)->CalculateJacobian(jacobian, det);
        mCellDensityOnCoarseElements[elem_index] /= rCoarseMesh.GetElement(elem_index)->GetVolume(det);
    }
}
void AveragedSourceParabolicPde<DIM>::SetupSourceTerms(TetrahedralMesh<DIM,DIM>& rCoarseMesh, std::map<CellPtr, unsigned>* pCellPdeElementMap) // must be called before solve {…}
 
template<unsigned DIM>
double AveragedSourceParabolicPde<DIM>::ComputeDuDtCoefficientFunction(const ChastePoint<DIM>& )
{
    return mDuDtCoefficient;
}
double AveragedSourceParabolicPde<DIM>::ComputeDuDtCoefficientFunction(const ChastePoint<DIM>& ) {…}
 
template<unsigned DIM>
double AveragedSourceParabolicPde<DIM>::ComputeSourceTerm(const ChastePoint<DIM>& rX, double u, Element<DIM,DIM>* pElement)
{
    assert(!mCellDensityOnCoarseElements.empty());
 
    // The source term is (a*u + b)*density
    double source_term = (mLinearSourceCoefficient * u + mConstantSourceCoefficient) * mCellDensityOnCoarseElements[pElement->GetIndex()];
   
    return source_term;
}
double AveragedSourceParabolicPde<DIM>::ComputeSourceTerm(const ChastePoint<DIM>& rX, double u, Element<DIM,DIM>* pElement) {…}
 
// LCOV_EXCL_START
template<unsigned DIM>
double AveragedSourceParabolicPde<DIM>::ComputeSourceTermAtNode(const Node<DIM>& rNode, double u)
{
    NEVER_REACHED;
}
double AveragedSourceParabolicPde<DIM>::ComputeSourceTermAtNode(const Node<DIM>& rNode, double u) {…}
// LCOV_EXCL_STOP
 
template<unsigned DIM>
c_matrix<double,DIM,DIM> AveragedSourceParabolicPde<DIM>::ComputeDiffusionTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement)
{
    return mDiffusionCoefficient*identity_matrix<double>(DIM);
}
c_matrix<double,DIM,DIM> AveragedSourceParabolicPde<DIM>::ComputeDiffusionTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement) {…}
 
template<unsigned DIM>
double AveragedSourceParabolicPde<DIM>::GetUptakeRateForElement(unsigned elementIndex)
{
    return this->mCellDensityOnCoarseElements[elementIndex];
}
double AveragedSourceParabolicPde<DIM>::GetUptakeRateForElement(unsigned elementIndex) {…}
 
// Explicit instantiation
template class AveragedSourceParabolicPde<1>;
template class AveragedSourceParabolicPde<2>;
template class AveragedSourceParabolicPde<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(AveragedSourceParabolicPde)