CellwiseSourceEllipticPde.cpp

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#include "CellwiseSourceEllipticPde.hpp"
 
template<unsigned DIM>
CellwiseSourceEllipticPde<DIM>::CellwiseSourceEllipticPde(AbstractCellPopulation<DIM,DIM>& rCellPopulation,
                                                          const double constantSourceCoefficient,
                                                          const double linearSourceCoefficient,
                                                          const double diffusionCoefficient,
                                                          const bool scaleByCellVolume)
    : mrCellPopulation(rCellPopulation),
      mConstantSourceCoefficient(constantSourceCoefficient),
      mLinearSourceCoefficient(linearSourceCoefficient),
      mDiffusionCoefficient(diffusionCoefficient),
      mScaleByCellVolume(scaleByCellVolume)
{
}
CellwiseSourceEllipticPde<DIM>::CellwiseSourceEllipticPde(AbstractCellPopulation<DIM,DIM>& rCellPopulation, {…}
 
template<unsigned DIM>
const AbstractCellPopulation<DIM>& CellwiseSourceEllipticPde<DIM>::rGetCellPopulation() const
{
    return mrCellPopulation;
}
const AbstractCellPopulation<DIM>& CellwiseSourceEllipticPde<DIM>::rGetCellPopulation() const {…}
 
template<unsigned DIM>
double CellwiseSourceEllipticPde<DIM>::GetConstantCoefficient() const
{
    return mConstantSourceCoefficient;
}
double CellwiseSourceEllipticPde<DIM>::GetConstantCoefficient() const {…}
 
template<unsigned DIM>
double CellwiseSourceEllipticPde<DIM>::GetLinearCoefficient() const
{
    return mLinearSourceCoefficient;
}
double CellwiseSourceEllipticPde<DIM>::GetLinearCoefficient() const {…}
 
template<unsigned DIM>
double CellwiseSourceEllipticPde<DIM>::GetDiffusionCoefficient() const
{
    return mDiffusionCoefficient;
}
double CellwiseSourceEllipticPde<DIM>::GetDiffusionCoefficient() const {…}
 
template<unsigned DIM>
bool CellwiseSourceEllipticPde<DIM>::GetScaleByCellVolume() const
{
    return mScaleByCellVolume;
}
bool CellwiseSourceEllipticPde<DIM>::GetScaleByCellVolume() const {…}
 
// LCOV_EXCL_START
template<unsigned DIM>
double CellwiseSourceEllipticPde<DIM>::ComputeConstantInUSourceTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement)
{
    NEVER_REACHED;
}
double CellwiseSourceEllipticPde<DIM>::ComputeConstantInUSourceTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement) {…}
 
template<unsigned DIM>
double CellwiseSourceEllipticPde<DIM>::ComputeLinearInUCoeffInSourceTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement)
{
    NEVER_REACHED;
}
double CellwiseSourceEllipticPde<DIM>::ComputeLinearInUCoeffInSourceTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement) {…}
// LCOV_EXCL_STOP
 
template<unsigned DIM>
double CellwiseSourceEllipticPde<DIM>::ComputeLinearInUCoeffInSourceTermAtNode(const Node<DIM>& rNode)
{
    double linear_source_coefficient = 0.0;
 
    if (mLinearSourceCoefficient != 0.0)
    {
        if (mrCellPopulation.IsPdeNodeAssociatedWithNonApoptoticCell(rNode.GetIndex()))
        {
            double cell_volume = 1.0;
 
            // Scale by volume if wanted
            if (mScaleByCellVolume)
            {   
                CellPtr p_cell = mrCellPopulation.GetCellUsingLocationIndex(rNode.GetIndex());
                cell_volume = mrCellPopulation.GetVolumeOfCell(p_cell);
                 
                if (cell_volume <1e-6)
                {
                    EXCEPTION("The volume of one of the cells is " << cell_volume << 
                              " 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).");
                }
            }
            linear_source_coefficient = mLinearSourceCoefficient/cell_volume;
        }
    }
 
    return linear_source_coefficient;
}
double CellwiseSourceEllipticPde<DIM>::ComputeLinearInUCoeffInSourceTermAtNode(const Node<DIM>& rNode) {…}
 
template<unsigned DIM>
double CellwiseSourceEllipticPde<DIM>::ComputeConstantInUSourceTermAtNode(const Node<DIM>& rNode)
{
    double constant_source_coefficient = 0.0;
 
    if (mConstantSourceCoefficient != 0.0)
    {
        if (mrCellPopulation.IsPdeNodeAssociatedWithNonApoptoticCell(rNode.GetIndex()))
        {
            double cell_volume = 1.0;
 
            // Scale by volume if wanted
            if (mScaleByCellVolume)
            {   
                CellPtr p_cell = mrCellPopulation.GetCellUsingLocationIndex(rNode.GetIndex());
                cell_volume = mrCellPopulation.GetVolumeOfCell(p_cell);
                if (cell_volume <1e-6)
                {
                    EXCEPTION("The volume of one of the cells is " << cell_volume << 
                              " 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).");
                }
            }
            constant_source_coefficient = mConstantSourceCoefficient/cell_volume;
        }
    }
 
    return constant_source_coefficient;
}
double CellwiseSourceEllipticPde<DIM>::ComputeConstantInUSourceTermAtNode(const Node<DIM>& rNode) {…}
 
template<unsigned DIM>
c_matrix<double,DIM,DIM> CellwiseSourceEllipticPde<DIM>::ComputeDiffusionTerm(const ChastePoint<DIM>& rX)
{
    return mDiffusionCoefficient*identity_matrix<double>(DIM);
}
c_matrix<double,DIM,DIM> CellwiseSourceEllipticPde<DIM>::ComputeDiffusionTerm(const ChastePoint<DIM>& rX) {…}
 
// Explicit instantiation
template class CellwiseSourceEllipticPde<1>;
template class CellwiseSourceEllipticPde<2>;
template class CellwiseSourceEllipticPde<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(CellwiseSourceEllipticPde)