CellwiseSourceParabolicPde.cpp

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*/
 
#include "CellwiseSourceParabolicPde.hpp"
 
template<unsigned DIM>
CellwiseSourceParabolicPde<DIM>::CellwiseSourceParabolicPde(AbstractCellPopulation<DIM,DIM>& rCellPopulation,
                                                            const double constantSourceCoefficient,
                                                            const double linearSourceCoefficient,
                                                            const double diffusionCoefficient,
                                                            const double duDtCoefficient,
                                                            const bool scaleByCellVolume)
    : mrCellPopulation(rCellPopulation),
      mConstantSourceCoefficient(constantSourceCoefficient),
      mLinearSourceCoefficient(linearSourceCoefficient),
      mDiffusionCoefficient(diffusionCoefficient),
      mDuDtCoefficient(duDtCoefficient),
      mScaleByCellVolume(scaleByCellVolume)
{
}
CellwiseSourceParabolicPde<DIM>::CellwiseSourceParabolicPde(AbstractCellPopulation<DIM,DIM>& rCellPopulation, {…}
 
template<unsigned DIM>
const AbstractCellPopulation<DIM,DIM>& CellwiseSourceParabolicPde<DIM>::rGetCellPopulation() const
{
    return mrCellPopulation;
}
const AbstractCellPopulation<DIM,DIM>& CellwiseSourceParabolicPde<DIM>::rGetCellPopulation() const {…}
 
template<unsigned DIM>
double CellwiseSourceParabolicPde<DIM>::GetConstantCoefficient() const
{
    return mConstantSourceCoefficient;
}
double CellwiseSourceParabolicPde<DIM>::GetConstantCoefficient() const {…}
 
template<unsigned DIM>
double CellwiseSourceParabolicPde<DIM>::GetLinearCoefficient() const
{
    return mLinearSourceCoefficient;
}
double CellwiseSourceParabolicPde<DIM>::GetLinearCoefficient() const {…}
 
template<unsigned DIM>
double CellwiseSourceParabolicPde<DIM>::GetDiffusionCoefficient() const
{
    return mDiffusionCoefficient;
}
double CellwiseSourceParabolicPde<DIM>::GetDiffusionCoefficient() const {…}
 
template<unsigned DIM>
double CellwiseSourceParabolicPde<DIM>::GetDuDtCoefficient() const
{
    return mDuDtCoefficient;
}
double CellwiseSourceParabolicPde<DIM>::GetDuDtCoefficient() const {…}
 
template<unsigned DIM>
bool CellwiseSourceParabolicPde<DIM>::GetScaleByCellVolume() const
{
    return mScaleByCellVolume;
}
bool CellwiseSourceParabolicPde<DIM>::GetScaleByCellVolume() const {…}
 
template<unsigned DIM>
double CellwiseSourceParabolicPde<DIM>::ComputeDuDtCoefficientFunction(const ChastePoint<DIM>& )
{
    return mDuDtCoefficient;
}
double CellwiseSourceParabolicPde<DIM>::ComputeDuDtCoefficientFunction(const ChastePoint<DIM>& ) {…}
 
// LCOV_EXCL_START
template<unsigned DIM>
double CellwiseSourceParabolicPde<DIM>::ComputeSourceTerm(const ChastePoint<DIM>& rX, double u, Element<DIM,DIM>* pElement)
{
    NEVER_REACHED;
}
double CellwiseSourceParabolicPde<DIM>::ComputeSourceTerm(const ChastePoint<DIM>& rX, double u, Element<DIM,DIM>* pElement) {…}
// LCOV_EXCL_STOP
 
template<unsigned DIM>
double CellwiseSourceParabolicPde<DIM>::ComputeSourceTermAtNode(const Node<DIM>& rNode, double u)
{
    double source_term = 0.0;
 
    if (mConstantSourceCoefficient != 0.0 || 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).");
                }
            }
 
            // At cells the source term is a*u + b
            source_term = (mLinearSourceCoefficient * u + mConstantSourceCoefficient)/cell_volume;
        }
    }
 
 
    return source_term;
}
double CellwiseSourceParabolicPde<DIM>::ComputeSourceTermAtNode(const Node<DIM>& rNode, double u) {…}
 
template<unsigned DIM>
c_matrix<double,DIM,DIM> CellwiseSourceParabolicPde<DIM>::ComputeDiffusionTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement)
{
    return mDiffusionCoefficient*identity_matrix<double>(DIM);
}
c_matrix<double,DIM,DIM> CellwiseSourceParabolicPde<DIM>::ComputeDiffusionTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement) {…}
 
// Explicit instantiation
template class CellwiseSourceParabolicPde<1>;
template class CellwiseSourceParabolicPde<2>;
template class CellwiseSourceParabolicPde<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(CellwiseSourceParabolicPde)