Chaste Release::3.1
AveragedSourcePde.cpp
00001 /*
00002 
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00034 */
00035 
00036 #include "AveragedSourcePde.hpp"
00037 #include "ApoptoticCellProperty.hpp"
00038 #include "PetscTools.hpp"
00039 
00040 template<unsigned DIM>
00041 AveragedSourcePde<DIM>::AveragedSourcePde(AbstractCellPopulation<DIM>& rCellPopulation, double coefficient)
00042     : mrCellPopulation(rCellPopulation),
00043       mCoefficient(coefficient)
00044 {
00045 }
00046 
00047 template<unsigned DIM>
00048 const AbstractCellPopulation<DIM>& AveragedSourcePde<DIM>::rGetCellPopulation() const
00049 {
00050     return mrCellPopulation;
00051 }
00052 
00053 template<unsigned DIM>
00054 double AveragedSourcePde<DIM>::GetCoefficient() const
00055 {
00056     return mCoefficient;
00057 }
00058 
00059 template<unsigned DIM>
00060 void AveragedSourcePde<DIM>::SetupSourceTerms(TetrahedralMesh<DIM,DIM>& rCoarseMesh, std::map< CellPtr, unsigned >* pCellPdeElementMap) // must be called before solve
00061 {
00062     // Allocate memory
00063     mCellDensityOnCoarseElements.resize(rCoarseMesh.GetNumElements());
00064     for (unsigned elem_index=0; elem_index<mCellDensityOnCoarseElements.size(); elem_index++)
00065     {
00066         mCellDensityOnCoarseElements[elem_index] = 0.0;
00067     }
00068 
00069     // Loop over cells, find which coarse element it is in, and add 1 to mSourceTermOnCoarseElements[elem_index]
00070     for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = mrCellPopulation.Begin();
00071          cell_iter != mrCellPopulation.End();
00072          ++cell_iter)
00073     {
00074         unsigned elem_index = 0;
00075         const ChastePoint<DIM>& r_position_of_cell = mrCellPopulation.GetLocationOfCellCentre(*cell_iter);
00076 
00077         if (pCellPdeElementMap != NULL)
00078         {
00079             elem_index = (*pCellPdeElementMap)[*cell_iter];
00080         }
00081         else
00082         {
00083             elem_index = rCoarseMesh.GetContainingElementIndex(r_position_of_cell);
00084         }
00085 
00086         // Update element map if cell has moved
00087         bool cell_is_apoptotic = cell_iter->template HasCellProperty<ApoptoticCellProperty>();
00088 
00089         if (!cell_is_apoptotic)
00090         {
00091             mCellDensityOnCoarseElements[elem_index] += 1.0;
00092         }
00093     }
00094 
00095     // Then divide each entry of mSourceTermOnCoarseElements by the element's area
00096     c_matrix<double, DIM, DIM> jacobian;
00097     double det;
00098     for (unsigned elem_index=0; elem_index<mCellDensityOnCoarseElements.size(); elem_index++)
00099     {
00100         rCoarseMesh.GetElement(elem_index)->CalculateJacobian(jacobian, det);
00101         mCellDensityOnCoarseElements[elem_index] /= rCoarseMesh.GetElement(elem_index)->GetVolume(det);
00102     }
00103 }
00104 
00105 template<unsigned DIM>
00106 double AveragedSourcePde<DIM>::ComputeConstantInUSourceTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement)
00107 {
00108     return 0.0;
00109 }
00110 
00111 template<unsigned DIM>
00112 double AveragedSourcePde<DIM>::ComputeLinearInUCoeffInSourceTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement) // now takes in element
00113 {
00114     assert(!mCellDensityOnCoarseElements.empty());
00115     return mCoefficient * mCellDensityOnCoarseElements[pElement->GetIndex()];
00116 }
00117 
00118 template<unsigned DIM>
00119 c_matrix<double,DIM,DIM> AveragedSourcePde<DIM>::ComputeDiffusionTerm(const ChastePoint<DIM>& rX)
00120 {
00121     return identity_matrix<double>(DIM);
00122 }
00123 
00124 template<unsigned DIM>
00125 double AveragedSourcePde<DIM>::GetUptakeRateForElement(unsigned elementIndex)
00126 {
00127     return this->mCellDensityOnCoarseElements[elementIndex];
00128 }
00129 
00131 // Explicit instantiation
00133 
00134 template class AveragedSourcePde<1>;
00135 template class AveragedSourcePde<2>;
00136 template class AveragedSourcePde<3>;
00137 
00138 // Serialization for Boost >= 1.36
00139 #include "SerializationExportWrapperForCpp.hpp"
00140 EXPORT_TEMPLATE_CLASS_SAME_DIMS(AveragedSourcePde)