Chaste  Release::2018.1
VolumeDependentAveragedSourceEllipticPde.cpp
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36 #include "VolumeDependentAveragedSourceEllipticPde.hpp"
37 #include "ApoptoticCellProperty.hpp"
38 
39 template<unsigned DIM>
41  : AveragedSourceEllipticPde<DIM>(rCellPopulation, coefficient)
42 {
43  assert(bool(dynamic_cast<NodeBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))));
45 }
46 
47 template<unsigned DIM>
48 void VolumeDependentAveragedSourceEllipticPde<DIM>::SetupSourceTerms(TetrahedralMesh<DIM,DIM>& rCoarseMesh, std::map< CellPtr, unsigned >* pCellPdeElementMap) // must be called before solve
49 {
50  // Allocate memory
51  this->mCellDensityOnCoarseElements.resize(rCoarseMesh.GetNumElements());
52  for (unsigned elem_index=0; elem_index<this->mCellDensityOnCoarseElements.size(); elem_index++)
53  {
54  this->mCellDensityOnCoarseElements[elem_index] = 0.0;
55  }
56 
57  // Loop over cells, find which coarse element it is in, and add volume to the mSourceTermOnCoarseElements[elem_index];
58  for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->mrCellPopulation.Begin();
59  cell_iter != this->mrCellPopulation.End();
60  ++cell_iter)
61  {
62  unsigned elem_index = 0;
63  const ChastePoint<DIM>& r_position_of_cell = this->mrCellPopulation.GetLocationOfCellCentre(*cell_iter);
64 
65  if (pCellPdeElementMap != nullptr)
66  {
67  elem_index = (*pCellPdeElementMap)[*cell_iter];
68  }
69  else
70  {
71  elem_index = rCoarseMesh.GetContainingElementIndex(r_position_of_cell);
72  }
73 
74  unsigned node_index = this->mrCellPopulation.GetLocationIndexUsingCell(*cell_iter);
75 
76  Node<DIM>* p_node = this->mrCellPopulation.GetNode(node_index);
77  double radius = p_node->GetRadius();
78 
79  // Uptake normalised to 1 for unit cell
80  double cell_weight = radius*radius;
81 
82  bool cell_is_apoptotic = cell_iter->template HasCellProperty<ApoptoticCellProperty>();
83  if (!cell_is_apoptotic)
84  {
85  this->mCellDensityOnCoarseElements[elem_index] += cell_weight;
86  }
87  }
88 
89  // Then divide each entry of mSourceTermOnCoarseElements by the element's area
90  c_matrix<double, DIM, DIM> jacobian;
91  double det;
92  for (unsigned elem_index=0; elem_index<this->mCellDensityOnCoarseElements.size(); elem_index++)
93  {
94  rCoarseMesh.GetElement(elem_index)->CalculateJacobian(jacobian, det);
95  this->mCellDensityOnCoarseElements[elem_index] /= rCoarseMesh.GetElement(elem_index)->GetVolume(det);
96  }
97 }
98 
99 // Explicit instantiation
103 
104 // Serialization for Boost >= 1.36
Definition: Node.hpp:58
virtual unsigned GetNumElements() const
Element< ELEMENT_DIM, SPACE_DIM > * GetElement(unsigned index) const
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
AbstractCellPopulation< DIM > & mrCellPopulation
void SetupSourceTerms(TetrahedralMesh< DIM, DIM > &rCoarseMesh, std::map< CellPtr, unsigned > *pCellPdeElementMap=nullptr)
unsigned GetContainingElementIndex(const ChastePoint< SPACE_DIM > &rTestPoint, bool strict=false, std::set< unsigned > testElements=std::set< unsigned >(), bool onlyTryWithTestElements=false)
VolumeDependentAveragedSourceEllipticPde(AbstractCellPopulation< DIM > &rCellPopulation, double coefficient=0.0)
double GetRadius()
Definition: Node.cpp:248