Chaste  Release::3.4
DeltaNotchTrackingModifier.cpp
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35 
36 #include "DeltaNotchTrackingModifier.hpp"
37 #include "DeltaNotchSrnModel.hpp"
38 
39 template<unsigned DIM>
42 {
43 }
44 
45 template<unsigned DIM>
47 {
48 }
49 
50 template<unsigned DIM>
52 {
53  UpdateCellData(rCellPopulation);
54 }
55 
56 template<unsigned DIM>
57 void DeltaNotchTrackingModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
58 {
59  /*
60  * We must update CellData in SetupSolve(), otherwise it will not have been
61  * fully initialised by the time we enter the main time loop.
62  */
63  UpdateCellData(rCellPopulation);
64 }
65 
66 template<unsigned DIM>
68 {
69  // Make sure the cell population is updated
70  rCellPopulation.Update();
71 
72  // First recover each cell's Notch and Delta concentrations from the ODEs and store in CellData
73  for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
74  cell_iter != rCellPopulation.End();
75  ++cell_iter)
76  {
77  DeltaNotchSrnModel* p_model = static_cast<DeltaNotchSrnModel*>(cell_iter->GetSrnModel());
78  double this_delta = p_model->GetDelta();
79  double this_notch = p_model->GetNotch();
80 
81  // Note that the state variables must be in the same order as listed in DeltaNotchOdeSystem
82  cell_iter->GetCellData()->SetItem("notch", this_notch);
83  cell_iter->GetCellData()->SetItem("delta", this_delta);
84  }
85 
86  // Next iterate over the population to compute and store each cell's neighbouring Delta concentration in CellData
87  for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
88  cell_iter != rCellPopulation.End();
89  ++cell_iter)
90  {
91  // Get the set of neighbouring location indices
92  std::set<unsigned> neighbour_indices = rCellPopulation.GetNeighbouringLocationIndices(*cell_iter);
93 
94  // Compute this cell's average neighbouring Delta concentration and store in CellData
95  if (!neighbour_indices.empty())
96  {
97  double mean_delta = 0.0;
98  for (std::set<unsigned>::iterator iter = neighbour_indices.begin();
99  iter != neighbour_indices.end();
100  ++iter)
101  {
102  CellPtr p_cell = rCellPopulation.GetCellUsingLocationIndex(*iter);
103  double this_delta = p_cell->GetCellData()->GetItem("delta");
104  mean_delta += this_delta/neighbour_indices.size();
105  }
106  cell_iter->GetCellData()->SetItem("mean delta", mean_delta);
107  }
108  else
109  {
110  // If this cell has no neighbours, such as an isolated cell in a CaBasedCellPopulation, store 0.0 for the cell data
111  cell_iter->GetCellData()->SetItem("mean delta", 0.0);
112  }
113  }
114 }
115 
116 template<unsigned DIM>
118 {
119  // No parameters to output, so just call method on direct parent class
121 }
122 
123 // Explicit instantiation
124 template class DeltaNotchTrackingModifier<1>;
125 template class DeltaNotchTrackingModifier<2>;
126 template class DeltaNotchTrackingModifier<3>;
127 
128 // Serialization for Boost >= 1.36
void UpdateCellData(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual CellPtr GetCellUsingLocationIndex(unsigned index)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
virtual void OutputSimulationModifierParameters(out_stream &rParamsFile)=0
virtual std::set< unsigned > GetNeighbouringLocationIndices(CellPtr pCell)=0
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void Update(bool hasHadBirthsOrDeaths=true)=0
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)