Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
DeltaNotchEdgeTrackingModifier.cpp
1/*
2
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34*/
35
36#include "DeltaNotchEdgeTrackingModifier.hpp"
37#include "CellSrnModel.hpp"
38#include "DeltaNotchInteriorSrnModel.hpp"
39#include "DeltaNotchEdgeSrnModel.hpp"
40
41template<unsigned DIM>
46
47template<unsigned DIM>
51
52template<unsigned DIM>
54{
55 // Update the cell
56 this->UpdateCellData(rCellPopulation);
57}
58
59template<unsigned DIM>
61{
62 /*
63 * We must update CellData in SetupSolve(), otherwise it will not have been
64 * fully initialised by the time we enter the main time loop.
65 */
66 UpdateCellData(rCellPopulation);
67}
68
69template<unsigned DIM>
71{
72 // Recovers each cell's edge levels of notch and delta, and those of its neighbor's
73 // Then saves them
74 for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
75 cell_iter != rCellPopulation.End();
76 ++cell_iter)
77 {
78 auto p_cell_edge_model = static_cast<CellSrnModel*>(cell_iter->GetSrnModel());
79
80 /* Cells edge data */
81 std::vector<double> notch_vec;
82 std::vector<double> delta_vec;
83 for (unsigned i = 0 ; i < p_cell_edge_model->GetNumEdgeSrn(); i++)
84 {
85 boost::shared_ptr<DeltaNotchEdgeSrnModel> p_model
86 = boost::static_pointer_cast<DeltaNotchEdgeSrnModel>(p_cell_edge_model->GetEdgeSrn(i));
87 double this_delta = p_model->GetDelta();
88 double this_notch = p_model->GetNotch();
89 delta_vec.push_back(this_delta);
90 notch_vec.push_back(this_notch);
91 }
92 // Note that the state variables must be in the same order as listed in DeltaNotchOdeSystem
93 cell_iter->GetCellEdgeData()->SetItem("edge notch", notch_vec);
94 cell_iter->GetCellEdgeData()->SetItem("edge delta", delta_vec);
95
96 /* Cell interior data */
97 //We're not using interior model so interiors are set to 0
98 cell_iter->GetCellData()->SetItem("interior delta", 0);
99 cell_iter->GetCellData()->SetItem("interior notch", 0);
100 }
101
102 // After the edge data is filled, fill the edge neighbour data
103 for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
104 cell_iter != rCellPopulation.End();
105 ++cell_iter)
106 {
107 auto p_cell_edge_model = static_cast<CellSrnModel*>(cell_iter->GetSrnModel());
108 const unsigned num_cell_edges = p_cell_edge_model->GetNumEdgeSrn();
109 std::vector<double> neigh_mean_delta(num_cell_edges);
110
111 for (unsigned i=0; i<num_cell_edges; ++i)
112 {
113 // Get neighbouring cell's values of delta on this
114 auto elemNeighbours = rCellPopulation.GetNeighbouringEdgeIndices(*cell_iter, i);
115 double mean_delta = 0;
116 for (auto neighbourIndex: elemNeighbours)
117 {
118 auto neighbourCell = rCellPopulation.GetCellUsingLocationIndex(neighbourIndex.first);
119 std::vector<double> neighbour_delta_vec = neighbourCell->GetCellEdgeData()->GetItem("edge delta");
120 mean_delta += neighbour_delta_vec[neighbourIndex.second];
121 }
122 if (elemNeighbours.size() > 0)
123 {
124 mean_delta = mean_delta/elemNeighbours.size();
125 }
126 neigh_mean_delta[i] = mean_delta;
127 }
128 cell_iter->GetCellEdgeData()->SetItem("neighbour delta", neigh_mean_delta);
129 }
130
131}
132
133template<unsigned DIM>
135{
136 // No parameters to output, so just call method on direct parent class
138}
139
140// Explicit instantiation
144
145// Serialization for Boost >= 1.36
147
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void OutputSimulationModifierParameters(out_stream &rParamsFile)=0
virtual std::set< std::pair< unsigned, unsigned > > GetNeighbouringEdgeIndices(CellPtr pCell, unsigned pEdgeIndex)
virtual CellPtr GetCellUsingLocationIndex(unsigned index)
unsigned GetNumEdgeSrn() const
void UpdateCellData(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
void OutputSimulationModifierParameters(out_stream &rParamsFile)