Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
DeltaNotchTrackingModifier.cpp
1/*
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34*/
35
36#include "DeltaNotchTrackingModifier.hpp"
37#include "DeltaNotchSrnModel.hpp"
38
39template<unsigned DIM>
44
45template<unsigned DIM>
49
50template<unsigned DIM>
52{
53 UpdateCellData(rCellPopulation);
54}
55
56template<unsigned DIM>
57void 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
66template<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
116template<unsigned DIM>
118{
119 // No parameters to output, so just call method on direct parent class
121}
122
123// Explicit instantiation
124template class DeltaNotchTrackingModifier<1>;
125template class DeltaNotchTrackingModifier<2>;
126template class DeltaNotchTrackingModifier<3>;
127
128// Serialization for Boost >= 1.36
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void OutputSimulationModifierParameters(out_stream &rParamsFile)=0
virtual std::set< unsigned > GetNeighbouringLocationIndices(CellPtr pCell)=0
virtual void Update(bool hasHadBirthsOrDeaths=true)=0
virtual CellPtr GetCellUsingLocationIndex(unsigned index)
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
void UpdateCellData(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void OutputSimulationModifierParameters(out_stream &rParamsFile)