DeltaNotchEdgeInteriorTrackingModifier.cpp

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#include "DeltaNotchEdgeInteriorTrackingModifier.hpp"
#include "CellSrnModel.hpp"
#include "DeltaNotchInteriorSrnModel.hpp"
#include "DeltaNotchEdgeSrnModel.hpp"
 
template<unsigned DIM>
DeltaNotchEdgeInteriorTrackingModifier<DIM>::DeltaNotchEdgeInteriorTrackingModifier()
    : AbstractCellBasedSimulationModifier<DIM>()
{
}
 
template<unsigned DIM>
DeltaNotchEdgeInteriorTrackingModifier<DIM>::~DeltaNotchEdgeInteriorTrackingModifier()
{
}
 
template<unsigned DIM>
void DeltaNotchEdgeInteriorTrackingModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    UpdateCellData(rCellPopulation);
}
 
template<unsigned DIM>
void DeltaNotchEdgeInteriorTrackingModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
{
    /*
     * We must update CellData in SetupSolve(), otherwise it will not have been
     * fully initialised by the time we enter the main time loop.
     */
    UpdateCellData(rCellPopulation);
}
 
template<unsigned DIM>
void DeltaNotchEdgeInteriorTrackingModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // First recover each cell's Notch and Delta concentrations from the ODEs and store
    // in CellData and CellEdgeData
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        auto p_cell_edge_model = static_cast<CellSrnModel*>(cell_iter->GetSrnModel());
 
        /* Cell Edges delta notch collection */
        std::vector<double> notch_vec;
        std::vector<double> delta_vec;
 
 
        for (unsigned i = 0 ; i  < p_cell_edge_model->GetNumEdgeSrn(); i++)
        {
            auto p_model = boost::static_pointer_cast<DeltaNotchEdgeSrnModel>(p_cell_edge_model->GetEdgeSrn(i));
            double edge_delta = p_model->GetDelta();
            double edge_notch = p_model->GetNotch();
 
            delta_vec.push_back(edge_delta);
            notch_vec.push_back(edge_notch);
        }
        // Note that the state variables must be in the same order as listed in DeltaNotchOdeSystem
        cell_iter->GetCellEdgeData()->SetItem("edge delta", delta_vec);
        cell_iter->GetCellEdgeData()->SetItem("edge notch", notch_vec);
 
        /* Interior delta notch collection */
        //Filling interior delta/notch value, interior model must be specified for this edge-interior example
        assert(p_cell_edge_model->GetInteriorSrn() != nullptr);
        auto p_interior_model = boost::static_pointer_cast<DeltaNotchInteriorSrnModel>(p_cell_edge_model->GetInteriorSrn());
 
        // Note that the state variables must be in the same order as listed in DeltaNotchOdeSystem
        cell_iter->GetCellData()->SetItem("interior delta", p_interior_model->GetDelta());
        cell_iter->GetCellData()->SetItem("interior notch", p_interior_model->GetNotch());
    }
 
    // After the edge data is filled, fill the edge neighbour data
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        auto p_cell_edge_model = static_cast<CellSrnModel*>(cell_iter->GetSrnModel());
        const unsigned num_cell_edges = p_cell_edge_model->GetNumEdgeSrn();
        std::vector<double> neigh_mean_delta(num_cell_edges);
 
        // Cell interior
        double total_edge_delta = 0;
        double total_edge_notch = 0;
 
        auto edges_delta = cell_iter->GetCellEdgeData()->GetItem("edge delta");
        auto edges_notch = cell_iter->GetCellEdgeData()->GetItem("edge notch");
 
        for (unsigned i = 0 ; i  < p_cell_edge_model->GetNumEdgeSrn(); i++)
        {
            total_edge_delta += edges_delta[i];
            total_edge_notch += edges_notch[i];
        }
 
        cell_iter->GetCellData()->SetItem("total neighbour edge delta", total_edge_delta);
        cell_iter->GetCellData()->SetItem("total edge notch", total_edge_notch);
 
        // Cell edge
        for (unsigned i=0; i<num_cell_edges; ++i)
        {
            // Get neighbouring cell's values of delta on this
            auto elemNeighbours = rCellPopulation.GetNeighbouringEdgeIndices(*cell_iter, i);
            double mean_delta = 0;
            for (auto neighbourIndex: elemNeighbours)
            {
                auto neighbourCell = rCellPopulation.GetCellUsingLocationIndex(neighbourIndex.first);
                std::vector<double> neighbour_delta_vec = neighbourCell->GetCellEdgeData()->GetItem("edge delta");
                mean_delta += neighbour_delta_vec[neighbourIndex.second];
            }
            if (elemNeighbours.size() > 0)
            {
                mean_delta = mean_delta/elemNeighbours.size();
            }
            neigh_mean_delta[i] = mean_delta;
        }
        cell_iter->GetCellEdgeData()->SetItem("neighbour delta", neigh_mean_delta);
    }
}
 
template<unsigned DIM>
void DeltaNotchEdgeInteriorTrackingModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    // No parameters to output, so just call method on direct parent class
    AbstractCellBasedSimulationModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}
 
 
// Explicit instantiation
template class DeltaNotchEdgeInteriorTrackingModifier<1>;
template class DeltaNotchEdgeInteriorTrackingModifier<2>;
template class DeltaNotchEdgeInteriorTrackingModifier<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(DeltaNotchEdgeInteriorTrackingModifier)