DeltaNotchEdgeTrackingModifier.cpp

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*/
 
#include "DeltaNotchEdgeTrackingModifier.hpp"
#include "CellSrnModel.hpp"
#include "DeltaNotchEdgeSrnModel.hpp"
 
template<unsigned DIM>
DeltaNotchEdgeTrackingModifier<DIM>::DeltaNotchEdgeTrackingModifier()
        : AbstractCellBasedSimulationModifier<DIM>()
{
}
 
template<unsigned DIM>
DeltaNotchEdgeTrackingModifier<DIM>::~DeltaNotchEdgeTrackingModifier()
{
}
 
template<unsigned DIM>
void DeltaNotchEdgeTrackingModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Update the cell
    this->UpdateCellData(rCellPopulation);
}
 
template<unsigned DIM>
void DeltaNotchEdgeTrackingModifier<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 DeltaNotchEdgeTrackingModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Recovers each cell's edge levels of notch and delta, and those of its neighbor's
    // Then saves them
    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());
 
        /* Cells edge data */
        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 this_delta = p_model->GetDelta();
            double this_notch = p_model->GetNotch();
            delta_vec.push_back(this_delta);
            notch_vec.push_back(this_notch);
        }
        // Note that the state variables must be in the same order as listed in DeltaNotchOdeSystem
        cell_iter->GetCellEdgeData()->SetItem("edge notch", notch_vec);
        cell_iter->GetCellEdgeData()->SetItem("edge delta", delta_vec);
 
        /* Cell interior data */
        //We're not using interior model so interiors are set to 0
        cell_iter->GetCellData()->SetItem("interior delta", 0);
        cell_iter->GetCellData()->SetItem("interior notch", 0);
    }
 
    // 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);
 
        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 DeltaNotchEdgeTrackingModifier<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 DeltaNotchEdgeTrackingModifier<1>;
template class DeltaNotchEdgeTrackingModifier<2>;
template class DeltaNotchEdgeTrackingModifier<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
 
EXPORT_TEMPLATE_CLASS_SAME_DIMS(DeltaNotchEdgeTrackingModifier)