DeltaNotchOffLatticeSimulation.cpp

/*

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#include "DeltaNotchOffLatticeSimulation.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "MeshBasedCellPopulation.hpp"
#include "DeltaNotchCellCycleModel.hpp"

template<unsigned DIM>
DeltaNotchOffLatticeSimulation<DIM>::DeltaNotchOffLatticeSimulation(AbstractCellPopulation<DIM>& rCellPopulation,
                                                                  bool deleteCellPopulationInDestructor,
                                                                  bool initialiseCells)
    : OffLatticeSimulation<DIM>(rCellPopulation, deleteCellPopulationInDestructor, initialiseCells)
{
}

template<unsigned DIM>
DeltaNotchOffLatticeSimulation<DIM>::~DeltaNotchOffLatticeSimulation()
{
}

template<unsigned DIM>
void DeltaNotchOffLatticeSimulation<DIM>::SetupSolve()
{
    OffLatticeSimulation<DIM>::SetupSolve();
    UpdateCellData();
}

template<unsigned DIM>
void DeltaNotchOffLatticeSimulation<DIM>::UpdateAtEndOfTimeStep()
{
    OffLatticeSimulation<DIM>::UpdateAtEndOfTimeStep();
    UpdateCellData();
}

template<unsigned DIM>
void DeltaNotchOffLatticeSimulation<DIM>::UpdateCellData()
{
    // Make sure the cell population is updated
    this->mrCellPopulation.Update();

    // First store each cell's Notch and Delta concentrations in CellData
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->mrCellPopulation.Begin();
         cell_iter != this->mrCellPopulation.End();
         ++cell_iter)
    {
        DeltaNotchCellCycleModel* p_model = static_cast<DeltaNotchCellCycleModel*>(cell_iter->GetCellCycleModel());
        double this_delta = p_model->GetDelta();
        double this_notch = p_model->GetNotch();

        // Note that the state variables must be in the same order as listed in DeltaNotchOdeSystem
        cell_iter->GetCellData()->SetItem("notch", this_notch);
        cell_iter->GetCellData()->SetItem("delta", this_delta);
    }

    // Next iterate over the population to compute and store each cell's neighbouring Delta concentration in CellData
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->mrCellPopulation.Begin();
         cell_iter != this->mrCellPopulation.End();
         ++cell_iter)
    {
        // Get the location index corresponding to this cell
        unsigned index = this->mrCellPopulation.GetLocationIndexUsingCell(*cell_iter);

        // Get the set of neighbouring location indices
        std::set<unsigned> neighbour_indices;
        if (dynamic_cast<AbstractCentreBasedCellPopulation<DIM>*>(&(this->mrCellPopulation)))
        {
            neighbour_indices = this->mrCellPopulation.GetNeighbouringNodeIndices(index);
        }
        else
        {
            neighbour_indices = static_cast<VertexBasedCellPopulation<DIM>*>(&(this->mrCellPopulation))->rGetMesh().GetNeighbouringElementIndices(index);
        }

        // Compute this cell's average neighbouring Delta concentration and store in CellData
        if (!neighbour_indices.empty())
        {
            double mean_delta = 0.0;
            for (std::set<unsigned>::iterator iter = neighbour_indices.begin();
                 iter != neighbour_indices.end();
                 ++iter)
            {
                CellPtr p_cell = this->mrCellPopulation.GetCellUsingLocationIndex(*iter);
                double this_delta = p_cell->GetCellData()->GetItem("delta");
                mean_delta += this_delta/neighbour_indices.size();
            }
            cell_iter->GetCellData()->SetItem("mean delta", mean_delta);
        }
        else
        {
            // If simulation trips at this assertion it is because at least one of the cells has no neighbours (as defined by mesh/population/interaction distance)
            NEVER_REACHED;
        }
    }
}

// Explicit instantiation

template class DeltaNotchOffLatticeSimulation<1>;
template class DeltaNotchOffLatticeSimulation<2>;
template class DeltaNotchOffLatticeSimulation<3>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(DeltaNotchOffLatticeSimulation)