CryptSimulation1d.cpp

/*

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*/

#include "CryptSimulation1d.hpp"
#include "WntConcentration.hpp"
#include "SmartPointers.hpp"

CryptSimulation1d::CryptSimulation1d(AbstractCellPopulation<1>& rCellPopulation,
                  bool deleteCellPopulationInDestructor,
                  bool initialiseCells)
    : OffLatticeSimulation<1>(rCellPopulation,
                          deleteCellPopulationInDestructor,
                          initialiseCells)
{
    mpStaticCastCellPopulation = static_cast<MeshBasedCellPopulation<1>*>(&mrCellPopulation);

    if (!mDeleteCellPopulationInDestructor)
    {
        // Pass a CryptSimulationBoundaryCondition object into mBoundaryConditions
        MAKE_PTR_ARGS(CryptSimulationBoundaryCondition<1>, p_bc, (&rCellPopulation));
        AddCellPopulationBoundaryCondition(p_bc);
    }
}

CryptSimulation1d::~CryptSimulation1d()
{
}

c_vector<double, 1> CryptSimulation1d::CalculateCellDivisionVector(CellPtr pParentCell)
{
    // Location of parent and daughter cells
    c_vector<double, 1> parent_coords = mpStaticCastCellPopulation->GetLocationOfCellCentre(pParentCell);
    c_vector<double, 1> daughter_coords;

    // Get separation parameter
    double separation = mpStaticCastCellPopulation->GetMeinekeDivisionSeparation();

    // Make a random direction vector of the required length
    c_vector<double, 1> random_vector;

    /*
     * Pick a random direction and move the parent cell backwards by 0.5*separation
     * in that direction and return the position of the daughter cell 0.5*separation
     * forwards in that direction.
     */

    double random_direction = -1.0 + 2.0*(RandomNumberGenerator::Instance()->ranf() < 0.5);
    random_vector(0) = 0.5*separation*random_direction;
    c_vector<double, 1> proposed_new_parent_coords = parent_coords - random_vector;
    c_vector<double, 1> proposed_new_daughter_coords = parent_coords + random_vector;

    if (   (proposed_new_parent_coords(0) >= 0.0)
        && (proposed_new_daughter_coords(0) >= 0.0))
    {
        // We are not too close to the bottom of the cell population, so move parent
        parent_coords = proposed_new_parent_coords;
        daughter_coords = proposed_new_daughter_coords;
    }
    else
    {
        proposed_new_daughter_coords = parent_coords + 2.0*random_vector;
        while (proposed_new_daughter_coords(0) < 0.0)
        {
            double random_direction = -1.0 + 2.0*(RandomNumberGenerator::Instance()->ranf() < 0.5);
            random_vector(0) = 0.5*separation*random_direction;
            proposed_new_daughter_coords = parent_coords + random_vector;
        }
        daughter_coords = proposed_new_daughter_coords;
    }

    assert(daughter_coords(0) >= 0.0); // to make sure dividing cells stay in the cell population
    assert(parent_coords(0) >= 0.0);   // to make sure dividing cells stay in the cell population

    // Set the parent to use this location
    ChastePoint<1> parent_coords_point(parent_coords);

    unsigned node_index = mpStaticCastCellPopulation->GetLocationIndexUsingCell(pParentCell);
    mrCellPopulation.SetNode(node_index, parent_coords_point);

    return daughter_coords;
}

void CryptSimulation1d::OutputSimulationParameters(out_stream& rParamsFile)
{
    // No parameters to output

    // Call method on direct parent class
    OffLatticeSimulation<1>::OutputSimulationParameters(rParamsFile);
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(CryptSimulation1d)