SurfaceAreaConstraintPottsUpdateRule.cpp

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#include "SurfaceAreaConstraintPottsUpdateRule.hpp"

template<unsigned DIM>
SurfaceAreaConstraintPottsUpdateRule<DIM>::SurfaceAreaConstraintPottsUpdateRule()
    : AbstractPottsUpdateRule<DIM>(),
      mDeformationEnergyParameter(0.5), // Educated guess
      mMatureCellTargetSurfaceArea(16.0) // Defaults to a 4*4 cell size
{
}

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

template<unsigned DIM>
double SurfaceAreaConstraintPottsUpdateRule<DIM>::EvaluateHamiltonianContribution(unsigned currentNodeIndex,
                                                                        unsigned targetNodeIndex,
                                                                        PottsBasedCellPopulation<DIM>& rCellPopulation)
{
    double delta_H = 0.0;

    // This method only works in 2D and 3D at present
    assert(DIM == 2 || DIM == 3);

    std::set<unsigned> containing_elements = rCellPopulation.GetNode(currentNodeIndex)->rGetContainingElementIndices();
    std::set<unsigned> new_location_containing_elements = rCellPopulation.GetNode(targetNodeIndex)->rGetContainingElementIndices();

    bool current_node_contained = !containing_elements.empty();
    bool target_node_contained = !new_location_containing_elements.empty();

    // Every node must each be in at most one element
    assert(new_location_containing_elements.size() < 2);

    if (!current_node_contained && !target_node_contained)
    {
        EXCEPTION("At least one of the current node or target node must be in an element.");
    }

    if (current_node_contained && target_node_contained)
    {
        if (*(new_location_containing_elements.begin()) == *(containing_elements.begin()))
        {
            EXCEPTION("The current node and target node must not be in the same element.");
        }
    }

    // Iterate over nodes neighbouring the target node to work out the change in surface area
    unsigned neighbours_in_same_element_as_current_node = 0;
    unsigned neighbours_in_same_element_as_target_node = 0;
    std::set<unsigned> target_neighbouring_node_indices = rCellPopulation.rGetMesh().GetVonNeumannNeighbouringNodeIndices(targetNodeIndex);
    for (std::set<unsigned>::iterator iter = target_neighbouring_node_indices.begin();
         iter != target_neighbouring_node_indices.end();
         ++iter)
    {
        std::set<unsigned> neighbouring_node_containing_elements = rCellPopulation.rGetMesh().GetNode(*iter)->rGetContainingElementIndices();

        // Every node must each be in at most one element
        assert(neighbouring_node_containing_elements.size() < 2);

        bool neighbouring_node_contained = !neighbouring_node_containing_elements.empty();

        if (neighbouring_node_contained && target_node_contained)
        {
            unsigned neighbour_element = (*neighbouring_node_containing_elements.begin());
            unsigned target_element = (*new_location_containing_elements.begin());
            if (target_element == neighbour_element)
            {
                neighbours_in_same_element_as_target_node++;
            }
        }
        if (neighbouring_node_contained && current_node_contained)
        {
            unsigned neighbour_element = (*neighbouring_node_containing_elements.begin());
            unsigned current_element = (*containing_elements.begin());
            if (current_element == neighbour_element)
            {
                neighbours_in_same_element_as_current_node++;
            }
        }
    }

    if (DIM == 2)
    {
        assert(neighbours_in_same_element_as_current_node<5);
        assert(neighbours_in_same_element_as_target_node<5);

        double change_in_surface_area[5] = {4,2,0,-2,-4};

        if (current_node_contained) // current node is in an element
        {
            unsigned current_element = (*containing_elements.begin());
            double current_surface_area = rCellPopulation.rGetMesh().GetSurfaceAreaOfElement(current_element);
            double current_surface_area_difference = current_surface_area - mMatureCellTargetSurfaceArea;
            double current_surface_area_difference_after_switch = current_surface_area_difference + change_in_surface_area[neighbours_in_same_element_as_current_node];

            delta_H += mDeformationEnergyParameter*(current_surface_area_difference_after_switch*current_surface_area_difference_after_switch - current_surface_area_difference*current_surface_area_difference);
        }
        if (target_node_contained) // target node is in an element
        {
            unsigned target_element = (*new_location_containing_elements.begin());
            double target_surface_area = rCellPopulation.rGetMesh().GetSurfaceAreaOfElement(target_element);
            double target_surface_area_difference = target_surface_area - mMatureCellTargetSurfaceArea;
            double target_surface_area_difference_after_switch = target_surface_area_difference - change_in_surface_area[neighbours_in_same_element_as_target_node];

            delta_H += mDeformationEnergyParameter*(target_surface_area_difference_after_switch*target_surface_area_difference_after_switch - target_surface_area_difference*target_surface_area_difference);
        }
    }
    else if (DIM==3)
    {
        assert(neighbours_in_same_element_as_current_node < 7);
        assert(neighbours_in_same_element_as_target_node < 7);

        double change_in_surface_area[7] = {6,4,2,0,-2,-4,-6};

        if (current_node_contained) // current node is in an element
        {
            unsigned current_element = (*containing_elements.begin());
            double current_surface_area = rCellPopulation.rGetMesh().GetSurfaceAreaOfElement(current_element);
            double current_surface_area_difference = current_surface_area - mMatureCellTargetSurfaceArea;
            double current_surface_area_difference_after_switch = current_surface_area_difference + change_in_surface_area[neighbours_in_same_element_as_current_node];

            delta_H += mDeformationEnergyParameter*(current_surface_area_difference_after_switch*current_surface_area_difference_after_switch - current_surface_area_difference*current_surface_area_difference);
        }
        if (target_node_contained) // target node is in an element
        {
            unsigned target_element = (*new_location_containing_elements.begin());
            double target_surface_area = rCellPopulation.rGetMesh().GetSurfaceAreaOfElement(target_element);
            double target_surface_area_difference = target_surface_area - mMatureCellTargetSurfaceArea;
            double target_surface_area_difference_after_switch = target_surface_area_difference - change_in_surface_area[neighbours_in_same_element_as_target_node];

            delta_H += mDeformationEnergyParameter*(target_surface_area_difference_after_switch*target_surface_area_difference_after_switch - target_surface_area_difference*target_surface_area_difference);
        }
    }

    return delta_H;
}

template<unsigned DIM>
double SurfaceAreaConstraintPottsUpdateRule<DIM>::GetDeformationEnergyParameter()
{
    return mDeformationEnergyParameter;
}

template<unsigned DIM>
void SurfaceAreaConstraintPottsUpdateRule<DIM>::SetDeformationEnergyParameter(double deformationEnergyParameter)
{
    mDeformationEnergyParameter = deformationEnergyParameter;
}

template<unsigned DIM>
double SurfaceAreaConstraintPottsUpdateRule<DIM>::GetMatureCellTargetSurfaceArea() const
{
    return mMatureCellTargetSurfaceArea;
}

template<unsigned DIM>
void SurfaceAreaConstraintPottsUpdateRule<DIM>::SetMatureCellTargetSurfaceArea(double matureCellTargetSurfaceArea)
{
    assert(matureCellTargetSurfaceArea >= 0.0);
    mMatureCellTargetSurfaceArea = matureCellTargetSurfaceArea;
}

template<unsigned DIM>
void SurfaceAreaConstraintPottsUpdateRule<DIM>::OutputUpdateRuleParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<DeformationEnergyParameter>" << mDeformationEnergyParameter << "</DeformationEnergyParameter>\n";
    *rParamsFile << "\t\t\t<MatureCellTargetSurfaceArea>" << mMatureCellTargetSurfaceArea << "</MatureCellTargetSurfaceArea>\n";

    // Call method on direct parent class
    AbstractPottsUpdateRule<DIM>::OutputUpdateRuleParameters(rParamsFile);
}

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

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