AdhesionPottsUpdateRule.cpp

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#include "AdhesionPottsUpdateRule.hpp"

template<unsigned DIM>
AdhesionPottsUpdateRule<DIM>::AdhesionPottsUpdateRule()
    : AbstractPottsUpdateRule<DIM>(),
      mCellCellAdhesionEnergyParameter(0.1), // Educated guess
      mCellBoundaryAdhesionEnergyParameter(0.2) // Educated guess
{
}

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

template<unsigned DIM>
double AdhesionPottsUpdateRule<DIM>::EvaluateHamiltonianContribution(unsigned currentNodeIndex,
                                                                unsigned targetNodeIndex,
                                                                PottsBasedCellPopulation<DIM>& rCellPopulation)
{
    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 contact energy contribution
    double delta_H = 0.0;
    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)
            {
                // The nodes are currently contained in different elements
                delta_H -= GetCellCellAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(target_element), rCellPopulation.GetCellUsingLocationIndex(neighbour_element));
            }
        }
        else if (neighbouring_node_contained && !target_node_contained)
        {
            // The neighbouring node is contained in a Potts element, but the target node is not
            unsigned neighbour_element = (*neighbouring_node_containing_elements.begin());
            delta_H -= GetCellBoundaryAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(neighbour_element));
        }
        else if (!neighbouring_node_contained && target_node_contained)
        {
            // The target node is contained in a Potts element, but the neighbouring node is not
            unsigned target_element = (*new_location_containing_elements.begin());
            delta_H -= GetCellBoundaryAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(target_element));
        }

        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)
            {
                // The nodes are currently contained in different elements
                delta_H += GetCellCellAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(current_element),rCellPopulation.GetCellUsingLocationIndex(neighbour_element));
            }
        }
        else if (neighbouring_node_contained && !current_node_contained)
        {
            // The neighbouring node is contained in a Potts element, but the current node is not
            unsigned neighbour_element = (*neighbouring_node_containing_elements.begin());
            delta_H += GetCellBoundaryAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(neighbour_element));
        }
        else if (!neighbouring_node_contained && current_node_contained)
        {
            // The current node is contained in a Potts element, but the neighbouring node is not
            unsigned current_element = (*containing_elements.begin());
            delta_H += GetCellBoundaryAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(current_element));
        }
    }

    return delta_H;
}

template<unsigned DIM>
double AdhesionPottsUpdateRule<DIM>::GetCellCellAdhesionEnergy(CellPtr pCellA, CellPtr pCellB)
{
    return GetCellCellAdhesionEnergyParameter();
}

template<unsigned DIM>
double AdhesionPottsUpdateRule<DIM>::GetCellBoundaryAdhesionEnergy(CellPtr pCell)
{
    return GetCellBoundaryAdhesionEnergyParameter();
}

template<unsigned DIM>
double AdhesionPottsUpdateRule<DIM>::GetCellCellAdhesionEnergyParameter()
{
    return mCellCellAdhesionEnergyParameter;
}

template<unsigned DIM>
double AdhesionPottsUpdateRule<DIM>::GetCellBoundaryAdhesionEnergyParameter()
{
    return mCellBoundaryAdhesionEnergyParameter;
}

template<unsigned DIM>
void AdhesionPottsUpdateRule<DIM>::SetCellCellAdhesionEnergyParameter(double cellCellAdhesionEnergyParameter)
{
    mCellCellAdhesionEnergyParameter = cellCellAdhesionEnergyParameter;
}

template<unsigned DIM>
void AdhesionPottsUpdateRule<DIM>::SetCellBoundaryAdhesionEnergyParameter(double cellBoundaryAdhesionEnergyParameter)
{
    mCellBoundaryAdhesionEnergyParameter = cellBoundaryAdhesionEnergyParameter;
}

template<unsigned DIM>
void AdhesionPottsUpdateRule<DIM>::OutputUpdateRuleParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<CellCellAdhesionEnergyParameter>" << mCellCellAdhesionEnergyParameter << "</CellCellAdhesionEnergyParameter>\n";
    *rParamsFile << "\t\t\t<CellBoundaryAdhesionEnergyParameter>" << mCellBoundaryAdhesionEnergyParameter << "</CellBoundaryAdhesionEnergyParameter>\n";

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

// Explicit instantiation
template class AdhesionPottsUpdateRule<1>;
template class AdhesionPottsUpdateRule<2>;
template class AdhesionPottsUpdateRule<3>;

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