AbstractOnLatticeCellPopulation.cpp

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*/

#include "AbstractOnLatticeCellPopulation.hpp"

template<unsigned DIM>
AbstractOnLatticeCellPopulation<DIM>::AbstractOnLatticeCellPopulation(AbstractMesh<DIM, DIM>& rMesh,
                                                                    std::vector<CellPtr>& rCells,
                                                                  const std::vector<unsigned> locationIndices,
                                                                  bool deleteMesh)
    : AbstractCellPopulation<DIM>(rMesh, rCells, locationIndices),
      mDeleteMesh(deleteMesh),
      mUpdateNodesInRandomOrder(true),
      mIterateRandomlyOverUpdateRuleCollection(false)
{
    std::list<CellPtr>::iterator it = this->mCells.begin();
    for (unsigned i=0; it != this->mCells.end(); ++it, ++i)
    {
        unsigned index = locationIndices.empty() ? i : locationIndices[i]; // assume that the ordering matches
        AbstractCellPopulation<DIM>::AddCellUsingLocationIndex(index, *it);
    }
}

template<unsigned DIM>
AbstractOnLatticeCellPopulation<DIM>::AbstractOnLatticeCellPopulation(AbstractMesh<DIM, DIM>& rMesh)
    : AbstractCellPopulation<DIM>(rMesh),
      mDeleteMesh(true),
      mUpdateNodesInRandomOrder(true),
      mIterateRandomlyOverUpdateRuleCollection(false)
{
}

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

template<unsigned DIM>
bool AbstractOnLatticeCellPopulation<DIM>::GetUpdateNodesInRandomOrder()
{
    return mUpdateNodesInRandomOrder;
}

template<unsigned DIM>
void AbstractOnLatticeCellPopulation<DIM>::SetUpdateNodesInRandomOrder(bool updateNodesInRandomOrder)
{
    mUpdateNodesInRandomOrder = updateNodesInRandomOrder;
}

template<unsigned DIM>
void AbstractOnLatticeCellPopulation<DIM>::SetIterateRandomlyOverUpdateRuleCollection(bool iterateRandomly)
{
    mIterateRandomlyOverUpdateRuleCollection = iterateRandomly;
}

template<unsigned DIM>
bool AbstractOnLatticeCellPopulation<DIM>::GetIterateRandomlyOverUpdateRuleCollection()
{
    return mIterateRandomlyOverUpdateRuleCollection;
}

template<unsigned DIM>
void AbstractOnLatticeCellPopulation<DIM>::SetNode(unsigned nodeIndex, ChastePoint<DIM>& rNewLocation)
{
    EXCEPTION("SetNode() cannot be called on a subclass of AbstractOnLatticeCellPopulation.");
}

template<unsigned DIM>
std::set<unsigned> AbstractOnLatticeCellPopulation<DIM>::GetNeighbouringNodeIndices(unsigned index)
{
    EXCEPTION("Cannot call GetNeighbouringNodeIndices() on a subclass of AbstractOnLatticeCellPopulation, need to go through the PottsMesh instead");
    std::set<unsigned> neighbouring_node_indices;
    return neighbouring_node_indices;
}

template<unsigned DIM>
void AbstractOnLatticeCellPopulation<DIM>::OutputCellPopulationParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t<UpdateNodesInRandomOrder>" << mUpdateNodesInRandomOrder << "</UpdateNodesInRandomOrder>\n";
    *rParamsFile << "\t\t<IterateRandomlyOverUpdateRuleCollection>" << mIterateRandomlyOverUpdateRuleCollection << "</IterateRandomlyOverUpdateRuleCollection>\n";

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

template<unsigned DIM>
double AbstractOnLatticeCellPopulation<DIM>::GetDefaultTimeStep()
{
    return 0.1;
}

template<unsigned DIM>
const std::vector<boost::shared_ptr<AbstractUpdateRule<DIM> > > AbstractOnLatticeCellPopulation<DIM>::GetUpdateRuleCollection() const
{
    return mUpdateRuleCollection;
}

template<unsigned DIM>
void AbstractOnLatticeCellPopulation<DIM>::RemoveAllUpdateRules()
{
    mUpdateRuleCollection.clear();
}

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