NodesOnlyMesh.cpp

/*

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*/

#include <map>
#include "NodesOnlyMesh.hpp"

template<unsigned SPACE_DIM>
NodesOnlyMesh<SPACE_DIM>::NodesOnlyMesh()
        : MutableMesh<SPACE_DIM, SPACE_DIM>(),
          mpBoxCollection(NULL)
{
}

template<unsigned SPACE_DIM>
NodesOnlyMesh<SPACE_DIM>::~NodesOnlyMesh()
{
    Clear();
    ClearBoxCollection();
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ConstructNodesWithoutMesh(const std::vector<Node<SPACE_DIM>*>& rNodes)
{
    this->Clear();
    mpBoxCollection = NULL;

    for (unsigned i=0; i<rNodes.size(); i++)
    {
        assert(!rNodes[i]->IsDeleted());
        c_vector<double, SPACE_DIM> location = rNodes[i]->rGetLocation();

        Node<SPACE_DIM>* p_node_copy = new Node<SPACE_DIM>(i, location);
        this->mNodes.push_back(p_node_copy);

        mCellRadii.push_back(0.5);
    }
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ConstructNodesWithoutMesh(const AbstractMesh<SPACE_DIM,SPACE_DIM>& rGeneratingMesh)
{
    ConstructNodesWithoutMesh(rGeneratingMesh.mNodes);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::Clear()
{
    // Call Clear() on the parent class
    MutableMesh<SPACE_DIM,SPACE_DIM>::Clear();

    // Clear the cell radii
    mCellRadii.clear();
}

template<unsigned SPACE_DIM>
double NodesOnlyMesh<SPACE_DIM>::GetCellRadius(unsigned index)
{
    assert(index < mCellRadii.size());
    return mCellRadii[index];
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::SetCellRadius(unsigned index, double radius)
{
    assert(index < mCellRadii.size());
    mCellRadii[index] = radius;
}

template<unsigned SPACE_DIM>
BoxCollection<SPACE_DIM>* NodesOnlyMesh<SPACE_DIM>::GetBoxCollection()
{
    return mpBoxCollection;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ClearBoxCollection()
{
    if (mpBoxCollection != NULL)
    {
        delete mpBoxCollection;
    }
    mpBoxCollection = NULL;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::SetUpBoxCollection(double cutOffLength, c_vector<double, 2*SPACE_DIM> domainSize)
{
    mpBoxCollection = new BoxCollection<SPACE_DIM>(cutOffLength, domainSize);
    mpBoxCollection->SetupLocalBoxesHalfOnly();

    //Put the nodes in the boxes.
    for (unsigned i=0; i< this->GetNumNodes(); i++)
    {
        unsigned box_index = mpBoxCollection->CalculateContainingBox(this->GetNode(i));
        mpBoxCollection->rGetBox(box_index).AddNode(this->GetNode(i));
    }
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::SetMaximumInteractionDistance(double maximumInteractionDistance)
{
    mMaximumInteractionDistance = maximumInteractionDistance;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::CalculateNodePairs(std::set<std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>*> >& rNodePairs, std::map<unsigned, std::set<unsigned> >& rNodeNeighbours)
{
    assert(mpBoxCollection != NULL);
    mpBoxCollection->CalculateNodePairs(this->mNodes, rNodePairs, rNodeNeighbours);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ReMesh(NodeMap& map)
{
    // Store the node locations
    std::vector<c_vector<double, SPACE_DIM> > old_node_locations;
    std::vector<double> old_cell_radii;
    bool copy_radii = !mCellRadii.empty();

    unsigned new_index = 0;
    for (unsigned i=0; i<this->GetNumAllNodes(); i++)
    {
        if (this->mNodes[i]->IsDeleted())
        {
            map.SetDeleted(i);
        }
        else
        {
            map.SetNewIndex(i, new_index);
            old_node_locations.push_back(this->mNodes[i]->rGetLocation());
            if (copy_radii)
            {
                old_cell_radii.push_back(mCellRadii[i]);
            }

            new_index++;
        }
    }
    // Remove current data
    this->Clear();

    // Replace radius data
    mCellRadii = old_cell_radii;

    // Construct the nodes
    for (unsigned node_index=0; node_index<old_node_locations.size(); node_index++)
    {
        Node<SPACE_DIM>* p_node = new Node<SPACE_DIM>(node_index, old_node_locations[node_index], false);
        this->mNodes.push_back(p_node);
    }
}

template<unsigned SPACE_DIM>
unsigned NodesOnlyMesh<SPACE_DIM>::AddNode(Node<SPACE_DIM>* pNewNode)
{
    // Call method on parent class
    unsigned new_node_index = MutableMesh<SPACE_DIM, SPACE_DIM>::AddNode(pNewNode);

    // Then update mCellRadii
    if (new_node_index >= mCellRadii.size())
    {
        mCellRadii.resize(new_node_index+1);
    }
    SetCellRadius(new_node_index, 0.5);

    return new_node_index;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::DeleteNode(unsigned index)
{
    if (this->mNodes[index]->IsDeleted())
    {
        EXCEPTION("Trying to delete a deleted node");
    }

    this->mNodes[index]->MarkAsDeleted();
    this->mDeletedNodeIndices.push_back(index);

    mCellRadii[index] = DOUBLE_UNSET;
}

// Explicit instantiation

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

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