NodesOnlyMesh.hpp

/*

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 * Redistributions in binary form must reproduce the above copyright notice,
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*/

#ifndef NODESONLYMESH_HPP_
#define NODESONLYMESH_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/map.hpp>

#include "SmartPointers.hpp"
#include "PetscTools.hpp"
#include "DistributedBoxCollection.hpp"
#include "MutableMesh.hpp"
template<unsigned SPACE_DIM>
class NodesOnlyMesh: public MutableMesh<SPACE_DIM, SPACE_DIM>
{
private:

    friend class TestNodesOnlyMesh;

    friend class boost::serialization::access;

    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        archive & mMaximumInteractionDistance;
        archive & mMinimumNodeDomainBoundarySeparation;
        std::vector<unsigned> indices = GetAllNodeIndices();
        archive & indices;
        archive & boost::serialization::base_object<MutableMesh<SPACE_DIM, SPACE_DIM> >(*this);
    }

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        archive & mMaximumInteractionDistance;
        archive & mMinimumNodeDomainBoundarySeparation;
        std::vector<unsigned> indices;
        archive & indices;
        archive & boost::serialization::base_object<MutableMesh<SPACE_DIM, SPACE_DIM> >(*this);
        // Re-index the nodes according to what we've just read
        assert(GetNumNodes() == indices.size());
        this->mNodesMapping.clear();
        for (unsigned i=0; i<this->mNodes.size(); i++)
        {
            unsigned new_index = indices[i];
            this->mNodes[i]->SetIndex(new_index);
            this->mNodesMapping[new_index] = i;
        }
        mMaxAddedNodeIndex = *(std::max_element(indices.begin(), indices.end()));
        mIndexCounter = mMaxAddedNodeIndex + 1; // Next available fresh index
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()
    std::vector<boost::shared_ptr<Node<SPACE_DIM> > > mHaloNodes;

    double mMaximumInteractionDistance;

    std::map<unsigned, unsigned> mNodesMapping;

    std::map<unsigned, unsigned> mHaloNodesMapping;

    unsigned mIndexCounter;

    double mMinimumNodeDomainBoundarySeparation;

    std::vector<unsigned> mDeletedGlobalNodeIndices;

    std::vector<unsigned> mNodesToSendRight;

    std::vector<unsigned> mNodesToSendLeft;

    std::vector<bool> mLocalInitialNodes;

    unsigned mMaxAddedNodeIndex;

    DistributedBoxCollection<SPACE_DIM>* mpBoxCollection;

    bool mCalculateNodeNeighbours;

    unsigned GetNextAvailableIndex();

    void EnlargeBoxCollection();

    bool IsANodeCloseToDomainBoundary();

     void SetUpBoxCollection(const std::vector<Node<SPACE_DIM>* >& rNodes);

     void RemoveDeletedNodes(NodeMap& map);

     void UpdateNodeIndices();

     void AddNodeWithFixedIndex(Node<SPACE_DIM>* pNewNode);

protected:

    void ClearBoxCollection();

     virtual void SetUpBoxCollection(double cutOffLength, c_vector<double, 2*SPACE_DIM> domainSize, int numLocalRows = PETSC_DECIDE, bool isPeriodic = false);

     DistributedBoxCollection<SPACE_DIM>* GetBoxCollection();

public:

    NodesOnlyMesh();

    virtual ~NodesOnlyMesh();

    void ConstructNodesWithoutMesh(const std::vector<Node<SPACE_DIM>*>& rNodes, double maxInteractionDistance);

    void ConstructNodesWithoutMesh(const std::vector<boost::shared_ptr<Node<SPACE_DIM> > >& rNodes, double maxInteractionDistance);

    void ConstructNodesWithoutMesh(const AbstractMesh<SPACE_DIM,SPACE_DIM>& rGeneratingMesh, double maxInteractionDistance);

    std::vector<bool>& rGetInitiallyOwnedNodes();

    void Clear();

    unsigned SolveNodeMapping(unsigned index) const;

    Node<SPACE_DIM>* GetNodeOrHaloNode(unsigned index) const;

    bool IsOwned(c_vector<double, SPACE_DIM>& location);

    unsigned GetNumNodes() const;

    virtual unsigned GetMaximumNodeIndex();

    void SetMaximumInteractionDistance(double maxDistance);

    double GetMaximumInteractionDistance();

    double GetWidth(const unsigned& rDimension) const;

    void SetCalculateNodeNeighbours(bool calculateNodeNeighbours);

    void CalculateInteriorNodePairs(std::vector<std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>*> >& rNodePairs);

    void CalculateBoundaryNodePairs(std::vector<std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>*> >& rNodePairs);

    void ReMesh(NodeMap& rMap);

    void SetInitialBoxCollection(const c_vector<double, 2*SPACE_DIM> domainSize, double maxInteractionDistance);

    void UpdateBoxCollection();

    void ResizeBoxCollection();

    void AddNodesToBoxes();

    void AddHaloNodesToBoxes();

    void CalculateNodesOutsideLocalDomain();

    std::vector<unsigned>& rGetNodesToSendLeft();

    std::vector<unsigned>& rGetNodesToSendRight();

    std::vector<unsigned>& rGetHaloNodesToSendRight();

    std::vector<unsigned>& rGetHaloNodesToSendLeft();

    void AddHaloNode(boost::shared_ptr<Node<SPACE_DIM> > pNewNode);

    void ClearHaloNodes();

    void SetNode(unsigned nodeIndex, ChastePoint<SPACE_DIM> point, bool concreteMove = false);

    unsigned AddNode(Node<SPACE_DIM>* pNewNode);

    void AddMovedNode(boost::shared_ptr<Node<SPACE_DIM> > pMovedNode);

    void DeleteNode(unsigned index);

    void DeleteMovedNode(unsigned index);

    void SetMinimumNodeDomainBoundarySeparation(double separation);

    void LoadBalanceMesh();

    void ConstructFromMeshReader(AbstractMeshReader<SPACE_DIM, SPACE_DIM>& rMeshReader);

    std::vector<unsigned> GetAllNodeIndices() const;
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(NodesOnlyMesh)

#endif /*NODESONLYMESH_HPP_*/