NodesOnlyMesh.hpp

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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,  c_vector<bool,SPACE_DIM> isDimPeriodic  = zero_vector<bool>(SPACE_DIM));
 
     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();
 
    bool GetIsPeriodicAcrossProcsFromBoxCollection() const;
 
    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_*/