NodesOnlyMesh.hpp

/*

Copyright (c) 2005-2015, University of Oxford.
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This file is part of Chaste.

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modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
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   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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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 "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 serialize(Archive & archive, const unsigned int version)
    {
        archive & mMaximumInteractionDistance;
        archive & mMinimumNodeDomainBoundarySeparation;
        archive & boost::serialization::base_object<MutableMesh<SPACE_DIM, SPACE_DIM> >(*this);
    }

    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 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, std::map<unsigned, std::set<unsigned> >& rNodeNeighbours);

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

    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();

    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);
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(NodesOnlyMesh)

#endif /*NODESONLYMESH_HPP_*/