NodesOnlyMesh.hpp

/*

Copyright (c) 2005-2016, University of Oxford.
All rights reserved.

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Redistribution and use in source and binary forms, with or without
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,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   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
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#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();

    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);
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(NodesOnlyMesh)

#endif /*NODESONLYMESH_HPP_*/