NodesOnlyMesh.hpp

/*

Copyright (c) 2005-2012, 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,
   this list of conditions and the following disclaimer in the documentation
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 * 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
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*/

#ifndef NODESONLYMESH_HPP_
#define NODESONLYMESH_HPP_

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

template<unsigned SPACE_DIM>
class NodesOnlyMesh: public MutableMesh<SPACE_DIM, SPACE_DIM>
{
private:

    std::vector<double> mCellRadii;

    BoxCollection<SPACE_DIM>* mpBoxCollection;

    double mMaximumInteractionDistance;


    friend class TestNodesOnlyMesh;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<MutableMesh<SPACE_DIM, SPACE_DIM> >(*this);
        /*
         * Note that the MutableMesh archiver does a remesh. If there are deleted nodes
         * then we want to wait for them to be re-numbered before archiving the radii.
         */
        archive & mCellRadii;
    }

public:

    NodesOnlyMesh();

    ~NodesOnlyMesh();

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

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

    void Clear();

    double GetCellRadius(unsigned index);

    void SetCellRadius(unsigned index, double radius);

    BoxCollection<SPACE_DIM>* GetBoxCollection();

    void ClearBoxCollection();

    void SetUpBoxCollection(double cutOffLength, c_vector<double, 2*SPACE_DIM> domainSize);

    void SetMaximumInteractionDistance(double maximumInteractionDistance);

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

    void ReMesh(NodeMap& rMap);

    unsigned AddNode(Node<SPACE_DIM>* pNewNode);

    void DeleteNode(unsigned index);
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(NodesOnlyMesh)

#endif /*NODESONLYMESH_HPP_*/