Cylindrical2dMesh.hpp

/*

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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.

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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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*/
#ifndef CYLINDRICAL2DMESH_HPP_
#define CYLINDRICAL2DMESH_HPP_

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

#include <cmath>
#include <map>

#include "MutableMesh.hpp"
#include "TrianglesMeshWriter.hpp"

class Cylindrical2dMesh : public MutableMesh<2,2>
{
    friend class TestCylindrical2dMesh;
private:

    double mWidth;

    double mTop;

    double mBottom;

    std::vector<unsigned> mLeftOriginals;

    std::vector<unsigned> mLeftImages;

    std::map<unsigned, unsigned> mImageToLeftOriginalNodeMap;

    std::vector<unsigned> mRightOriginals;

    std::vector<unsigned> mRightImages;

    std::map<unsigned, unsigned> mImageToRightOriginalNodeMap;

    std::set<unsigned> mLeftPeriodicBoundaryElementIndices;

    std::set<unsigned> mRightPeriodicBoundaryElementIndices;

    std::vector<unsigned > mTopHaloNodes;

    std::vector<unsigned > mBottomHaloNodes;

    bool mMismatchedBoundaryElements;

    void UpdateTopAndBottom();

    void CreateHaloNodes();

    void CreateMirrorNodes();

    void ReconstructCylindricalMesh();

    void DeleteHaloNodes();

    void CorrectNonPeriodicMesh();

    void GenerateVectorsOfElementsStraddlingPeriodicBoundaries();

    unsigned GetCorrespondingNodeIndex(unsigned nodeIndex);

    void UseTheseElementsToDecideMeshing(std::set<unsigned>& rMainSideElements);

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<MutableMesh<2,2> >(*this);
        archive & mWidth;
        archive & mTop;
        archive & mBottom;
    }

public:

    Cylindrical2dMesh(double width);

    Cylindrical2dMesh(double width, std::vector<Node<2>*> nodes);

    ~Cylindrical2dMesh();

    void ReMesh(NodeMap& rMap);

    c_vector<double, 2> GetVectorFromAtoB(const c_vector<double, 2>& rLocation1, const c_vector<double, 2>& rLocation2);

    void SetNode(unsigned index, ChastePoint<2> point, bool concreteMove);

    double GetWidth(const unsigned& rDimension) const;

    unsigned AddNode(Node<2>* pNewNode);

    bool GetInstanceOfMismatchedBoundaryNodes();
};

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const Cylindrical2dMesh * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const double width = t->GetWidth(0);
    ar & width;
}

template<class Archive>
inline void load_construct_data(
    Archive & ar, Cylindrical2dMesh * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    double width;
    ar & width;

    // Invoke inplace constructor to initialise instance
    ::new(t)Cylindrical2dMesh(width);
}
}
} // namespace ...

#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(Cylindrical2dMesh)

#endif /*CYLINDRICAL2DMESH_HPP_*/