Cylindrical2dMesh.hpp

/*

Copyright (C) University of Oxford, 2005-2011

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.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#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 BOOST_PFTO 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_*/