QuadraticMesh.hpp

/*

Copyright (C) University of Oxford, 2005-2010

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 QUADRATICMESH_HPP_
#define QUADRATICMESH_HPP_

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

#include "TetrahedralMesh.hpp"
#include "TrianglesMeshReader.hpp"

#include <vector>

template<unsigned DIM>
class QuadraticMesh : public TetrahedralMesh<DIM, DIM>
{
private:

    std::vector<bool> mIsInternalNode;

    unsigned mNumVertices;


    void AddNodesToBoundaryElements(TrianglesMeshReader<DIM,DIM>* pMeshReader);

    void AddNodeToBoundaryElement(BoundaryElement<DIM-1,DIM>* pBoundaryElement,
                                  Element<DIM,DIM>* pElement,
                                  unsigned internalNode);

    void AddExtraBoundaryNodes(BoundaryElement<DIM-1,DIM>* pBoundaryElement,
                               Element<DIM,DIM>* pElement,
                               unsigned nodeIndexOppositeToFace);

    void HelperMethod1(unsigned boundaryElemNode0, unsigned boundaryElemNode1,
                       Element<DIM,DIM>* pElement,
                       unsigned node0, unsigned node1, unsigned node2,
                       unsigned& rOffset,
                       bool& rReverse);

    void HelperMethod2(BoundaryElement<DIM-1,DIM>* pBoundaryElement,
                       Element<DIM,DIM>* pElement,
                       unsigned internalNode0, unsigned internalNode1, unsigned internalNode2,
                       unsigned offset,
                       bool reverse);

    void RunMesherAndReadMesh(std::string binary, std::string outputDir, std::string fileStem);

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<TetrahedralMesh<DIM, DIM> >(*this);
    }

public:

    QuadraticMesh()
    {
        this->mMeshIsLinear=false;
    }

    void ConstructFromMeshReader(AbstractMeshReader<DIM, DIM>& rMeshReader);

    QuadraticMesh(double xEnd, double yEnd, unsigned numElemX, unsigned numElemY);

    QuadraticMesh(double xEnd, double yEnd, double zEnd,
                  unsigned numElemX, unsigned numElemY, unsigned numElemZ);

    void WriteBoundaryElementFile(std::string directory, std::string fileName);

    unsigned GetNumVertices();
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(QuadraticMesh);


#endif /*QUADRATICMESH_HPP_*/