VertexMesh.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,
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 * Redistributions in binary form must reproduce the above copyright notice,
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   software without specific prior written permission.

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*/
#ifndef VERTEXMESH_HPP_
#define VERTEXMESH_HPP_

// Forward declaration prevents circular include chain
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class VertexMeshWriter;

#include <iostream>
#include <map>
#include <algorithm>

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

#include "AbstractMesh.hpp"
#include "ArchiveLocationInfo.hpp"
#include "VertexMeshReader.hpp"
#include "VertexMeshWriter.hpp"
#include "VertexElement.hpp"
#include "VertexElementMap.hpp"
#include "TetrahedralMesh.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class VertexMesh : public AbstractMesh<ELEMENT_DIM, SPACE_DIM>
{
    friend class TestVertexMesh;

protected:

    std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*> mElements;

    std::vector<VertexElement<ELEMENT_DIM-1, SPACE_DIM>*> mFaces;

    std::map<unsigned, unsigned> mVoronoiElementIndexMap;

    TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* mpDelaunayMesh;

    unsigned SolveNodeMapping(unsigned index) const;

    unsigned SolveElementMapping(unsigned index) const;

    unsigned SolveBoundaryElementMapping(unsigned index) const;

    void GenerateVerticesFromElementCircumcentres(TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rMesh);

    //                        2D-specific methods                       //

    bool ElementIncludesPoint(const c_vector<double, SPACE_DIM>& rTestPoint, unsigned elementIndex);

    unsigned GetLocalIndexForElementEdgeClosestToPoint(const c_vector<double, SPACE_DIM>& rTestPoint, unsigned elementIndex);

    friend class boost::serialization::access;

    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        archive & boost::serialization::base_object<AbstractMesh<ELEMENT_DIM,SPACE_DIM> >(*this);

        // Create a mesh writer pointing to the correct file and directory
        VertexMeshWriter<ELEMENT_DIM, SPACE_DIM> mesh_writer(ArchiveLocationInfo::GetArchiveRelativePath(),
                                                             ArchiveLocationInfo::GetMeshFilename(),
                                                             false);
        mesh_writer.WriteFilesUsingMesh(*(const_cast<VertexMesh<ELEMENT_DIM, SPACE_DIM>*>(this)));
    }

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractMesh<ELEMENT_DIM,SPACE_DIM> >(*this);

        VertexMeshReader<ELEMENT_DIM,SPACE_DIM> mesh_reader(ArchiveLocationInfo::GetArchiveDirectory() + ArchiveLocationInfo::GetMeshFilename());
        this->ConstructFromMeshReader(mesh_reader);
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()

public:

    //                            Iterators                             //

    class VertexElementIterator;

    inline VertexElementIterator GetElementIteratorBegin(bool skipDeletedElements=true);

    inline VertexElementIterator GetElementIteratorEnd();

    //                             Methods                              //

    VertexMesh(std::vector<Node<SPACE_DIM>*> nodes,
               std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*> vertexElements);

    VertexMesh(std::vector<Node<SPACE_DIM>*> nodes,
               std::vector<VertexElement<ELEMENT_DIM-1,SPACE_DIM>*> faces,
               std::vector<VertexElement<ELEMENT_DIM,SPACE_DIM>*> vertexElements);

    VertexMesh(TetrahedralMesh<2,2>& rMesh, bool isPeriodic=false);

    VertexMesh(TetrahedralMesh<3,3>& rMesh);

    VertexMesh();

    virtual ~VertexMesh();

    virtual unsigned GetNumNodes() const;

    virtual unsigned GetNumElements() const;

    unsigned GetNumAllElements() const;

    virtual unsigned GetNumFaces() const;

    VertexElement<ELEMENT_DIM, SPACE_DIM>* GetElement(unsigned index) const;

    VertexElement<ELEMENT_DIM-1, SPACE_DIM>* GetFace(unsigned index) const;

    virtual c_vector<double, SPACE_DIM> GetCentroidOfElement(unsigned index);

    void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM,SPACE_DIM>& rMeshReader);

    virtual void Clear();

    unsigned GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(unsigned elementIndex);

    unsigned GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex(unsigned nodeIndex);

    virtual c_vector<double, SPACE_DIM> GetVectorFromAtoB(const c_vector<double, SPACE_DIM>& rLocationA,
                                                          const c_vector<double, SPACE_DIM>& rLocationB);

    virtual double GetVolumeOfElement(unsigned index);

    virtual double GetSurfaceAreaOfElement(unsigned index);

    //                        2D-specific methods                       //

    c_vector<double, SPACE_DIM> GetAreaGradientOfElementAtNode(VertexElement<ELEMENT_DIM,SPACE_DIM>* pElement, unsigned localIndex);

    c_vector<double, SPACE_DIM> GetPreviousEdgeGradientOfElementAtNode(VertexElement<ELEMENT_DIM,SPACE_DIM>* pElement, unsigned localIndex);

    c_vector<double, SPACE_DIM> GetNextEdgeGradientOfElementAtNode(VertexElement<ELEMENT_DIM,SPACE_DIM>* pElement, unsigned localIndex);

    c_vector<double, SPACE_DIM> GetPerimeterGradientOfElementAtNode(VertexElement<ELEMENT_DIM,SPACE_DIM>* pElement, unsigned localIndex);

    virtual c_vector<double, 3> CalculateMomentsOfElement(unsigned index);

    double GetEdgeLength(unsigned elementIndex1, unsigned elementIndex2);

    //                        3D-specific methods                       //

    c_vector<double, SPACE_DIM> GetUnitNormalToFace(VertexElement<ELEMENT_DIM-1, SPACE_DIM>* pFace);

    virtual double GetAreaOfFace(VertexElement<ELEMENT_DIM-1, SPACE_DIM>* pFace);

    c_vector<double, SPACE_DIM> GetShortAxisOfElement(unsigned index);

    std::set<unsigned> GetNeighbouringNodeIndices(unsigned nodeIndex);

    std::set<unsigned> GetNeighbouringNodeNotAlsoInElement(unsigned nodeIndex, unsigned elemIndex);

    std::set<unsigned> GetNeighbouringElementIndices(unsigned elementIndex);

    //                         Nested classes                           //

    class VertexElementIterator
    {
    public:
        inline VertexElement<ELEMENT_DIM, SPACE_DIM>& operator*();

        inline VertexElement<ELEMENT_DIM, SPACE_DIM>* operator->();

        inline bool operator!=(const VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator& rOther);

        inline VertexElementIterator& operator++();

        VertexElementIterator(VertexMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                        typename std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM> *>::iterator elementIter,
                        bool skipDeletedElements=true);

    private:
        VertexMesh& mrMesh;

        typename std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM> *>::iterator mElementIter;

        bool mSkipDeletedElements;

        inline bool IsAtEnd();

        inline bool IsAllowedElement();
    };
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(VertexMesh)



// VertexElementIterator class implementation - most methods are inlined    //

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator VertexMesh<ELEMENT_DIM, SPACE_DIM>::GetElementIteratorBegin(
        bool skipDeletedElements)
{
    return VertexElementIterator(*this, mElements.begin(), skipDeletedElements);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator VertexMesh<ELEMENT_DIM, SPACE_DIM>::GetElementIteratorEnd()
{
    return VertexElementIterator(*this, mElements.end());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VertexElement<ELEMENT_DIM, SPACE_DIM>& VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator::operator*()
{
    assert(!IsAtEnd());
    return **mElementIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VertexElement<ELEMENT_DIM, SPACE_DIM>* VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator::operator->()
{
    assert(!IsAtEnd());
    return *mElementIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator::operator!=(const VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator& rOther)
{
    return mElementIter != rOther.mElementIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator& VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator::operator++()
{
    do
    {
        ++mElementIter;
    }
    while (!IsAtEnd() && !IsAllowedElement());

    return (*this);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator::VertexElementIterator(
        VertexMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
        typename std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM> *>::iterator elementIter,
        bool skipDeletedElements)
    : mrMesh(rMesh),
      mElementIter(elementIter),
      mSkipDeletedElements(skipDeletedElements)
{
    if (mrMesh.mElements.empty())
    {
        // Cope with empty meshes
        mElementIter = mrMesh.mElements.end();
    }
    else
    {
        // Make sure we start at an allowed element
        if (mElementIter == mrMesh.mElements.begin() && !IsAllowedElement())
        {
            ++(*this);
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator::IsAtEnd()
{
    return mElementIter == mrMesh.mElements.end();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator::IsAllowedElement()
{
    return !(mSkipDeletedElements && (*this)->IsDeleted());
}


#endif /*VERTEXMESH_HPP_*/