VertexMesh.hpp

/*

Copyright (c) 2005-2015, University of Oxford.
All rights reserved.

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.

Redistribution and use in source and binary forms, with or without
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
   and/or other materials provided with the distribution.
 * 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
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/
#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);

    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:

    class VertexElementIterator;

    inline VertexElementIterator GetElementIteratorBegin(bool skipDeletedElements=true);

    inline VertexElementIterator GetElementIteratorEnd();

    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);

    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);

    double GetElongationShapeFactorOfElement(unsigned elementIndex);

    double CalculateUnitNormalToFaceWithArea(VertexElement<ELEMENT_DIM-1, SPACE_DIM>* pFace, c_vector<double, SPACE_DIM>& rNormal);

    virtual double CalculateAreaOfFace(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);

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

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

        inline bool operator!=(const typename 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 typename 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_*/