VertexMesh.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 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_*/