VertexMesh.hpp

/*
 
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This file is part of Chaste.
 
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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 <algorithm>
#include <iostream>
#include <map>
 
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/split_member.hpp>
#include <boost/serialization/vector.hpp>
#include "ChasteSerialization.hpp"
 
#include "AbstractMesh.hpp"
#include "Edge.hpp"
#include "EdgeHelper.hpp"
#include "ArchiveLocationInfo.hpp"
#include "TetrahedralMesh.hpp"
#include "VertexElement.hpp"
#include "VertexElementMap.hpp"
#include "VertexMeshReader.hpp"
#include "VertexMeshWriter.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;
 
    EdgeHelper<SPACE_DIM> mEdgeHelper;
 
    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 GenerateEdgesFromElements(std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*>& rElements);
 
    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, 
               bool isBounded = false,
               bool scaleBoundByEdgeLength = true,
               double maxDelaunayEdgeLength = DBL_MAX,
               bool offsetNewBoundaryNodes = false);
 
    VertexMesh(TetrahedralMesh<3, 3>& rMesh);
 
    VertexMesh();
 
    virtual ~VertexMesh();
 
    unsigned GetNumEdges() const;
 
    Edge<SPACE_DIM>* GetEdge(unsigned index) const;
 
    const EdgeHelper<SPACE_DIM>& rGetEdgeHelper() const;
 
    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);
 
    unsigned GetRosetteRankOfElement(unsigned index);
 
    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);
 
    virtual VertexMesh<ELEMENT_DIM, SPACE_DIM>* GetMeshForVtk();
 
    bool IsNearExistingNodes(c_vector<double,SPACE_DIM> newNodeLocation, std::vector<Node<SPACE_DIM> *> nodesToCheck, double minClearance);
 
    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_*/