PottsMesh.hpp

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*/

#ifndef POTTSMESH_HPP_
#define POTTSMESH_HPP_

// Forward declaration prevents circular include chain
template<unsigned DIM>
class PottsMeshWriter;

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

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

#include "AbstractMesh.hpp"
#include "ArchiveLocationInfo.hpp"
#include "PottsMeshReader.hpp"
#include "PottsMeshWriter.hpp"
#include "PottsElement.hpp"

template<unsigned DIM>
class PottsMesh : public AbstractMesh<DIM, DIM>
{
    friend class TestPottsMesh;

protected:
    std::vector<PottsElement<DIM>*> mElements;

    std::vector<unsigned> mDeletedElementIndices;

    std::vector< std::set<unsigned> > mVonNeumannNeighbouringNodeIndices;

    std::vector< std::set<unsigned> > mMooreNeighbouringNodeIndices;

    unsigned SolveNodeMapping(unsigned index) const;

    unsigned SolveElementMapping(unsigned index) const;

    unsigned SolveBoundaryElementMapping(unsigned index) const;

    friend class boost::serialization::access;

    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        // NOTE - Subclasses must archive their member variables BEFORE calling this method.
        archive & mDeletedElementIndices;
        archive & mVonNeumannNeighbouringNodeIndices;
        archive & mMooreNeighbouringNodeIndices;
        archive & boost::serialization::base_object<AbstractMesh<DIM, DIM> >(*this);

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

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        // NOTE - Subclasses must archive their member variables BEFORE calling this method.
        archive & mDeletedElementIndices;
        archive & mVonNeumannNeighbouringNodeIndices;
        archive & mMooreNeighbouringNodeIndices;
        archive & boost::serialization::base_object<AbstractMesh<DIM, DIM> >(*this);

        PottsMeshReader<DIM> mesh_reader(ArchiveLocationInfo::GetArchiveDirectory() + ArchiveLocationInfo::GetMeshFilename());
        this->ConstructFromMeshReader(mesh_reader);
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()

public:

    //                            Iterators                             //

    class PottsElementIterator;

    inline PottsElementIterator GetElementIteratorBegin(bool skipDeletedElements=true);

    inline PottsElementIterator GetElementIteratorEnd();

    //                             Methods                              //

    PottsMesh(std::vector<Node<DIM>*> nodes,
              std::vector<PottsElement<DIM>*> pottsElements,
              std::vector< std::set<unsigned> > vonNeumannNeighbouringNodeIndices,
              std::vector< std::set<unsigned> > mooreNeighbouringNodeIndices);

    PottsMesh();

    virtual ~PottsMesh();

    virtual unsigned GetNumNodes() const;

    virtual unsigned GetNumElements() const;

    unsigned GetNumAllElements() const;

    PottsElement<DIM>* GetElement(unsigned index) const;

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

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

    virtual void Clear();

    virtual double GetVolumeOfElement(unsigned index);

    virtual double GetSurfaceAreaOfElement(unsigned index);

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

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

    void DeleteNode(unsigned index);

    void DeleteElement(unsigned index);

    void RemoveDeletedElements();

    unsigned DivideElement(PottsElement<DIM>* pElement,
                           bool placeOriginalElementBelow=false);

    unsigned AddElement(PottsElement<DIM>* pNewElement);

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




    //                         Nested classes                           //

    class PottsElementIterator
    {
    public:
        inline PottsElement<DIM>& operator*();

        inline PottsElement<DIM>* operator->();

        inline bool operator!=(const typename PottsMesh<DIM>::PottsElementIterator& rOther);

        inline PottsElementIterator& operator++();

        PottsElementIterator(PottsMesh<DIM>& rMesh,
                             typename std::vector<PottsElement<DIM> *>::iterator elementIter,
                             bool skipDeletedElements=true);

    private:
        PottsMesh<DIM>& mrMesh;

        typename std::vector<PottsElement<DIM> *>::iterator mElementIter;

        bool mSkipDeletedElements;

        inline bool IsAtEnd();

        inline bool IsAllowedElement();
    };
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(PottsMesh)

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

template<unsigned DIM>
typename PottsMesh<DIM>::PottsElementIterator PottsMesh<DIM>::GetElementIteratorBegin(
        bool skipDeletedElements)
{
    return PottsElementIterator(*this, mElements.begin(), skipDeletedElements);
}

template<unsigned DIM>
typename PottsMesh<DIM>::PottsElementIterator PottsMesh<DIM>::GetElementIteratorEnd()
{
    return PottsElementIterator(*this, mElements.end());
}
template<unsigned DIM>
PottsElement<DIM>& PottsMesh<DIM>::PottsElementIterator::operator*()
{
    assert(!IsAtEnd());
    return **mElementIter;
}

template<unsigned DIM>
PottsElement<DIM>* PottsMesh<DIM>::PottsElementIterator::operator->()
{
    assert(!IsAtEnd());
    return *mElementIter;
}

template<unsigned DIM>
bool PottsMesh<DIM>::PottsElementIterator::operator!=(const typename PottsMesh<DIM>::PottsElementIterator& rOther)
{
    return mElementIter != rOther.mElementIter;
}

template<unsigned DIM>
typename PottsMesh<DIM>::PottsElementIterator& PottsMesh<DIM>::PottsElementIterator::operator++()
{
    do
    {
        ++mElementIter;
    }
    while (!IsAtEnd() && !IsAllowedElement());

    return (*this);
}

template<unsigned DIM>
PottsMesh<DIM>::PottsElementIterator::PottsElementIterator(
        PottsMesh<DIM>& rMesh,
        typename std::vector<PottsElement<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 DIM>
bool PottsMesh<DIM>::PottsElementIterator::IsAtEnd()
{
    return mElementIter == mrMesh.mElements.end();
}

template<unsigned DIM>
bool PottsMesh<DIM>::PottsElementIterator::IsAllowedElement()
{
    return !(mSkipDeletedElements && (*this)->IsDeleted());
}

#endif /*POTTSMESH_HPP_*/