SemMesh.hpp

/*

Copyright (c) 2005-2012, 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 SEMMESH_HPP_
#define SEMMESH_HPP_

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

#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 "SemMeshReader.hpp"
#include "SemMeshWriter.hpp"
#include "PottsElement.hpp"

template<unsigned DIM>
class SemMesh : public AbstractMesh<DIM, DIM>
{
    friend class TestSemMesh;

protected:

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

    std::vector<unsigned> mDeletedElementIndices;

    std::vector<unsigned> mDeletedNodeIndices;

    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 & mDeletedNodeIndices;
        archive & boost::serialization::base_object<AbstractMesh<DIM, DIM> >(*this);

        // Create a mesh writer pointing to the correct file and directory
        SemMeshWriter<DIM> mesh_writer(ArchiveLocationInfo::GetArchiveRelativePath(),
                                         ArchiveLocationInfo::GetMeshFilename(),
                                         false);
        mesh_writer.WriteFilesUsingMesh(*(const_cast<SemMesh<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 & mDeletedNodeIndices;
        archive & boost::serialization::base_object<AbstractMesh<DIM, DIM> >(*this);

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

public:

    //                            Iterators                             //

    class SemElementIterator;

    inline SemElementIterator GetElementIteratorBegin(bool skipDeletedElements=true);

    inline SemElementIterator GetElementIteratorEnd();

    //                             Methods                              //

    SemMesh( std::vector<Node<DIM>*> nodes,
            std::vector<PottsElement<DIM>*> pottsElements);

    SemMesh();

    virtual ~SemMesh();

    virtual unsigned GetNumNodes() const;

    virtual unsigned GetNumAllNodes() const;

    virtual unsigned GetNumElements() const;

    unsigned GetNumAllElements() const;

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

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

    virtual void Clear();

    void ReMesh();

    void DeleteElement(unsigned index);

    unsigned AddElement(PottsElement<DIM>* pNewElement, std::vector<Node<DIM>* > pNewNodes);

    //                         Nested classes                           //

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

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

        inline bool operator!=(const SemMesh<DIM>::SemElementIterator& rOther);

        inline SemElementIterator& operator++();

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

    private:
        SemMesh<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(SemMesh)


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

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

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

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

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

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

    return (*this);
}

template<unsigned DIM>
SemMesh<DIM>::SemElementIterator::SemElementIterator(
        SemMesh<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 SemMesh<DIM>::SemElementIterator::IsAtEnd()
{
    return mElementIter == mrMesh.mElements.end();
}

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

#endif /*SEMMESH_HPP_*/