PottsMesh.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 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 c_vector<double, DIM> GetVectorFromAtoB(const c_vector<double, DIM>& rLocationA,
                                                    const c_vector<double, DIM>& rLocationB);

    virtual double GetVolumeOfElement(unsigned index);

    virtual double GetSurfaceAreaOfElement(unsigned index);

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

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

    void DeleteElement(unsigned index);

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

    unsigned AddElement(PottsElement<DIM>* pNewElement);

    //                         Nested classes                           //

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

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

        inline bool operator!=(const 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 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_*/