AbstractTetrahedralMesh.hpp

/*

Copyright (C) University of Oxford, 2005-2009

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 ABSTRACTTETRAHEDRALMESH_HPP_
#define ABSTRACTTETRAHEDRALMESH_HPP_

#include <boost/serialization/access.hpp>
#include <boost/serialization/is_abstract.hpp>
#include <boost/serialization/base_object.hpp>

#include <vector>
#include <string>
#include <cassert>

#include "AbstractMesh.hpp"
#include "BoundaryElement.hpp"
#include "Element.hpp"
#include "AbstractMeshReader.hpp"
#include "TrianglesMeshReader.hpp"
#include "TrianglesMeshWriter.hpp"
#include "ArchiveLocationInfo.hpp"

#include <boost/serialization/split_member.hpp>

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractTetrahedralMesh : public AbstractMesh<ELEMENT_DIM, SPACE_DIM>
{
private:
    virtual unsigned SolveElementMapping(unsigned index) const = 0;

    virtual unsigned SolveBoundaryElementMapping(unsigned index) const = 0;

    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.
        TrianglesMeshWriter<ELEMENT_DIM,SPACE_DIM> mesh_writer(ArchiveLocationInfo::GetArchiveRelativePath(),
                                                               ArchiveLocationInfo::GetMeshFilename(),
                                                               false);
        if (this->IsMeshChanging())
        {
            mesh_writer.WriteFilesUsingMesh(*this);
        }
        else
        {
            try
            {
                // If this mesh object has been constructed from a mesh reader we can get reference to it
                TrianglesMeshReader<ELEMENT_DIM,SPACE_DIM> mesh_reader(this->GetMeshFileBaseName());
                mesh_writer.WriteFilesUsingMeshReader(mesh_reader, this->rGetNodePermutation());
            }
            catch(Exception& e)
            {
                NEVER_REACHED;
            }
        }
    }

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractMesh<ELEMENT_DIM,SPACE_DIM> >(*this);
        TrianglesMeshReader<ELEMENT_DIM,SPACE_DIM> mesh_reader(ArchiveLocationInfo::GetArchiveDirectory() + ArchiveLocationInfo::GetMeshFilename());
        this->ConstructFromMeshReader(mesh_reader);
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()


protected:  // Give access of these variables to subclasses

    std::vector<Element<ELEMENT_DIM, SPACE_DIM> *> mElements;

    std::vector<BoundaryElement<ELEMENT_DIM-1, SPACE_DIM> *> mBoundaryElements;

public:

    //                            Iterators                             //

    typedef typename std::vector<BoundaryElement<ELEMENT_DIM-1, SPACE_DIM> *>::const_iterator BoundaryElementIterator;

    class ElementIterator;

    inline ElementIterator GetElementIteratorBegin(bool skipDeletedElements=true);

    inline ElementIterator GetElementIteratorEnd();

    //                             Methods                              //

    AbstractTetrahedralMesh();

    virtual ~AbstractTetrahedralMesh();


    virtual unsigned GetNumElements() const;

    virtual unsigned GetNumBoundaryElements() const;

    unsigned GetNumAllElements() const;

    unsigned GetNumAllBoundaryElements() const;

    Element<ELEMENT_DIM, SPACE_DIM>* GetElement(unsigned index) const;

    BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>* GetBoundaryElement(unsigned index) const;

    virtual void SetElementOwnerships(unsigned lo, unsigned hi);

    virtual void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                         bool cullInternalFaces=false)=0;

    BoundaryElementIterator GetBoundaryElementIteratorBegin() const;

    BoundaryElementIterator GetBoundaryElementIteratorEnd() const;

    virtual void GetInverseJacobianForElement(unsigned elementIndex, c_matrix<double, SPACE_DIM, ELEMENT_DIM>& rJacobian,
                                              double& rJacobianDeterminant,
                                              c_matrix<double, ELEMENT_DIM, SPACE_DIM>& rInverseJacobian) const;

    virtual void GetWeightedDirectionForBoundaryElement(unsigned elementIndex,
                                                        c_vector<double, SPACE_DIM>& rWeightedDirection,
                                                        double& rJacobianDeterminant) const;


    //                         Nested classes                           //


    class ElementIterator
    {
    public:
        inline Element<ELEMENT_DIM, SPACE_DIM>& operator*();

        inline Element<ELEMENT_DIM, SPACE_DIM>* operator->();

        inline bool operator!=(const AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator& rOther);

        inline ElementIterator& operator++();

        ElementIterator(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                        typename std::vector<Element<ELEMENT_DIM, SPACE_DIM> *>::iterator elementIter,
                        bool skipDeletedElements=true);

    private:
        AbstractTetrahedralMesh& mrMesh;

        typename std::vector<Element<ELEMENT_DIM, SPACE_DIM> *>::iterator mElementIter;

        bool mSkipDeletedElements;

        inline bool IsAtEnd();

        inline bool IsAllowedElement();
    };

};

namespace boost
{
namespace serialization
{
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
struct is_abstract<AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> >
{
    typedef mpl::bool_<true> type;
    BOOST_STATIC_CONSTANT(bool, value=true);
};
}
}


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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetElementIteratorBegin(
        bool skipDeletedElements)
{
    return ElementIterator(*this, mElements.begin(), skipDeletedElements);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetElementIteratorEnd()
{
    return ElementIterator(*this, mElements.end());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Element<ELEMENT_DIM, SPACE_DIM>& AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::operator*()
{
    assert(!IsAtEnd());
    return **mElementIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Element<ELEMENT_DIM, SPACE_DIM>* AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::operator->()
{
    assert(!IsAtEnd());
    return *mElementIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::operator!=(const AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator& rOther)
{
    return mElementIter != rOther.mElementIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator& AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::operator++()
{
    do
    {
        ++mElementIter;
    }
    while (!IsAtEnd() && !IsAllowedElement());

    return (*this);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::ElementIterator(
        AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
        typename std::vector<Element<ELEMENT_DIM, SPACE_DIM> *>::iterator elementIter,
        bool skipDeletedElements)
    : mrMesh(rMesh),
      mElementIter(elementIter),
      mSkipDeletedElements(skipDeletedElements)
{
    if (mrMesh.mElements.size() == 0)
    {
        // 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 AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::IsAtEnd()
{
    return mElementIter == mrMesh.mElements.end();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::IsAllowedElement()
{
    return !(mSkipDeletedElements && (*this)->IsDeleted());
}


#endif /*ABSTRACTTETRAHEDRALMESH_HPP_*/

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