Node.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
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This file is part of Chaste.

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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,
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   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

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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
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*/

#ifndef _NODE_HPP_
#define _NODE_HPP_

#include "UblasVectorInclude.hpp"

#include <set>
#include <vector>

#include "ChasteSerialization.hpp"
#include "ChastePoint.hpp"

//#include <boost/serialization/vector.hpp>
//#include <boost/serialization/set.hpp>

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractTetrahedralMesh;

template<unsigned SPACE_DIM>
class Node
{
private:

    unsigned mIndex;

    unsigned mRegion;

    c_vector<double, SPACE_DIM> mLocation;

    bool mIsBoundaryNode;

    bool mIsInternal;

    bool mIsDeleted;

    std::set<unsigned> mElementIndices;

    std::set<unsigned> mBoundaryElementIndices;

    std::vector<double> mNodeAttributes;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        //archive & mLocation; //earlier versions of boost are unable to do this. See #1709
//        archive & mIndex;
        archive & mRegion;
//        archive & mIsBoundaryNode;
//        archive & mIsInternal;
//        archive & mIsDeleted;
//        archive & mElementIndices;
//        archive & mBoundaryElementIndices;
//        archive & mNodeAttributes;
    }

    void CommonConstructor(unsigned index, bool isBoundaryNode);

public:

    Node(unsigned index, ChastePoint<SPACE_DIM> point, bool isBoundaryNode=false);

    Node(unsigned index, std::vector<double> coords, bool isBoundaryNode=false);

    Node(unsigned index, c_vector<double, SPACE_DIM> location, bool isBoundaryNode=false);

    Node(unsigned index, bool isBoundaryNode=false, double v1=0, double v2=0, double v3=0);

    Node(unsigned index,  double *location, bool isBoundaryNode=false);

    void SetPoint(ChastePoint<SPACE_DIM> point);

    void SetIndex(unsigned index);

    void AddNodeAttribute(double attribute);

    void SetAsBoundaryNode(bool value=true);

    ChastePoint<SPACE_DIM> GetPoint() const;

    const c_vector<double, SPACE_DIM>& rGetLocation() const;

    c_vector<double, SPACE_DIM>& rGetModifiableLocation();

    unsigned GetIndex() const;

    bool IsBoundaryNode() const;

    void AddElement(unsigned index);

    void RemoveElement(unsigned index);

    void RemoveBoundaryElement(unsigned index);

    void AddBoundaryElement(unsigned index);

    std::set<unsigned>& rGetContainingElementIndices();

    std::vector<double>& rGetNodeAttributes();

    std::set<unsigned>& rGetContainingBoundaryElementIndices();

    unsigned GetNumContainingElements() const;

    unsigned GetNumBoundaryElements() const;

    void MarkAsDeleted();

    bool IsDeleted() const;

    void MarkAsInternal();

    bool IsInternal() const;

    template <unsigned ELEMENT_DIM>
    bool IsFlagged(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rMesh)
    {
        bool in_flagged_element = false;
        for (ContainingElementIterator it = ContainingElementsBegin();
             it != ContainingElementsEnd();
             ++it)
        {
            if (rMesh.GetElement(*it)->IsFlagged())
            {
                in_flagged_element = true;
                break;
            }
        }
        return in_flagged_element;
    }

    void SetRegion(unsigned region);

    unsigned GetRegion() const;

    class ContainingElementIterator
    {
    public:
        ContainingElementIterator(std::set<unsigned>::const_iterator indexIterator)
            : mIndexIterator(indexIterator)
        {}
        const unsigned& operator*() const
        {
            return *mIndexIterator;
        }
        bool operator!=(const ContainingElementIterator& rOther) const
        {
            return mIndexIterator != rOther.mIndexIterator;
        }
        bool operator==(const ContainingElementIterator& rOther) const
        {
            return !operator!=(rOther);
        }
        ContainingElementIterator& operator++()
        {
            ++mIndexIterator;
            return *this;
        }
    private:
        std::set<unsigned>::const_iterator mIndexIterator;  
    };

    ContainingElementIterator ContainingElementsBegin() const
    {
        return ContainingElementIterator(mElementIndices.begin());
    }

    ContainingElementIterator ContainingElementsEnd() const
    {
        return ContainingElementIterator(mElementIndices.end());
    }

    class ContainingBoundaryElementIterator
    {
    public:
        ContainingBoundaryElementIterator(std::set<unsigned>::const_iterator indexIterator)
            : mIndexIterator(indexIterator)
        {}
        const unsigned& operator*() const
        {
            return *mIndexIterator;
        }
        bool operator!=(const ContainingBoundaryElementIterator& rOther) const
        {
            return mIndexIterator != rOther.mIndexIterator;
        }
        bool operator==(const ContainingBoundaryElementIterator& rOther) const
        {
            return !operator!=(rOther);
        }
        ContainingBoundaryElementIterator& operator++()
        {
            ++mIndexIterator;
            return *this;
        }
    private:
        std::set<unsigned>::const_iterator mIndexIterator;  
    };

    ContainingBoundaryElementIterator ContainingBoundaryElementsBegin() const
    {
        return ContainingBoundaryElementIterator(mBoundaryElementIndices.begin());
    }

    ContainingBoundaryElementIterator ContainingBoundaryElementsEnd() const
    {
        return ContainingBoundaryElementIterator(mBoundaryElementIndices.end());
    }
};

#include "SerializationExportWrapper.hpp"
// Declare identifier for the serializer
EXPORT_TEMPLATE_CLASS_SAME_DIMS(Node)

namespace boost
{
namespace serialization
{
template<class Archive, unsigned SPACE_DIM>
inline void save_construct_data(
    Archive & ar, const Node<SPACE_DIM> * t, const BOOST_PFTO unsigned int file_version)
{

    // Save data required to construct instance
    for (unsigned i = 0; i < SPACE_DIM; i++)
    {
        //we archive coordinates of mLocation one by one
        //this is because earlier version of boost (<1.40, I think) cannot archive c_vectors
        double coord = t->rGetLocation()[i];
        ar & coord;
    }
    unsigned index = t->GetIndex();
    ar << index;

    bool is_boundary = t->IsBoundaryNode();
    ar << is_boundary;
}
template<class Archive, unsigned SPACE_DIM>
inline void load_construct_data(
    Archive & ar, Node<SPACE_DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance of Node
    c_vector<double,SPACE_DIM> location;
    for (unsigned i=0; i<SPACE_DIM; i++)
    {
        double coordinate;
        ar & coordinate;//resume coordinates one by one
        location[i] = coordinate;
    }

    unsigned index;
    ar >> index;

    bool is_boundary;
    ar >> is_boundary;

    // Invoke inplace constructor to initialise instance
    ::new(t)Node<SPACE_DIM>(index, location, is_boundary);
}
}
} // namespace ...

#endif //_NODE_HPP_