MutableMesh.hpp

/*

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 * Redistributions in binary form must reproduce the above copyright notice,
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*/

#ifndef MUTABLEMESH_HPP_
#define MUTABLEMESH_HPP_

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

#include "TetrahedralMesh.hpp"
#include "NodeMap.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class MutableMesh : public TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>
{
    friend class boost::serialization::access;

    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        archive & boost::serialization::base_object<TetrahedralMesh<ELEMENT_DIM, SPACE_DIM> >(*this);

        // Assume that the first node is indicative of the rest.
        bool does_have_attributes = this->mNodes[0]->HasNodeAttributes();

        archive & does_have_attributes;

        if (does_have_attributes)
        {
            for (unsigned i=0; i<this->mNodes.size(); i++)
            {
                double radius;
                radius = this->mNodes[i]->GetRadius();
                archive & radius;

                bool is_particle;
                is_particle = this->mNodes[i]->IsParticle();
                archive & is_particle;
            }
        }
    }

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<TetrahedralMesh<ELEMENT_DIM, SPACE_DIM> >(*this);

        bool does_have_attributes;

        archive & does_have_attributes;

        if (does_have_attributes)
        {
            for (unsigned i=0; i<this->mNodes.size(); i++)
            {
                double radius;
                archive & radius;
                this->mNodes[i]->SetRadius(radius);

                bool is_particle;
                archive & is_particle;

                if (is_particle)
                {
                    this->mNodes[i]->SetIsParticle(true);
                }
            }
        }

        // If ELEMENT_DIM=SPACEDIM Do a remesh after archiving has finished to get right number of boundary nodes etc.
        // NOTE - Subclasses must archive their member variables BEFORE calling this method.
        if(ELEMENT_DIM==SPACE_DIM)
        {
            NodeMap map(this->GetNumNodes());
            this->ReMesh(map);
            assert(map.IsIdentityMap()); // Otherwise the mesh will get VERY confused.
        }
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()

protected:

    std::vector<unsigned> mDeletedElementIndices;

    std::vector<unsigned> mDeletedBoundaryElementIndices;

    std::vector<unsigned> mDeletedNodeIndices;

    bool mAddedNodes;

private:

#define COVERAGE_IGNORE

    bool CheckIsVoronoi(Element<ELEMENT_DIM, SPACE_DIM>* pElement, double maxPenetration);
#undef COVERAGE_IGNORE

public:

    MutableMesh();

    MutableMesh(std::vector<Node<SPACE_DIM> *> nodes);

    virtual ~MutableMesh();

    void Clear();

    unsigned GetNumNodes() const;

    unsigned GetNumElements() const;

    unsigned GetNumBoundaryElements() const;


    void RescaleMeshFromBoundaryNode(ChastePoint<1> updatedPoint, unsigned boundaryNodeIndex);

    virtual unsigned AddNode(Node<SPACE_DIM>* pNewNode);

    unsigned AddElement(Element<ELEMENT_DIM,SPACE_DIM>* pNewElement);

    virtual void SetNode(unsigned index, ChastePoint<SPACE_DIM> point, bool concreteMove=true);

    void MoveMergeNode(unsigned index, unsigned targetIndex, bool concreteMove=true);

#define COVERAGE_IGNORE

    virtual void DeleteNode(unsigned index);

    virtual void DeleteElement(unsigned index);
#undef COVERAGE_IGNORE

    void DeleteNodePriorToReMesh(unsigned index);

    unsigned RefineElement(Element<ELEMENT_DIM,SPACE_DIM>* pElement, ChastePoint<SPACE_DIM> point);

    void DeleteBoundaryNodeAt(unsigned index);

#define COVERAGE_IGNORE

    void ReIndex(NodeMap& map);
#undef COVERAGE_IGNORE

    virtual void ReMesh(NodeMap& map);

    void ReMesh();

#define COVERAGE_IGNORE

    std::vector<c_vector<unsigned, 5> > SplitLongEdges(double cutoffLength);
#undef COVERAGE_IGNORE

#define COVERAGE_IGNORE

    c_vector<unsigned, 3> SplitEdge(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB);
#undef COVERAGE_IGNORE

#define COVERAGE_IGNORE

    bool CheckIsVoronoi(double maxPenetration=0.0);
#undef COVERAGE_IGNORE
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(MutableMesh)

#endif /*MUTABLEMESH_HPP_*/