MutableVertexMesh.hpp

/*

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This file is part of Chaste.

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 * Redistributions in binary form must reproduce the above copyright notice,
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   software without specific prior written permission.

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*/
#ifndef MUTABLEVERTEXMESH_HPP_
#define MUTABLEVERTEXMESH_HPP_

// Forward declaration prevents circular include chain
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class VertexMeshWriter;

#include <iostream>
#include <map>
#include <algorithm>

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

#include "VertexMesh.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class MutableVertexMesh : public VertexMesh<ELEMENT_DIM, SPACE_DIM>
{
    friend class TestMutableVertexMesh;
    friend class TestMutableVertexMeshReMesh;

protected:

    double mCellRearrangementThreshold;

    double mCellRearrangementRatio;

    double mT2Threshold;

    bool mCheckForInternalIntersections;

    std::vector<unsigned> mDeletedNodeIndices;

    std::vector<unsigned> mDeletedElementIndices;

    std::vector< c_vector<double, SPACE_DIM> > mLocationsOfT1Swaps;

    std::vector< c_vector<double, SPACE_DIM> > mLocationsOfT2Swaps;

    std::vector< c_vector<double, SPACE_DIM> > mLocationsOfT3Swaps;

    unsigned DivideElement(VertexElement<ELEMENT_DIM,SPACE_DIM>* pElement,
                           unsigned nodeAIndex,
                           unsigned nodeBIndex,
                           bool placeOriginalElementBelow=false);

    bool CheckForSwapsFromShortEdges(VertexElementMap& rElementMap);

    bool CheckForIntersections();

    virtual void IdentifySwapType(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB, VertexElementMap& rElementMap);

    void PerformNodeMerge(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB);

    void PerformT1Swap(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB, std::set<unsigned>& rElementsContainingNodes);

    void PerformIntersectionSwap(Node<SPACE_DIM>* pNode, unsigned elementIndex);

    void PerformT2Swap(VertexElement<ELEMENT_DIM,SPACE_DIM>& rElement);

    void PerformT3Swap(Node<SPACE_DIM>* pNode, unsigned elementIndex);

    void PerformVoidRemoval(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB, Node<SPACE_DIM>* pNodeC);

    friend class boost::serialization::access;

    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // NOTE - Subclasses must archive their member variables BEFORE calling this method.
        archive & mCellRearrangementThreshold;
        archive & mCellRearrangementRatio;
        archive & mT2Threshold;
        archive & mCheckForInternalIntersections;
        archive & mDeletedNodeIndices;
        archive & mDeletedElementIndices;

        archive & boost::serialization::base_object<VertexMesh<ELEMENT_DIM, SPACE_DIM> >(*this);
    }

public:

    MutableVertexMesh(std::vector<Node<SPACE_DIM>*> nodes,
                      std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*> vertexElements,
                      double cellRearrangementThreshold=0.01,
                      double t2Threshold=0.001,
                      double cellRearrangementRatio=1.5);

    MutableVertexMesh();

    virtual ~MutableVertexMesh();

    void SetCellRearrangementThreshold(double cellRearrangementThreshold);

    void SetT2Threshold(double t2Threshold);

    void SetCellRearrangementRatio(double cellRearrangementRatio);

    virtual void SetNode(unsigned nodeIndex, ChastePoint<SPACE_DIM> point);

    void SetCheckForInternalIntersections(bool checkForInternalIntersections);

    double GetCellRearrangementThreshold() const;

    double GetT2Threshold() const;

    double GetCellRearrangementRatio() const;

    unsigned GetNumNodes() const;

    unsigned GetNumElements() const;

    bool GetCheckForInternalIntersections() const;

    std::vector< c_vector<double, SPACE_DIM> > GetLocationsOfT1Swaps();

    std::vector< c_vector<double, SPACE_DIM> > GetLocationsOfT2Swaps();

    std::vector< c_vector<double, SPACE_DIM> > GetLocationsOfT3Swaps();

    void ClearLocationsOfT1Swaps();

    void ClearLocationsOfT2Swaps();

    void ClearLocationsOfT3Swaps();

    unsigned AddNode(Node<SPACE_DIM>* pNewNode);

    void DeleteElementPriorToReMesh(unsigned index);

    void DeleteNodePriorToReMesh(unsigned index);

    unsigned DivideElementAlongShortAxis(VertexElement<ELEMENT_DIM,SPACE_DIM>* pElement,
                                         bool placeOriginalElementBelow=false);

    unsigned DivideElementAlongGivenAxis(VertexElement<ELEMENT_DIM,SPACE_DIM>* pElement,
                                         c_vector<double, SPACE_DIM> axisOfDivision,
                                         bool placeOriginalElementBelow=false);

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

    bool CheckForT2Swaps(VertexElementMap& rElementMap);

    void Clear();

    void DivideEdge(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB);

    void RemoveDeletedNodesAndElements(VertexElementMap& rElementMap);

    void RemoveDeletedNodes();

    virtual void ReMesh(VertexElementMap& rElementMap);

    void ReMesh();
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(MutableVertexMesh)

#endif /*MUTABLEVERTEXMESH_HPP_*/