TetrahedralMesh.hpp

/*

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*/

#ifndef _TETRAHEDRALMESH_HPP_
#define _TETRAHEDRALMESH_HPP_

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

#include "UblasVectorInclude.hpp"
#include "UblasMatrixInclude.hpp"

#include <vector>
#include <string>
#include <set>

#include "AbstractTetrahedralMesh.hpp"
#include "AbstractMeshReader.hpp"
#include "ChastePoint.hpp"


class triangulateio; 

//   DECLARATION

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class TetrahedralMesh : public AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM>
{
    friend class TestTetrahedralMesh; // to give access to private methods (not variables)
    friend class TestCryptSimulation2d; // to give access to private methods (not variables)
private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
       archive & boost::serialization::base_object<AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> >(*this);
    }

protected:

    unsigned SolveNodeMapping(unsigned index) const;

    unsigned SolveElementMapping(unsigned index) const;

    unsigned SolveBoundaryElementMapping(unsigned index) const;

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

    std::vector< c_matrix<double, SPACE_DIM, ELEMENT_DIM> > mElementJacobians;

    std::vector< c_matrix<double, ELEMENT_DIM, SPACE_DIM> > mElementInverseJacobians;

    std::vector<double> mElementJacobianDeterminants;

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

    std::vector<double> mBoundaryElementJacobianDeterminants;

    template <class MESHER_IO>
    void ExportToMesher(NodeMap& map, MESHER_IO& mesherInput, int *elementList=NULL);

    template <class MESHER_IO>
    void ImportFromMesher(MESHER_IO& mesherOutput, unsigned numberOfElements, int *elementList, unsigned numberOfFaces, int *faceList, int *edgeMarkerList);


    void InitialiseTriangulateIo(triangulateio& mesherIo);

    void FreeTriangulateIo(triangulateio& mesherIo);

public:

    TetrahedralMesh();

    void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM,SPACE_DIM>& rMeshReader);

    void ReadNodesPerProcessorFile(const std::string& rNodesPerProcessorFile);

    bool CheckIsConforming();

    double GetVolume();

    double GetSurfaceArea();

    void RefreshMesh();

    void PermuteNodes();

    void PermuteNodes(const std::vector<unsigned>& perm);

    unsigned GetContainingElementIndex(const ChastePoint<SPACE_DIM>& rTestPoint,
                                       bool strict=false,
                                       std::set<unsigned> testElements=std::set<unsigned>(),
                                       bool onlyTryWithTestElements = false);


    unsigned GetContainingElementIndexWithInitialGuess(const ChastePoint<SPACE_DIM>& rTestPoint, unsigned startingElementGuess, bool strict=false);

    unsigned GetNearestElementIndex(const ChastePoint<SPACE_DIM>& rTestPoint);

    unsigned GetNearestElementIndexFromTestElements(const ChastePoint<SPACE_DIM>& rTestPoint,
                                                    std::set<unsigned> testElements);


    std::vector<unsigned> GetContainingElementIndices(const ChastePoint<SPACE_DIM>& rTestPoint);

    virtual void Clear();

    std::set<unsigned> CalculateBoundaryOfFlaggedRegion();

    double GetAngleBetweenNodes(unsigned indexA, unsigned indexB);

    void UnflagAllElements();

    void FlagElementsNotContainingNodes(const std::set<unsigned> rNodes);

    virtual void RefreshJacobianCachedData();

    virtual void GetJacobianForElement(unsigned elementIndex, c_matrix<double, SPACE_DIM, SPACE_DIM>& rJacobian, double& rJacobianDeterminant) 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 GetWeightedDirectionForElement(unsigned elementIndex, c_vector<double, SPACE_DIM>& rWeightedDirection, double& rJacobianDeterminant) const;

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

    class EdgeIterator
    {
    public:
        Node<SPACE_DIM>* GetNodeA();
        Node<SPACE_DIM>* GetNodeB();

        bool operator!=(const TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::EdgeIterator& rOther);

        EdgeIterator& operator++();

        EdgeIterator(TetrahedralMesh& rMesh, unsigned elemIndex);




    private:
        std::set< std::pair<unsigned, unsigned> > mEdgesVisited;

        TetrahedralMesh& mrMesh;   
        unsigned mElemIndex;       
        unsigned mNodeALocalIndex; 
        unsigned mNodeBLocalIndex; 
    };

    EdgeIterator EdgesBegin();

    EdgeIterator EdgesEnd();
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(TetrahedralMesh)

#endif //_TETRAHEDRALMESH_HPP_