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"
 
 
struct 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=nullptr);
 
    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 GetContainingElementIndexWithInitialGuess(const ChastePoint<SPACE_DIM>& rTestPoint, unsigned startingElementGuess, bool strict=false);
 
    unsigned GetNearestElementIndex(const ChastePoint<SPACE_DIM>& rTestPoint);
 
    std::vector<unsigned> GetContainingElementIndices(const ChastePoint<SPACE_DIM>& rTestPoint);
 
    virtual void Clear();
 
    double GetAngleBetweenNodes(unsigned indexA, unsigned indexB);
 
    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 typename 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_