TetrahedralMesh.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#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)
    template <unsigned A_DIMENSION> friend class NodesOnlyMesh; //NodesOnlyMesh is able to grab the node information in order to copy
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_

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