TetrahedralMesh.hpp

/*

Copyright (C) University of Oxford, 2005-2009

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 <iostream>
#include <vector>
#include <map>
#include <set>
#include <algorithm>

#include <boost/serialization/access.hpp>

//Jonathan Shewchuk's triangle
#define REAL double
#define VOID void
#include "triangle.h"
#undef REAL

#include "AbstractMesh.hpp"
#include "AbstractMeshReader.hpp"
#include "TrianglesMeshReader.hpp"
#include "Element.hpp"
#include "BoundaryElement.hpp"
#include "Node.hpp"
#include "NodeMap.hpp"
#include "Exception.hpp"
#include "OutputFileHandler.hpp"
#include "RandomNumberGenerator.hpp"
#include "PetscTools.hpp"

#include <boost/serialization/export.hpp>

//   DECLARATION

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class TetrahedralMesh : public AbstractMesh< 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)
    {
       // Don't do anything - this is just so subclasses can archive member variables.
    }        

//    std::vector<unsigned> mNodesPerProcessor;

    unsigned SolveNodeMapping(unsigned index) const;
    unsigned SolveElementMapping(unsigned index) const;
    unsigned SolveBoundaryElementMapping(unsigned index) const;    

protected:
    
    std::vector< c_vector<double, SPACE_DIM> > mElementWeightedDirections; 
    std::vector< c_matrix<double, SPACE_DIM, SPACE_DIM> > mElementJacobians;    
    std::vector< c_matrix<double, SPACE_DIM, SPACE_DIM> > mElementInverseJacobians;
    std::vector<double> mElementJacobianDeterminants;

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

    TetrahedralMesh();
    TetrahedralMesh(unsigned numElements);
    //TetrahedralMesh(std::vector<Node<SPACE_DIM> *> nodes);

    //virtual ~TetrahedralMesh();

    void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM,SPACE_DIM> &rMeshReader,
                                 bool cullInternalFaces=false);

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

    double CalculateVolume();
    double CalculateSurfaceArea();

    void Translate(c_vector<double, SPACE_DIM> displacement);
    void Translate(const double xMovement=0.0, const double yMovement=0.0, const double zMovement=0.0);
    void Scale(const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0);
    void Rotate(c_matrix<double , SPACE_DIM, SPACE_DIM> rotation_matrix);
    void Rotate(c_vector<double,3> axis, double angle);
    void RotateX(const double theta);
    void RotateY(const double theta);
    void RotateZ(const double theta);
    void Rotate(double theta)
    {
        RotateZ(theta);
    }

    void RefreshMesh(void);

    void PermuteNodes();

    void PermuteNodesWithMetisBinaries(unsigned numProcs);

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

    void ConstructLinearMesh(unsigned width);

    void ConstructRectangularMesh(unsigned width, unsigned height, bool stagger=true);

    void ConstructCuboid(unsigned width, unsigned height, unsigned depth, bool stagger=false);

    unsigned GetContainingElementIndex(ChastePoint<SPACE_DIM> testPoint, bool strict=false, std::set<unsigned> testElements=std::set<unsigned>());

    unsigned GetNearestElementIndex(ChastePoint<SPACE_DIM> testPoint);

    std::vector<unsigned> GetContainingElementIndices(ChastePoint<SPACE_DIM> testPoint);


//    /**
//     * Sets the ownership of each element according to which nodes are owned by the
//     * process.
//     * @param lo is the lowest node number owned by the process
//     * @param hi is one higher than the highest node number owned by the process
//     * ie. this process owns nodes [lo..hi)
//     * and element is "owned" if one or more of its nodes are owned
//     */
//    void SetElementOwnerships(unsigned lo, unsigned hi);

    virtual void Clear();

    std::set<unsigned> CalculateBoundaryOfFlaggedRegion();

    double GetDistanceBetweenNodes(unsigned indexA, unsigned indexB);

    virtual c_vector<double, SPACE_DIM> GetVectorFromAtoB(const c_vector<double, SPACE_DIM>& rLocationA, const c_vector<double, SPACE_DIM>& rLocationB);

    double GetAngleBetweenNodes(unsigned indexA, unsigned indexB);

    virtual double GetWidth(const unsigned& rDimension) const;

    c_vector<double,2> GetWidthExtremes(const unsigned& rDimension) const;

    void UnflagAllElements();


    void FlagElementsNotContainingNodes(std::set<unsigned> nodesList);

    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, SPACE_DIM>& rJacobian, double &rJacobianDeterminant, c_matrix<double, SPACE_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;


//    void GetJacobianForElement(unsigned elementIndex, c_matrix<double, SPACE_DIM, SPACE_DIM>& rJacobian) const;    
//    void GetInverseJacobianForElement(unsigned elementIndex, c_matrix<double, SPACE_DIM, SPACE_DIM>& rInverseJacobian) const;
//    void GetWeightedDirectionForElement(unsigned elementIndex, c_vector<double, SPACE_DIM>& rWeightedDirection) const;
//    double GetJacobianDeterminantForElement(unsigned elementIndex) const;    
//
//    void GetWeightedDirectionForBoundaryElement(unsigned elementIndex, c_vector<double, SPACE_DIM>& rWeightedDirection) const;       
//    double GetJacobianDeterminantForBoundaryElement(unsigned elementIndex) const;

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

        bool operator!=(const EdgeIterator& other);

        EdgeIterator& operator++();

        EdgeIterator(TetrahedralMesh& rMesh, unsigned elemIndex);

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

        TetrahedralMesh& mrMesh;

        unsigned mElemIndex;
        unsigned mNodeALocalIndex;
        unsigned mNodeBLocalIndex;
        unsigned mCellIndex;
        unsigned mNodeIndex;
        
    };

    EdgeIterator EdgesBegin();

    EdgeIterator EdgesEnd();
};



#endif //_TETRAHEDRALMESH_HPP_

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