AbstractMesh.hpp

/*

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*/

#ifndef ABSTRACTMESH_HPP_
#define ABSTRACTMESH_HPP_

#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"

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

#include <vector>
#include <string>
#include <cassert>

#include "Node.hpp"
#include "DistributedVectorFactory.hpp"
#include "ProcessSpecificArchive.hpp"
#include "ChasteCuboid.hpp"

#include <boost/utility.hpp>

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractMesh : private boost::noncopyable
{
    friend class TestDistributedTetrahedralMesh;
    template <unsigned A_DIMENSION> friend class NodesOnlyMesh; //NodesOnlyMesh is able to grab the node information in order to copy
    template <unsigned A_DIMENSION> friend class QuadraticMeshHelper;

private:
    virtual unsigned SolveNodeMapping(unsigned index) const = 0;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & mMeshChangesDuringSimulation;
        (*ProcessSpecificArchive<Archive>::Get()) & mpDistributedVectorFactory;
    }

protected:  // Give access of these variables to subclasses

    std::vector<Node<SPACE_DIM> *> mNodes;

    std::vector<Node<SPACE_DIM> *> mBoundaryNodes;

    DistributedVectorFactory* mpDistributedVectorFactory;

    std::vector<unsigned> mNodePermutation;

    std::string mMeshFileBaseName;

    bool mMeshChangesDuringSimulation;

    virtual void SetElementOwnerships();

    ChasteCuboid<SPACE_DIM> CalculateBoundingBox(const std::vector<Node<SPACE_DIM>* >& rNodes) const;

public:

    //                            Iterators                             //

    typedef typename std::vector<Node<SPACE_DIM> *>::const_iterator BoundaryNodeIterator;

    class NodeIterator;

    inline NodeIterator GetNodeIteratorBegin(bool skipDeletedNodes=true);

    inline NodeIterator GetNodeIteratorEnd();

    //                             Methods                              //

    AbstractMesh();

    virtual ~AbstractMesh();

    virtual unsigned GetNumNodes() const;

    unsigned GetNumBoundaryNodes() const;

    virtual unsigned GetNumAllNodes() const;

    unsigned GetNumNodeAttributes() const;

    Node<SPACE_DIM>* GetNode(unsigned index) const;

    virtual Node<SPACE_DIM>* GetNodeOrHaloNode(unsigned index) const;

    Node<SPACE_DIM>* GetNodeFromPrePermutationIndex(unsigned index) const;

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

    virtual DistributedVectorFactory * GetDistributedVectorFactory();

    virtual void SetDistributedVectorFactory(DistributedVectorFactory* pFactory);

    virtual void PermuteNodes();

    BoundaryNodeIterator GetBoundaryNodeIteratorBegin() const;

    BoundaryNodeIterator GetBoundaryNodeIteratorEnd() const;

    std::string GetMeshFileBaseName() const;

    bool IsMeshOnDisk() const;

    const std::vector<unsigned>& rGetNodePermutation() const;

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

    double GetDistanceBetweenNodes(unsigned indexA, unsigned indexB);

    virtual double GetWidth(const unsigned& rDimension) const;

    virtual ChasteCuboid<SPACE_DIM> CalculateBoundingBox() const;

    virtual void Scale(const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0);

     void Translate(const c_vector<double, SPACE_DIM>& rDisplacement);

     void Translate(const double xMovement=0.0, const double yMovement=0.0, const double zMovement=0.0);

     void Rotate(c_matrix<double , SPACE_DIM, SPACE_DIM> rotationMatrix);

     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);

    virtual void RefreshMesh();

    bool IsMeshChanging() const;

    unsigned CalculateMaximumContainingElementsPerProcess() const;

    void SetMeshHasChangedSinceLoading();

    //                         Nested classes                           //

    class NodeIterator
    {
    public:
        inline Node<SPACE_DIM>& operator*();

        inline Node<SPACE_DIM>* operator->();

        inline bool operator!=(const typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator& rOther);

        inline NodeIterator& operator++();

        NodeIterator(AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                     typename std::vector<Node<SPACE_DIM> *>::iterator nodeIter,
                     bool skipDeletedNodes=true);
    private:
        AbstractMesh& mrMesh;

        typename std::vector<Node<SPACE_DIM> *>::iterator mNodeIter;

        bool mSkipDeletedNodes;

        inline bool IsAtEnd();

        inline bool IsAllowedNode();
    };


};

TEMPLATED_CLASS_IS_ABSTRACT_2_UNSIGNED(AbstractMesh)


//      NodeIterator class implementation - most methods are inlined        //

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNodeIteratorBegin(
        bool skipDeletedNodes)
{
    return NodeIterator(*this, mNodes.begin(), skipDeletedNodes);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNodeIteratorEnd()
{
    return NodeIterator(*this, mNodes.end());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Node<SPACE_DIM>& AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator::operator*()
{
    assert(!IsAtEnd());
    return **mNodeIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Node<SPACE_DIM>* AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator::operator->()
{
    assert(!IsAtEnd());
    return *mNodeIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator::operator!=(const typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator& rOther)
{
    return mNodeIter != rOther.mNodeIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator& AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator::operator++()
{
    do
    {
        ++mNodeIter;
    }
    while (!IsAtEnd() && !IsAllowedNode());

    return (*this);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator::NodeIterator(
        AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
        typename std::vector<Node<SPACE_DIM> *>::iterator nodeIter,
        bool skipDeletedNodes)
    : mrMesh(rMesh),
      mNodeIter(nodeIter),
      mSkipDeletedNodes(skipDeletedNodes)
{
    if (mrMesh.mNodes.size() == 0)
    {
        // Cope with empty meshes
        mNodeIter = mrMesh.mNodes.end();
    }
    else
    {
        // Make sure we start at an allowed node
        if (mNodeIter == mrMesh.mNodes.begin() && !IsAllowedNode())
        {
            ++(*this);
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator::IsAtEnd()
{
    return mNodeIter == mrMesh.mNodes.end();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator::IsAllowedNode()
{
    return !(mSkipDeletedNodes && (*this)->IsDeleted());
}


#endif /*ABSTRACTMESH_HPP_*/