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 unsigned GetNearestNodeIndex(const ChastePoint<SPACE_DIM>& rTestPoint);
 
    virtual void Scale(const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0);
 
    virtual 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);
 
    virtual 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_*/