AbstractMesh.hpp

/*

Copyright (c) 2005-2016, University of Oxford.
All rights reserved.

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.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#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_*/