AbstractMesh.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 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 : boost::noncopyable
{
    template <unsigned A_DIMENSION> friend class NodesOnlyMesh; //NodesOnlyMesh is able to grab the node information in order to copy
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> mNodesPermutation;

    std::string mMeshFileBaseName;

    bool mMeshChangesDuringSimulation;

    virtual void SetElementOwnerships();
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;

    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 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 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_*/