AbstractTetrahedralMesh.hpp

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#ifndef ABSTRACTTETRAHEDRALMESH_HPP_
#define ABSTRACTTETRAHEDRALMESH_HPP_

#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"
#include "ChasteSerializationVersion.hpp"
#include <boost/serialization/vector.hpp>
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/split_member.hpp>

#include <vector>
#include <string>
#include <cassert>
#include <boost/foreach.hpp>

#include "AbstractMesh.hpp"
#include "BoundaryElement.hpp"
#include "Element.hpp"
#include "GenericMeshReader.hpp"
#include "AbstractMeshReader.hpp"
#include "TrianglesMeshReader.hpp"
#include "TrianglesMeshWriter.hpp"
#include "ArchiveLocationInfo.hpp"
#include "FileFinder.hpp"


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractConductivityTensors;

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractTetrahedralMesh : public AbstractMesh<ELEMENT_DIM, SPACE_DIM>
{
    friend class AbstractConductivityTensors<ELEMENT_DIM, SPACE_DIM>; //A class which needs a global to local element mapping
    friend class CentroidWriter; //A test class which needs access to mElements in order to check that local/global indices match
protected:
    bool mMeshIsLinear;

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

    virtual unsigned SolveBoundaryElementMapping(unsigned index) const = 0;

    friend class boost::serialization::access;

    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        archive & boost::serialization::base_object<AbstractMesh<ELEMENT_DIM,SPACE_DIM> >(*this);
        archive & mMeshIsLinear;
        // Create a mesh writer pointing to the correct file and directory
        TrianglesMeshWriter<ELEMENT_DIM,SPACE_DIM> mesh_writer(ArchiveLocationInfo::GetArchiveRelativePath(),
                                                               ArchiveLocationInfo::GetMeshFilename(),
                                                               false);
        // Binary meshes have similar content to the original Triangle/Tetgen format, but take up less space on disk
        mesh_writer.SetWriteFilesAsBinary();

        // Archive the mesh permutation, so we can just copy the original mesh files whenever possible
        bool permutation_available = (this->rGetNodePermutation().size() != 0);
        archive & permutation_available;

        if (permutation_available)
        {
            const std::vector<unsigned>& rPermutation = this->rGetNodePermutation();
            archive & rPermutation;
        }

        if (!this->IsMeshOnDisk() || this->mMeshChangesDuringSimulation)
        {
            mesh_writer.WriteFilesUsingMesh(*(const_cast<AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>*>(this)));
        }
        else
        {
            unsigned order_of_element = (mMeshIsLinear?1:2);
            unsigned& order_of_boundary_element = order_of_element;

            // Mesh in disc, copy it to the archiving folder
            std::string original_file=this->GetMeshFileBaseName();
            std::auto_ptr<AbstractMeshReader<ELEMENT_DIM, SPACE_DIM> > p_original_mesh_reader
                = GenericMeshReader<ELEMENT_DIM, SPACE_DIM>(original_file, order_of_element, order_of_boundary_element);

            if (p_original_mesh_reader->IsFileFormatBinary())
            {
                // Mesh is in binary format, we can just copy the files across ignoring the mesh reader
                if (PetscTools::AmMaster())
                {
                    FileFinder mesh_base(this->GetMeshFileBaseName());
                    FileFinder mesh_folder = mesh_base.GetParent();
                    std::string mesh_leaf_name = mesh_base.GetLeafNameNoExtension();
                    std::vector<FileFinder> mesh_files = mesh_folder.FindMatches(mesh_leaf_name + ".*");
                    FileFinder dest_dir(ArchiveLocationInfo::GetArchiveDirectory());
                    BOOST_FOREACH(const FileFinder& r_mesh_file, mesh_files)
                    {
                        FileFinder dest_file(ArchiveLocationInfo::GetMeshFilename() + r_mesh_file.GetExtension(),
                                             dest_dir);
                        ABORT_IF_THROWS(r_mesh_file.CopyTo(dest_file));
                    }
                }
            }
            else
            {
                // Mesh in text format, use the mesh writer to "binarise" it
                mesh_writer.WriteFilesUsingMeshReaderAndMesh(*p_original_mesh_reader,
                                                             *(const_cast<AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>*>(this)));
            }
        }

        // Make sure that the files are written before slave processes proceed
        PetscTools::Barrier("AbstractTetrahedralMesh::save");
    }

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractMesh<ELEMENT_DIM,SPACE_DIM> >(*this);
        archive & mMeshIsLinear;

        bool permutation_available=false;
        std::vector<unsigned> permutation;

        if (version > 0)
        {
            archive & permutation_available;

            if (permutation_available)
            {
                archive & permutation;
            }
        }

        // Store the DistributedVectorFactory loaded from the archive
        DistributedVectorFactory* p_factory = this->mpDistributedVectorFactory;
        this->mpDistributedVectorFactory = NULL;

        // Check whether we're migrating, or if we can use the original partition for the mesh
        DistributedVectorFactory* p_our_factory = NULL;
        if (p_factory)
        {
            p_our_factory = p_factory->GetOriginalFactory();
        }
        if (p_our_factory && p_our_factory->GetNumProcs() == p_factory->GetNumProcs())
        {
            // Specify the node distribution
            this->SetDistributedVectorFactory(p_our_factory);
        }
        else
        {
            // Migrating; let the mesh re-partition if it likes
            p_our_factory = NULL;
        }

        if (mMeshIsLinear)
        {
            // I am a linear mesh
            TrianglesMeshReader<ELEMENT_DIM,SPACE_DIM> mesh_reader(ArchiveLocationInfo::GetArchiveDirectory() + ArchiveLocationInfo::GetMeshFilename());

            if (permutation_available)
            {
                mesh_reader.SetNodePermutation(permutation);
            }

            this->ConstructFromMeshReader(mesh_reader);
        }
        else
        {
            // I am a quadratic mesh and need quadratic information from the reader
            TrianglesMeshReader<ELEMENT_DIM,SPACE_DIM> mesh_reader(ArchiveLocationInfo::GetArchiveDirectory() + ArchiveLocationInfo::GetMeshFilename(), 2, 2);
            this->ConstructFromMeshReader(mesh_reader);
        }

        // Make sure we're using the correct vector factory
        if (p_factory)
        {
            if (!this->mpDistributedVectorFactory)
            {
                // If we're not using a DistributedTetrahedralMesh, ConstructFromMeshReader won't set
                // this->mpDistributedVectorFactory.
                this->mpDistributedVectorFactory = p_factory;
            }
            else
            {
                // We need to update p_factory to match this->mpDistributedVectorFactory, and then use
                // p_factory, since the rest of the code (e.g. AbstractCardiacPde) will be using p_factory.
                p_factory->SetFromFactory(this->mpDistributedVectorFactory);
                if (p_our_factory != this->mpDistributedVectorFactory)
                {
                    // Avoid memory leak
                    delete this->mpDistributedVectorFactory;
                }
                this->mpDistributedVectorFactory = p_factory;
            }
        }
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()

protected:  // Give access of these variables to subclasses

    std::vector<Element<ELEMENT_DIM, SPACE_DIM> *> mElements;

    std::vector<BoundaryElement<ELEMENT_DIM-1, SPACE_DIM> *> mBoundaryElements;

    void SetElementOwnerships();

public:

    //                            Iterators                             //

    typedef typename std::vector<BoundaryElement<ELEMENT_DIM-1, SPACE_DIM> *>::const_iterator BoundaryElementIterator;

    class ElementIterator;

    inline ElementIterator GetElementIteratorBegin(bool skipDeletedElements=true);

    inline ElementIterator GetElementIteratorEnd();

    //                             Methods                              //

    AbstractTetrahedralMesh();

    virtual ~AbstractTetrahedralMesh();


    virtual unsigned GetNumElements() const;

    virtual unsigned GetNumLocalElements() const;

    virtual unsigned GetNumBoundaryElements() const;

    virtual unsigned GetNumLocalBoundaryElements() const;

    unsigned GetNumAllElements() const;

    unsigned GetNumAllBoundaryElements() const;

    virtual unsigned GetNumCableElements() const;

    virtual unsigned GetNumVertices() const;

    virtual unsigned GetMaximumNodeIndex();

    Element<ELEMENT_DIM, SPACE_DIM>* GetElement(unsigned index) const;

    BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>* GetBoundaryElement(unsigned index) const;


    virtual void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader)=0;

    void ConstructFromMesh(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rOtherMesh);


    BoundaryElementIterator GetBoundaryElementIteratorBegin() const;

    BoundaryElementIterator GetBoundaryElementIteratorEnd() const;

    virtual void GetInverseJacobianForElement(unsigned elementIndex, c_matrix<double, SPACE_DIM, ELEMENT_DIM>& rJacobian,
                                              double& rJacobianDeterminant,
                                              c_matrix<double, ELEMENT_DIM, SPACE_DIM>& rInverseJacobian) const;

    virtual void GetWeightedDirectionForBoundaryElement(unsigned elementIndex,
                                                        c_vector<double, SPACE_DIM>& rWeightedDirection,
                                                        double& rJacobianDeterminant) const;

    void CheckOutwardNormals();

    virtual void ConstructLinearMesh(unsigned width);



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



    virtual void ConstructCuboid(unsigned width, unsigned height, unsigned depth);



    void ConstructRegularSlabMesh(double spaceStep, double width, double height=0, double depth=0);

    void ConstructRegularSlabMeshWithDimensionSplit(unsigned dimension, double spaceStep, double width, double height=0, double depth=0);


    virtual bool CalculateDesignatedOwnershipOfBoundaryElement( unsigned faceIndex );

    virtual bool CalculateDesignatedOwnershipOfElement( unsigned elementIndex );

    unsigned CalculateMaximumNodeConnectivityPerProcess() const;

    virtual void GetHaloNodeIndices(std::vector<unsigned>& rHaloIndices) const;

     void CalculateNodeExchange( std::vector<std::vector<unsigned> >& rNodesToSendPerProcess,
                                 std::vector<std::vector<unsigned> >& rNodesToReceivePerProcess);


     virtual c_vector<double, 2> CalculateMinMaxEdgeLengths();

     unsigned GetContainingElementIndex(const ChastePoint<SPACE_DIM>& rTestPoint,
                                        bool strict=false,
                                        std::set<unsigned> testElements=std::set<unsigned>(),
                                        bool onlyTryWithTestElements = false);

     unsigned GetNearestElementIndexFromTestElements(const ChastePoint<SPACE_DIM>& rTestPoint,
                                                     std::set<unsigned> testElements);



    //                         Nested classes                           //


    class ElementIterator
    {
    public:
        inline Element<ELEMENT_DIM, SPACE_DIM>& operator*();

        inline Element<ELEMENT_DIM, SPACE_DIM>* operator->();

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

        inline ElementIterator& operator++();

        ElementIterator(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                        typename std::vector<Element<ELEMENT_DIM, SPACE_DIM> *>::iterator elementIter,
                        bool skipDeletedElements=true);

    private:
        AbstractTetrahedralMesh& mrMesh;

        typename std::vector<Element<ELEMENT_DIM, SPACE_DIM> *>::iterator mElementIter;

        bool mSkipDeletedElements;

        inline bool IsAtEnd();

        inline bool IsAllowedElement();
    };

};

TEMPLATED_CLASS_IS_ABSTRACT_2_UNSIGNED(AbstractTetrahedralMesh)

namespace boost {
namespace serialization {
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
struct version<AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> >
{
    CHASTE_VERSION_CONTENT(1);
};
} // namespace serialization
} // namespace boost


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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetElementIteratorBegin(
        bool skipDeletedElements)
{
    return ElementIterator(*this, mElements.begin(), skipDeletedElements);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetElementIteratorEnd()
{
    return ElementIterator(*this, mElements.end());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Element<ELEMENT_DIM, SPACE_DIM>& AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::operator*()
{
    assert(!IsAtEnd());
    return **mElementIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Element<ELEMENT_DIM, SPACE_DIM>* AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::operator->()
{
    assert(!IsAtEnd());
    return *mElementIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::operator!=(const typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator& rOther)
{
    return mElementIter != rOther.mElementIter;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator& AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::operator++()
{
    do
    {
        ++mElementIter;
    }
    while (!IsAtEnd() && !IsAllowedElement());

    return (*this);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::ElementIterator(
        AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
        typename std::vector<Element<ELEMENT_DIM, SPACE_DIM> *>::iterator elementIter,
        bool skipDeletedElements)
    : mrMesh(rMesh),
      mElementIter(elementIter),
      mSkipDeletedElements(skipDeletedElements)
{
    if (mrMesh.mElements.size() == 0)
    {
        // Cope with empty meshes
        mElementIter = mrMesh.mElements.end();
    }
    else
    {
        // Make sure we start at an allowed element
        if (mElementIter == mrMesh.mElements.begin() && !IsAllowedElement())
        {
            ++(*this);
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::IsAtEnd()
{
    return mElementIter == mrMesh.mElements.end();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator::IsAllowedElement()
{
    return !(mSkipDeletedElements && (*this)->IsDeleted());
}



#endif /*ABSTRACTTETRAHEDRALMESH_HPP_*/