AbstractTetrahedralMesh.hpp

/*

Copyright (c) 2005-2018, 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 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::shared_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 = nullptr;

        // Check whether we're migrating, or if we can use the original partition for the mesh
        DistributedVectorFactory* p_our_factory = nullptr;
        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 = nullptr;
        }

        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_*/