ImmersedBoundaryMesh.hpp

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*/
 
#ifndef IMMERSEDBOUNDARYMESH_HPP_
#define IMMERSEDBOUNDARYMESH_HPP_
 
// Forward declaration prevents circular include chain
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class ImmersedBoundaryMeshWriter;
 
#include <set>
#include <vector>
 
#include <boost/polygon/voronoi.hpp>
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/split_member.hpp>
#include <boost/serialization/vector.hpp>
 
#include "AbstractMesh.hpp"
#include "ArchiveLocationInfo.hpp"
#include "ChasteSerialization.hpp"
#include "FluidSource.hpp"
#include "ImmersedBoundaryArray.hpp"
#include "ImmersedBoundaryElement.hpp"
#include "ImmersedBoundaryMeshReader.hpp"
#include "ImmersedBoundaryMeshWriter.hpp"
#include "Node.hpp"
 
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class ImmersedBoundaryMesh : public AbstractMesh<ELEMENT_DIM, SPACE_DIM>
{
    friend class TestImmersedBoundaryMesh;
 
protected:
    unsigned mNumGridPtsX;
 
    unsigned mNumGridPtsY;
 
    double mCharacteristicNodeSpacing;
 
    double mElementDivisionSpacing;
 
    double mNeighbourDist;
 
    double mSummaryOfNodeLocations;
 
    static constexpr double mVoronoiHalo = 0.1;
 
    std::vector<unsigned> mDeletedNodeIndices;
 
    std::vector<unsigned> mDeletedElementIndices;
 
    multi_array<double, 3> m2dVelocityGrids;
 
    multi_array<double, 4> m3dVelocityGrids;
 
    std::vector<ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>*> mElements;
 
    std::vector<ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>*> mLaminas;
 
    std::vector<std::shared_ptr<FluidSource<SPACE_DIM>>> mElementFluidSources;
 
    std::vector<std::shared_ptr<FluidSource<SPACE_DIM>>> mBalancingFluidSources;
 
    boost::polygon::voronoi_diagram<double> mNodeLocationsVoronoiDiagram;
 
    std::vector<unsigned> mVoronoiCellIdsIndexedByNodeIndex;
 
    unsigned SolveNodeMapping(unsigned index) const;
 
    unsigned SolveElementMapping(unsigned index) const;
 
    unsigned SolveBoundaryElementMapping(unsigned index) const;
 
    void TagBoundaryElements();
 
    unsigned DivideElement(ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>* pElement,
                           unsigned nodeAIndex,
                           unsigned nodeBIndex,
                           c_vector<double, SPACE_DIM> centroid,
                           c_vector<double, SPACE_DIM> axisOfDivision);
 
    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);
 
        // Create a mesh writer pointing to the correct file and directory
        ImmersedBoundaryMeshWriter<ELEMENT_DIM, SPACE_DIM> mesh_writer(ArchiveLocationInfo::GetArchiveRelativePath(),
                                                                       ArchiveLocationInfo::GetMeshFilename(),
                                                                       false);
        mesh_writer.WriteFilesUsingMesh(*(const_cast<ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>*>(this)));
    }
 
    template <class Archive>
    void load(Archive& archive, const unsigned int version)
    {
        archive& boost::serialization::base_object<AbstractMesh<ELEMENT_DIM, SPACE_DIM> >(*this);
 
        ImmersedBoundaryMeshReader<ELEMENT_DIM, SPACE_DIM> mesh_reader(ArchiveLocationInfo::GetArchiveDirectory() + ArchiveLocationInfo::GetMeshFilename());
        this->ConstructFromMeshReader(mesh_reader);
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()
 
public:
    class ImmersedBoundaryElementIterator;
 
    class ImmersedBoundaryLaminaIterator;
 
    const std::vector<Node<SPACE_DIM>*>& rGetNodes() const;
 
    inline ImmersedBoundaryElementIterator GetElementIteratorBegin(bool skipDeletedElements = true);
 
    inline ImmersedBoundaryElementIterator GetElementIteratorEnd();
 
    inline ImmersedBoundaryLaminaIterator GetLaminaIteratorBegin(bool skipDeletedLaminas = true);
 
    inline ImmersedBoundaryLaminaIterator GetLaminaIteratorEnd();
 
    ImmersedBoundaryMesh(std::vector<Node<SPACE_DIM>*> nodes,
                         std::vector<ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>*> elements,
                         std::vector<ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>*> laminas = {},
                         unsigned numGridPtsX = 128u,
                         unsigned numGridPtsY = 128u);
 
    ImmersedBoundaryMesh();
 
    virtual ~ImmersedBoundaryMesh();
 
    virtual unsigned GetNumNodes() const;
 
    virtual unsigned GetNumElements() const;
 
    unsigned GetNumAllElements() const;
 
    unsigned GetNumLaminas() const;
 
    unsigned GetNumGridPtsX() const;
 
    unsigned GetNumGridPtsY() const;
 
    double GetCharacteristicNodeSpacing() const;
 
    double GetSpacingRatio() const;
 
    unsigned GetMaxNodeIndex() const;
 
    unsigned GetMaxElementIndex() const;
 
    unsigned GetMaxLaminaIndex() const;
 
    c_vector<double, SPACE_DIM> GetVectorFromAtoB(const c_vector<double, SPACE_DIM>& rLocation1, const c_vector<double, SPACE_DIM>& rLocation2);
 
    void SetNode(unsigned nodeIndex, ChastePoint<SPACE_DIM> point);
 
    void ConformToGeometry(c_vector<double, SPACE_DIM>& rLocation);
 
    const multi_array<double, 3>& rGet2dVelocityGrids() const;
 
    //const multi_array<double, 4>& rGet3dVelocityGrids() const;
 
    multi_array<double, 3>& rGetModifiable2dVelocityGrids();
 
    void SetNumGridPtsX(unsigned meshPointsX);
 
    void SetNumGridPtsY(unsigned meshPointsY);
 
    void SetNumGridPtsXAndY(unsigned numGridPts);
 
    void SetCharacteristicNodeSpacing(double nodeSpacing);
 
    unsigned AddNode(Node<SPACE_DIM>* pNewNode);
 
    std::vector<std::shared_ptr<FluidSource<SPACE_DIM>>>& rGetElementFluidSources();
 
    std::vector<std::shared_ptr<FluidSource<SPACE_DIM>>>& rGetBalancingFluidSources();
 
    std::set<unsigned> GetNeighbouringNodeIndices(unsigned nodeIndex);
 
    ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>* GetElement(unsigned index) const;
 
    ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>* GetLamina(unsigned index) const;
 
    virtual c_vector<double, SPACE_DIM> GetCentroidOfElement(unsigned index);
 
    void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader);
 
    virtual void Clear();
 
    virtual double GetVolumeOfElement(unsigned index);
 
    virtual double GetSurfaceAreaOfElement(unsigned index);
 
    double GetVoronoiSurfaceAreaOfElement(unsigned elemIdx);
 
    double GetAverageNodeSpacingOfElement(unsigned index, bool recalculate = true);
 
    double GetAverageNodeSpacingOfLamina(unsigned index, bool recalculate = true);
 
    virtual c_vector<double, 3> CalculateMomentsOfElement(unsigned index);
 
    double GetElongationShapeFactorOfElement(unsigned elementIndex);
 
    double GetTortuosityOfMesh();
 
    double GetSkewnessOfElementMassDistributionAboutAxis(unsigned elemIndex, c_vector<double, SPACE_DIM> axis);
 
    ChasteCuboid<SPACE_DIM> CalculateBoundingBoxOfElement(unsigned index);
 
    c_vector<double, SPACE_DIM> GetShortAxisOfElement(unsigned index);
 
    unsigned DivideElementAlongGivenAxis(ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>* pElement,
                                         c_vector<double, SPACE_DIM> axisOfDivision,
                                         bool placeOriginalElementBelow = false);
 
    unsigned DivideElementAlongShortAxis(ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>* pElement,
                                         bool placeOriginalElementBelow = false);
 
    double GetElementDivisionSpacing();
 
    void SetElementDivisionSpacing(double elementDivisionSpacing);
 
    double GetNeighbourDist() const;
 
    void SetNeighbourDist(double neighbourDist);
 
    void UpdateNodeLocationsVoronoiDiagramIfOutOfDate();
 
    void ReMesh(bool randomOrder=false);
 
    void ReMeshElement(ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>* pElement, bool randomOrder);
 
    void ReMeshLamina(ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>* pLamina, bool randomOrder);
 
    bool NodesInDifferentElementOrLamina(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB);
 
    std::set<unsigned> GetNeighbouringElementIndices(unsigned elemIdx);
 
    double CalculateLengthOfVoronoiEdge(const boost::polygon::voronoi_diagram<double>::edge_type& rEdge);
 
    std::array<unsigned, 13> GetPolygonDistribution();
 
    const boost::polygon::voronoi_diagram<double>& rGetNodeLocationsVoronoiDiagram(bool update=true);
 
    const std::vector<unsigned int>& GetVoronoiCellIdsIndexedByNodeIndex() const;
 
    int ScaleUpToVoronoiCoordinate(double location) const;
 
    double ScaleDistanceDownFromVoronoi(const double distance) const;
 
 
    class ImmersedBoundaryElementIterator
    {
    public:
        inline ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>& operator*();
 
        inline ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>* operator->();
 
        inline bool operator!=(const typename ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator& rOther);
 
        inline ImmersedBoundaryElementIterator& operator++();
 
        ImmersedBoundaryElementIterator(ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                                        typename std::vector<ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>*>::iterator elementIter,
                                        bool skipDeletedElements = true);
 
    private:
        ImmersedBoundaryMesh& mrMesh;
 
        typename std::vector<ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>*>::iterator mElementIter;
 
        bool mSkipDeletedElements;
 
        inline bool IsAtEnd();
 
        inline bool IsAllowedElement();
    };
 
    class ImmersedBoundaryLaminaIterator
    {
    public:
        inline ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>& operator*();
 
        inline ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>* operator->();
 
        inline bool operator!=(const typename ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator& rOther);
 
        inline ImmersedBoundaryLaminaIterator& operator++();
 
        ImmersedBoundaryLaminaIterator(ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                                       typename std::vector<ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>*>::iterator laminaIter,
                                       bool skipDeletedLaminas = true);
 
    private:
        ImmersedBoundaryMesh& mrMesh;
 
        typename std::vector<ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>*>::iterator mLaminaIter;
 
        bool mSkipDeletedLaminas;
 
        inline bool IsAtEnd();
 
        inline bool IsAllowedLamina();
    };
};
 
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(ImmersedBoundaryMesh)
 
 
// ImmersedBoundaryElementIterator class implementation - most methods are inlined    //
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::GetElementIteratorBegin(
    bool skipDeletedElements)
{
    return ImmersedBoundaryElementIterator(*this, mElements.begin(), skipDeletedElements);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::GetElementIteratorEnd()
{
    return ImmersedBoundaryElementIterator(*this, mElements.end());
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>& ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator::operator*()
{
    assert(!IsAtEnd());
    return **mElementIter;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>* ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator::operator->()
{
    assert(!IsAtEnd());
    return *mElementIter;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator::operator!=(const typename ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator& rOther)
{
    return mElementIter != rOther.mElementIter;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator& ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator::operator++()
{
    do
    {
        ++mElementIter;
    } while (!IsAtEnd() && !IsAllowedElement());
 
    return (*this);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator::ImmersedBoundaryElementIterator(
    ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
    typename std::vector<ImmersedBoundaryElement<ELEMENT_DIM, SPACE_DIM>*>::iterator elementIter,
    bool skipDeletedElements)
        : mrMesh(rMesh),
          mElementIter(elementIter),
          mSkipDeletedElements(skipDeletedElements)
{
    if (mrMesh.mElements.empty())
    {
        // 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 ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator::IsAtEnd()
{
    return mElementIter == mrMesh.mElements.end();
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryElementIterator::IsAllowedElement()
{
    return !(mSkipDeletedElements && (*this)->IsDeleted());
}
 
// ImmersedBoundaryLaminaIterator class implementation - most methods are inlined    //
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::GetLaminaIteratorBegin(
    bool skipDeletedLaminas)
{
    return ImmersedBoundaryLaminaIterator(*this, mLaminas.begin(), skipDeletedLaminas);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::GetLaminaIteratorEnd()
{
    return ImmersedBoundaryLaminaIterator(*this, mLaminas.end());
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>& ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator::operator*()
{
    assert(!IsAtEnd());
    return **mLaminaIter;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>* ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator::operator->()
{
    assert(!IsAtEnd());
    return *mLaminaIter;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator::operator!=(const typename ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator& rOther)
{
    return mLaminaIter != rOther.mLaminaIter;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator& ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator::operator++()
{
    do
    {
        ++mLaminaIter;
    } while (!IsAtEnd() && !IsAllowedLamina());
 
    return (*this);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator::ImmersedBoundaryLaminaIterator(
    ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
    typename std::vector<ImmersedBoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>*>::iterator laminaIter,
    bool skipDeletedLaminas)
        : mrMesh(rMesh),
          mLaminaIter(laminaIter),
          mSkipDeletedLaminas(skipDeletedLaminas)
{
    if (mrMesh.mLaminas.empty())
    {
        // Cope with empty meshes
        mLaminaIter = mrMesh.mLaminas.end();
    }
    else
    {
        // Make sure we start at an allowed lamina
        if (mLaminaIter == mrMesh.mLaminas.begin() && !IsAllowedLamina())
        {
            ++(*this);
        }
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator::IsAtEnd()
{
    return mLaminaIter == mrMesh.mLaminas.end();
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>::ImmersedBoundaryLaminaIterator::IsAllowedLamina()
{
    return !(mSkipDeletedLaminas && (*this)->IsDeleted());
}
 
#endif /*IMMERSEDBOUNDARYMESH_HPP_*/