ImmersedBoundaryMesh.hpp

/*
 
Copyright (c) 2005-2024, 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 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;
 
    double mCellRearrangementThreshold;
 
    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 SetCellRearrangementThreshold(double cellRearrangementThreshold);
 
    double GetCellRearrangementThreshold();
 
    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_*/