#include <MeshGraphIO.h>

Inheritance diagram for Nektar::SpatialDomains::MeshGraphIO:

Public Member Functions
virtual	~MeshGraphIO ()=default

void	SetMeshGraph (MeshGraphSharedPtr &meshGraph)

void	WriteGeometry (const std::string &outfilename, bool defaultExp=false, const LibUtilities::FieldMetaDataMap &metadata=LibUtilities::NullFieldMetaDataMap)

void	ReadGeometry (bool fillGraph)

void	PartitionMesh (LibUtilities::SessionReaderSharedPtr session)

std::map< int, MeshEntity >	CreateMeshEntities ()
	Create mesh entities for this graph.

CompositeDescriptor	CreateCompositeDescriptor ()

Static Public Member Functions
static MeshGraphSharedPtr	Read (const LibUtilities::SessionReaderSharedPtr pSession, LibUtilities::DomainRangeShPtr rng=LibUtilities::NullDomainRangeShPtr, bool fillGraph=true, SpatialDomains::MeshGraphSharedPtr partitionedGraph=nullptr)

Protected Member Functions
std::string	GetCompositeString (CompositeSharedPtr comp)
	Returns a string representation of a composite.

	MeshGraphIO ()=default

virtual void	v_WriteGeometry (const std::string &outfilename, bool defaultExp=false, const LibUtilities::FieldMetaDataMap &metadata=LibUtilities::NullFieldMetaDataMap)=0

virtual void	v_ReadGeometry (bool fillGraph)=0

virtual void	v_PartitionMesh (LibUtilities::SessionReaderSharedPtr session)=0

Protected Attributes
LibUtilities::SessionReaderSharedPtr	m_session

MeshGraphSharedPtr	m_meshGraph

int	m_partition

bool	m_meshPartitioned = false

CompositeOrdering	m_compOrder

BndRegionOrdering	m_bndRegOrder

Detailed Description

Definition at line 48 of file MeshGraphIO.h.

Constructor & Destructor Documentation

◆ ~MeshGraphIO()

virtual Nektar::SpatialDomains::MeshGraphIO::~MeshGraphIO ( )

virtualdefault

◆ MeshGraphIO()

Nektar::SpatialDomains::MeshGraphIO::MeshGraphIO ( )

protecteddefault

Member Function Documentation

◆ CreateCompositeDescriptor()

CompositeDescriptor Nektar::SpatialDomains::MeshGraphIO::CreateCompositeDescriptor ( )

Definition at line 248 of file MeshGraphIO.cpp.

{
    auto meshComposites = &m_meshGraph->GetComposites();
    CompositeDescriptor ret;
 
    for (auto &comp : *meshComposites)
    {
        std::pair<LibUtilities::ShapeType, std::vector<int>> tmp;
        tmp.first = comp.second->m_geomVec[0]->GetShapeType();
 
        tmp.second.resize(comp.second->m_geomVec.size());
        for (size_t i = 0; i < tmp.second.size(); ++i)
        {
            tmp.second[i] = comp.second->m_geomVec[i]->GetGlobalID();
        }
 
        ret[comp.first] = tmp;
    }
 
    return ret;
}

References m_meshGraph.

Referenced by Nektar::SpatialDomains::MeshGraphIOHDF5::v_PartitionMesh(), and Nektar::SpatialDomains::MeshGraphIOXml::v_PartitionMesh().

◆ CreateMeshEntities()

std::map< int, MeshEntity > Nektar::SpatialDomains::MeshGraphIO::CreateMeshEntities ( )

Create mesh entities for this graph.

This function will create a map of all mesh entities of the current graph, which can then be used within the mesh partitioner to construct an appropriate partitioning.

Definition at line 130 of file MeshGraphIO.cpp.

{
    std::map<int, MeshEntity> elements;
    switch (m_meshGraph->GetMeshDimension())
    {
        case 1:
        {
            for (auto [id, geom] : m_meshGraph->GetGeomMap<SegGeom>())
            {
                MeshEntity e;
                e.id = e.origId = id;
                e.list.push_back(geom->GetVertex(0)->GetGlobalID());
                e.list.push_back(geom->GetVertex(1)->GetGlobalID());
                e.ghost        = false;
                elements[e.id] = e;
            }
        }
        break;
        case 2:
        {
            for (auto [id, geom] : m_meshGraph->GetGeomMap<TriGeom>())
            {
                if (m_meshGraph->CheckRange(*geom))
                {
                    MeshEntity e;
                    e.id = e.origId = id;
                    e.list.push_back(geom->GetEdge(0)->GetGlobalID());
                    e.list.push_back(geom->GetEdge(1)->GetGlobalID());
                    e.list.push_back(geom->GetEdge(2)->GetGlobalID());
                    e.ghost        = false;
                    elements[e.id] = e;
                }
            }
            for (auto [id, geom] : m_meshGraph->GetGeomMap<QuadGeom>())
            {
                if (m_meshGraph->CheckRange(*geom))
                {
                    MeshEntity e;
                    e.id = e.origId = id;
                    e.list.push_back(geom->GetEdge(0)->GetGlobalID());
                    e.list.push_back(geom->GetEdge(1)->GetGlobalID());
                    e.list.push_back(geom->GetEdge(2)->GetGlobalID());
                    e.list.push_back(geom->GetEdge(3)->GetGlobalID());
                    e.ghost        = false;
                    elements[e.id] = e;
                }
            }
        }
        break;
        case 3:
        {
            for (auto [id, geom] : m_meshGraph->GetGeomMap<TetGeom>())
            {
                if (m_meshGraph->CheckRange(*geom))
                {
                    MeshEntity e;
                    e.id = e.origId = id;
                    e.list.push_back(geom->GetFace(0)->GetGlobalID());
                    e.list.push_back(geom->GetFace(1)->GetGlobalID());
                    e.list.push_back(geom->GetFace(2)->GetGlobalID());
                    e.list.push_back(geom->GetFace(3)->GetGlobalID());
                    e.ghost        = false;
                    elements[e.id] = e;
                }
            }
            for (auto [id, geom] : m_meshGraph->GetGeomMap<PyrGeom>())
            {
                if (m_meshGraph->CheckRange(*geom))
                {
                    MeshEntity e;
                    e.id = e.origId = id;
                    e.list.push_back(geom->GetFace(0)->GetGlobalID());
                    e.list.push_back(geom->GetFace(1)->GetGlobalID());
                    e.list.push_back(geom->GetFace(2)->GetGlobalID());
                    e.list.push_back(geom->GetFace(3)->GetGlobalID());
                    e.list.push_back(geom->GetFace(4)->GetGlobalID());
                    e.ghost        = false;
                    elements[e.id] = e;
                }
            }
            for (auto [id, geom] : m_meshGraph->GetGeomMap<PrismGeom>())
            {
                if (m_meshGraph->CheckRange(*geom))
                {
                    MeshEntity e;
                    e.id = e.origId = id;
                    e.list.push_back(geom->GetFace(0)->GetGlobalID());
                    e.list.push_back(geom->GetFace(1)->GetGlobalID());
                    e.list.push_back(geom->GetFace(2)->GetGlobalID());
                    e.list.push_back(geom->GetFace(3)->GetGlobalID());
                    e.list.push_back(geom->GetFace(4)->GetGlobalID());
                    e.ghost        = false;
                    elements[e.id] = e;
                }
            }
            for (auto [id, geom] : m_meshGraph->GetGeomMap<HexGeom>())
            {
                if (m_meshGraph->CheckRange(*geom))
                {
                    MeshEntity e;
                    e.id = e.origId = id;
                    e.list.push_back(geom->GetFace(0)->GetGlobalID());
                    e.list.push_back(geom->GetFace(1)->GetGlobalID());
                    e.list.push_back(geom->GetFace(2)->GetGlobalID());
                    e.list.push_back(geom->GetFace(3)->GetGlobalID());
                    e.list.push_back(geom->GetFace(4)->GetGlobalID());
                    e.list.push_back(geom->GetFace(5)->GetGlobalID());
                    e.ghost        = false;
                    elements[e.id] = e;
                }
            }
        }
        break;
    }
 
    return elements;
}

References Nektar::SpatialDomains::MeshEntity::ghost, Nektar::SpatialDomains::MeshEntity::id, Nektar::SpatialDomains::MeshEntity::list, m_meshGraph, and Nektar::SpatialDomains::MeshEntity::origId.

Referenced by Nektar::SpatialDomains::MeshGraphIOXml::v_PartitionMesh().

◆ GetCompositeString()

std::string Nektar::SpatialDomains::MeshGraphIO::GetCompositeString ( CompositeSharedPtr comp )

protected

Returns a string representation of a composite.

Definition at line 273 of file MeshGraphIO.cpp.

{
    if (comp->m_geomVec.size() == 0)
    {
        return "";
    }
 
    // Create a map that gets around the issue of mapping faces -> F and edges
    // -> E inside the tag.
    std::map<LibUtilities::ShapeType, std::pair<std::string, std::string>>
        compMap;
    compMap[LibUtilities::ePoint]         = std::make_pair("V", "V");
    compMap[LibUtilities::eSegment]       = std::make_pair("S", "E");
    compMap[LibUtilities::eQuadrilateral] = std::make_pair("Q", "F");
    compMap[LibUtilities::eTriangle]      = std::make_pair("T", "F");
    compMap[LibUtilities::eTetrahedron]   = std::make_pair("A", "A");
    compMap[LibUtilities::ePyramid]       = std::make_pair("P", "P");
    compMap[LibUtilities::ePrism]         = std::make_pair("R", "R");
    compMap[LibUtilities::eHexahedron]    = std::make_pair("H", "H");
 
    std::stringstream s;
 
    Geometry *firstGeom = comp->m_geomVec[0];
    int shapeDim        = firstGeom->GetShapeDim();
    std::string tag     = (shapeDim < m_meshGraph->GetMeshDimension())
                              ? compMap[firstGeom->GetShapeType()].second
                              : compMap[firstGeom->GetShapeType()].first;
 
    std::vector<unsigned int> idxList;
    std::transform(comp->m_geomVec.begin(), comp->m_geomVec.end(),
                   std::back_inserter(idxList),
                   [](Geometry *geom) { return geom->GetGlobalID(); });
 
    s << " " << tag << "[" << ParseUtils::GenerateSeqString(idxList) << "] ";
    return s.str();
}

References Nektar::LibUtilities::eHexahedron, Nektar::LibUtilities::ePoint, Nektar::LibUtilities::ePrism, Nektar::LibUtilities::ePyramid, Nektar::LibUtilities::eQuadrilateral, Nektar::LibUtilities::eSegment, Nektar::LibUtilities::eTetrahedron, Nektar::LibUtilities::eTriangle, Nektar::ParseUtils::GenerateSeqString(), Nektar::SpatialDomains::Geometry::GetShapeDim(), Nektar::SpatialDomains::Geometry::GetShapeType(), and m_meshGraph.

Referenced by Nektar::SpatialDomains::MeshGraphIOHDF5::WriteComposites(), and Nektar::SpatialDomains::MeshGraphIOXml::WriteComposites().

◆ PartitionMesh()

void Nektar::SpatialDomains::MeshGraphIO::PartitionMesh ( LibUtilities::SessionReaderSharedPtr session )

inline

Definition at line 78 of file MeshGraphIO.h.

    {
        v_PartitionMesh(session);
    }

References v_PartitionMesh().

◆ Read()

MeshGraphSharedPtr Nektar::SpatialDomains::MeshGraphIO::Read	(	const LibUtilities::SessionReaderSharedPtr	pSession,
		LibUtilities::DomainRangeShPtr	rng = `LibUtilities::NullDomainRangeShPtr`,
		bool	fillGraph = `true`,
		SpatialDomains::MeshGraphSharedPtr	partitionedGraph = `nullptr`
	)

static

Definition at line 51 of file MeshGraphIO.cpp.

{
    LibUtilities::CommSharedPtr comm = session->GetComm();
    ASSERTL0(comm.get(), "Communication not initialised.");
 
    // Populate SessionReader. This should be done only on the root process so
    // that we can partition appropriately without all processes having to read
    // in the input file.
    const bool isRoot = comm->TreatAsRankZero();
    std::string geomType;
 
    if (isRoot)
    {
        // Parse the XML document.
        session->InitSession();
 
        // Get geometry type, i.e. XML (compressed/uncompressed) or HDF5.
        geomType = session->GetGeometryType();
 
        // Convert to a vector of chars so that we can broadcast.
        std::vector<char> v(geomType.c_str(),
                            geomType.c_str() + geomType.length());
 
        size_t length = v.size();
        comm->Bcast(length, 0);
        comm->Bcast(v, 0);
    }
    else
    {
        size_t length;
        comm->Bcast(length, 0);
 
        std::vector<char> v(length);
        comm->Bcast(v, 0);
 
        geomType = std::string(v.begin(), v.end());
    }
 
    // Every process then creates a mesh. Partitioning logic takes place inside
    // the PartitionMesh function so that we can support different options for
    // XML and HDF5.
    MeshGraphIOSharedPtr meshIO =
        GetMeshGraphIOFactory().CreateInstance(geomType);
    meshIO->m_meshGraph =
        MemoryManager<SpatialDomains::MeshGraph>::AllocateSharedPtr();
    meshIO->m_meshGraph->SetSession(session);
 
    // For Parallel-in-Time
    //    In contrast to XML, a pre-partitioned mesh directory (_xml) is not
    //    produced when partitionning the mesh for the fine solver when using
    //    HDF5. In order to guarantee the same partition on all time level,
    //    the fine mesh partition has to be copied explicitly.
    if (partitionedGraph && geomType == "HDF5")
    {
        meshIO->m_meshGraph->SetPartition(partitionedGraph);
        meshIO->m_meshPartitioned = true;
    }
 
    // set up domain range info before partitioning
    meshIO->m_meshGraph->SetDomainRange(rng);
 
    meshIO->PartitionMesh(session);
 
    // Finally, read the geometry information.
    meshIO->ReadGeometry(fillGraph);
 
    return meshIO->m_meshGraph;
}

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::LibUtilities::NekFactory< tKey, tBase, tParam >::CreateInstance(), and Nektar::SpatialDomains::GetMeshGraphIOFactory().

Referenced by Diffusion::Diffusion(), main(), MeshGraphIO_Read(), Nektar::SolverUtils::DriverParallelInTime::SetParallelInTimeEquationSystem(), Nektar::VarcoeffHashingTest::setupContFieldSolve(), Nektar::SolverUtils::CouplingCwipi::SetupReceive(), Nektar::SolverUtils::Driver::v_InitObject(), Nektar::FieldUtils::InputXml::v_Process(), Nektar::FieldUtils::ProcessDisplacement::v_Process(), Nektar::FieldUtils::ProcessInterpField::v_Process(), Nektar::FieldUtils::ProcessInterpPoints::v_Process(), Nektar::SolverUtils::FilterModalEnergy::v_Update(), and Nektar::VortexWaveInteraction::VortexWaveInteraction().

◆ ReadGeometry()

void Nektar::SpatialDomains::MeshGraphIO::ReadGeometry ( bool fillGraph )

inline

Definition at line 73 of file MeshGraphIO.h.

    {
        v_ReadGeometry(fillGraph);
    }

References v_ReadGeometry().

Referenced by Nektar::SpatialDomains::MeshGraphIOXml::v_PartitionMesh().

◆ SetMeshGraph()

void Nektar::SpatialDomains::MeshGraphIO::SetMeshGraph ( MeshGraphSharedPtr & meshGraph )

inline

Definition at line 59 of file MeshGraphIO.h.

    {
        m_meshGraph = meshGraph;
    }

References m_meshGraph.

Referenced by export_MeshGraphIO().

◆ v_PartitionMesh()

virtual void Nektar::SpatialDomains::MeshGraphIO::v_PartitionMesh ( LibUtilities::SessionReaderSharedPtr session )

protectedpure virtual

Implemented in Nektar::SpatialDomains::MeshGraphIOHDF5, and Nektar::SpatialDomains::MeshGraphIOXml.

Referenced by PartitionMesh().

◆ v_ReadGeometry()

virtual void Nektar::SpatialDomains::MeshGraphIO::v_ReadGeometry ( bool fillGraph )

protectedpure virtual

Implemented in Nektar::SpatialDomains::MeshGraphIOHDF5, and Nektar::SpatialDomains::MeshGraphIOXml.

Referenced by ReadGeometry().

◆ v_WriteGeometry()

virtual void Nektar::SpatialDomains::MeshGraphIO::v_WriteGeometry	(	const std::string &	outfilename,
		bool	defaultExp = `false`,
		const LibUtilities::FieldMetaDataMap &	metadata = `LibUtilities::NullFieldMetaDataMap`
	)

protectedpure virtual

Implemented in Nektar::SpatialDomains::MeshGraphIOHDF5, and Nektar::SpatialDomains::MeshGraphIOXml.

Referenced by WriteGeometry().

◆ WriteGeometry()

void Nektar::SpatialDomains::MeshGraphIO::WriteGeometry	(	const std::string &	outfilename,
		bool	defaultExp = `false`,
		const LibUtilities::FieldMetaDataMap &	metadata = `LibUtilities::NullFieldMetaDataMap`
	)

inline

Definition at line 64 of file MeshGraphIO.h.

    {
        v_WriteGeometry(outfilename, defaultExp, metadata);
    }

References v_WriteGeometry().

Referenced by export_MeshGraphIO().

Member Data Documentation

◆ m_bndRegOrder

BndRegionOrdering Nektar::SpatialDomains::MeshGraphIO::m_bndRegOrder

protected

Definition at line 93 of file MeshGraphIO.h.

Referenced by Nektar::SpatialDomains::MeshGraphIOHDF5::v_PartitionMesh(), Nektar::SpatialDomains::MeshGraphIOXml::v_PartitionMesh(), and Nektar::SpatialDomains::MeshGraphIOXml::WriteXMLGeometry().

◆ m_compOrder

CompositeOrdering Nektar::SpatialDomains::MeshGraphIO::m_compOrder

protected

Definition at line 92 of file MeshGraphIO.h.

Referenced by Nektar::SpatialDomains::MeshGraphIOHDF5::ReadComposites(), and Nektar::SpatialDomains::MeshGraphIOXml::v_PartitionMesh().

◆ m_meshGraph

MeshGraphSharedPtr Nektar::SpatialDomains::MeshGraphIO::m_meshGraph

protected

Definition at line 89 of file MeshGraphIO.h.

◆ m_meshPartitioned

bool Nektar::SpatialDomains::MeshGraphIO::m_meshPartitioned = false

protected

Definition at line 91 of file MeshGraphIO.h.

Referenced by Nektar::SpatialDomains::MeshGraphIOHDF5::v_PartitionMesh(), and Nektar::SpatialDomains::MeshGraphIOXml::v_ReadGeometry().

◆ m_partition

int Nektar::SpatialDomains::MeshGraphIO::m_partition

protected

Definition at line 90 of file MeshGraphIO.h.

Referenced by Nektar::SpatialDomains::MeshGraphIOXml::v_ReadGeometry().

◆ m_session

LibUtilities::SessionReaderSharedPtr Nektar::SpatialDomains::MeshGraphIO::m_session

protected

Definition at line 88 of file MeshGraphIO.h.

Referenced by Nektar::SpatialDomains::MeshGraphIOHDF5::ReadCurveMap(), Nektar::SpatialDomains::MeshGraphIOXml::SetupCompositeRange(), Nektar::SpatialDomains::MeshGraphIOHDF5::v_PartitionMesh(), Nektar::SpatialDomains::MeshGraphIOXml::v_PartitionMesh(), Nektar::SpatialDomains::MeshGraphIOXml::v_ReadGeometry(), Nektar::SpatialDomains::MeshGraphIOXml::v_WriteGeometry(), and Nektar::SpatialDomains::MeshGraphIOXml::WriteXMLGeometry().

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ~MeshGraphIO()

◆ MeshGraphIO()

Member Function Documentation

◆ CreateCompositeDescriptor()

◆ CreateMeshEntities()

◆ GetCompositeString()

◆ PartitionMesh()

◆ Read()

◆ ReadGeometry()

◆ SetMeshGraph()

◆ v_PartitionMesh()

◆ v_ReadGeometry()

◆ v_WriteGeometry()

◆ WriteGeometry()

Member Data Documentation

◆ m_bndRegOrder

◆ m_compOrder

◆ m_meshGraph

◆ m_meshPartitioned

◆ m_partition

◆ m_session