Nektar::Utilities::OutputGmsh Class Reference

Converter for Gmsh files. More...

#include <OutputGmsh.h>

Inheritance diagram for Nektar::Utilities::OutputGmsh:

Public Member Functions
	OutputGmsh (NekMeshUtils::MeshSharedPtr m)
virtual	~OutputGmsh ()
virtual void	Process ()
	Write mesh to output file. More...
Public Member Functions inherited from Nektar::NekMeshUtils::OutputModule
NEKMESHUTILS_EXPORT	OutputModule (MeshSharedPtr p_m)
NEKMESHUTILS_EXPORT void	OpenStream ()
	Open a file for output. More...
Public Member Functions inherited from Nektar::NekMeshUtils::Module
NEKMESHUTILS_EXPORT	Module (MeshSharedPtr p_m)
NEKMESHUTILS_EXPORT void	RegisterConfig (std::string key, std::string value=std::string())
	Register a configuration option with a module. More...
NEKMESHUTILS_EXPORT void	PrintConfig ()
	Print out all configuration options for a module. More...
NEKMESHUTILS_EXPORT void	SetDefaults ()
	Sets default configuration options for those which have not been set. More...
NEKMESHUTILS_EXPORT MeshSharedPtr	GetMesh ()
virtual NEKMESHUTILS_EXPORT void	ProcessVertices ()
	Extract element vertices. More...
virtual NEKMESHUTILS_EXPORT void	ProcessEdges (bool ReprocessEdges=true)
	Extract element edges. More...
virtual NEKMESHUTILS_EXPORT void	ProcessFaces (bool ReprocessFaces=true)
	Extract element faces. More...
virtual NEKMESHUTILS_EXPORT void	ProcessElements ()
	Generate element IDs. More...
virtual NEKMESHUTILS_EXPORT void	ProcessComposites ()
	Generate composites. More...
virtual NEKMESHUTILS_EXPORT void	ClearElementLinks ()

Static Public Member Functions
static std::shared_ptr< Module >	create (NekMeshUtils::MeshSharedPtr m)
	Creates an instance of this class. More...

Static Public Attributes
static NekMeshUtils::ModuleKey	className

Private Attributes
std::unordered_map< NekMeshUtils::ElmtConfig, unsigned int, ElmtConfigHash >	elmMap

Additional Inherited Members
Protected Member Functions inherited from Nektar::NekMeshUtils::Module
NEKMESHUTILS_EXPORT void	ReorderPrisms (PerMap &perFaces)
	Reorder node IDs so that prisms and tetrahedra are aligned correctly. More...
NEKMESHUTILS_EXPORT void	PrismLines (int prism, PerMap &perFaces, std::set< int > &prismsDone, std::vector< ElementSharedPtr > &line)
Protected Attributes inherited from Nektar::NekMeshUtils::OutputModule
io::filtering_ostream	m_mshFile
	Output stream. More...
std::ofstream	m_mshFileStream
	Input stream. More...
Protected Attributes inherited from Nektar::NekMeshUtils::Module
MeshSharedPtr	m_mesh
	Mesh object. More...
std::map< std::string, ConfigOption >	m_config
	List of configuration values. More...

Detailed Description

Converter for Gmsh files.

Definition at line 66 of file OutputGmsh.h.

Constructor & Destructor Documentation

OutputGmsh()

Nektar::Utilities::OutputGmsh::OutputGmsh

(

NekMeshUtils::MeshSharedPtr

m

)

Definition at line 55 of file OutputGmsh.cpp.

References elmMap, Nektar::Utilities::InputGmsh::GenElmMap(), and Nektar::NekMeshUtils::Module::m_config.

                                      : OutputModule(m)
{
    // Populate #InputGmsh::elmMap and use this to construct an
    // inverse mapping from %ElmtConfig to Gmsh ID.
    for (auto &it : InputGmsh::GenElmMap())
    {
        elmMap[it.second] = it.first;
    }

    m_config["order"] = ConfigOption(false, "-1", "Enforce a polynomial order");
}

~OutputGmsh()

Nektar::Utilities::OutputGmsh::~OutputGmsh ( )

virtual

Definition at line 67 of file OutputGmsh.cpp.

{
}

Member Function Documentation

create()

static std::shared_ptr<Module> Nektar::Utilities::OutputGmsh::create ( NekMeshUtils::MeshSharedPtr  m )

inlinestatic

Creates an instance of this class.

Definition at line 70 of file OutputGmsh.h.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr().

                                                                     {
        return MemoryManager<OutputGmsh>::AllocateSharedPtr(m);
    }

Process()

void Nektar::Utilities::OutputGmsh::Process ( )

virtual

Write mesh to output file.

Process a mesh to output to Gmsh MSH format.

Gmsh output is fairly straightforward. The file first contains a list of nodes, followed by a list of elements. Since Mesh::vertexSet only contains vertices of the linear elements, we first loop over the elements so that any high-order vertices can be enumerated and then added to the node list. We then print out the list of nodes and finally print the element list.

Implements Nektar::NekMeshUtils::Module.

Definition at line 81 of file OutputGmsh.cpp.

References Nektar::NekMeshUtils::HOTriangle< T >::Align(), Nektar::NekMeshUtils::HOQuadrilateral< T >::Align(), ASSERTL1, Nektar::Utilities::InputGmsh::CreateReordering(), Nektar::StdRegions::eForwards, elmMap, Nektar::LibUtilities::ePolyEvenlySpaced, Nektar::NekMeshUtils::Module::m_config, Nektar::NekMeshUtils::Module::m_mesh, Nektar::NekMeshUtils::OutputModule::m_mshFile, Nektar::NekMeshUtils::OutputModule::OpenStream(), Nektar::NekMeshUtils::HOTriangle< T >::surfVerts, and Nektar::NekMeshUtils::HOQuadrilateral< T >::surfVerts.

{
    if (m_mesh->m_verbose)
    {
        cout << "OutputGmsh: Writing file..." << endl;
    }

    std::unordered_map<int, vector<int> > orderingMap;

    // Open the file stream.
    OpenStream();

    // Write MSH header
    m_mshFile << "$MeshFormat" << endl
              << "2.2 0 8" << endl
              << "$EndMeshFormat" << endl;

    int id = m_mesh->m_vertexSet.size();
    vector<ElementSharedPtr> toComplete;

    int order = m_config["order"].as<int>();

    if (order != -1)
    {
        if (m_mesh->m_verbose)
        {
            cout << "Making mesh of order " << order << endl;
        }
    }
    else
    {
        // Do first pass over elements of expansion dimension to determine
        // which elements need completion.
        for (int i = 0; i < m_mesh->m_element[m_mesh->m_expDim].size(); ++i)
        {
            ElementSharedPtr e = m_mesh->m_element[m_mesh->m_expDim][i];
            if (e->GetMaxOrder() > order)
            {
                order = e->GetMaxOrder();
            }
        }
    }

    // Convert this mesh into a high-order mesh of uniform order.
    if (m_mesh->m_verbose)
    {
        cout << "Mesh order of " << order << " detected" << endl;
    }

    m_mesh->MakeOrder(order, LibUtilities::ePolyEvenlySpaced);

    // Add edge- and face-interior nodes to vertex set.
    for (auto &eIt : m_mesh->m_edgeSet)
    {
        m_mesh->m_vertexSet.insert(eIt->m_edgeNodes.begin(),
                                   eIt->m_edgeNodes.end());
    }

    for (auto &fIt : m_mesh->m_faceSet)
    {
        m_mesh->m_vertexSet.insert(fIt->m_faceNodes.begin(),
                                   fIt->m_faceNodes.end());
    }

    // Do second pass over elements for volume nodes.
    for (int d = 1; d <= 3; ++d)
    {
        for (int i = 0; i < m_mesh->m_element[d].size(); ++i)
        {
            ElementSharedPtr e = m_mesh->m_element[d][i];
            vector<NodeSharedPtr> volList = e->GetVolumeNodes();
            m_mesh->m_vertexSet.insert(volList.begin(), volList.end());
        }
    }

    // Create ordered set of nodes - not required but looks nicer.
    map<int, NodeSharedPtr> tmp;
    for (const auto &it : m_mesh->m_vertexSet)
    {
        tmp[it->GetID() + 1] = it;
    }

    // Write out nodes section.
    m_mshFile << "$Nodes" << endl << m_mesh->m_vertexSet.size() << endl;

    for (auto &it : tmp)
    {
        m_mshFile << it.first << " " << scientific << setprecision(10)
                  << it.second->m_x << " " << it.second->m_y << " "
                  << it.second->m_z << endl;
    }

    m_mshFile << "$EndNodes" << endl;

    // Write elements section. All other sections are not currently
    // supported (physical names etc).
    m_mshFile << "$Elements" << endl;
    m_mshFile << m_mesh->GetNumEntities() << endl;

    id = 1;

    for (int d = 1; d <= 3; ++d)
    {
        for (int i = 0; i < m_mesh->m_element[d].size(); ++i, ++id)
        {
            ElementSharedPtr e = m_mesh->m_element[d][i];

            // First output element ID and type.
            int elmtType = elmMap[e->GetConf()];
            m_mshFile << id << " " << elmtType << " ";

            // Write out number of element tags and then the tags
            // themselves.
            vector<int> tags = e->GetTagList();

            if (tags.size() == 1)
            {
                tags.push_back(tags[0]);
                tags.push_back(0);
            }

            m_mshFile << tags.size() << " ";

            for (int j = 0; j < tags.size(); ++j)
            {
                m_mshFile << tags[j] << " ";
            }

            // Finally write out node list. First write vertices, then
            // internal edge nodes, then face nodes.
            vector<NodeSharedPtr> nodeList = e->GetVertexList();
            vector<EdgeSharedPtr> edgeList = e->GetEdgeList();
            vector<FaceSharedPtr> faceList = e->GetFaceList();
            vector<NodeSharedPtr> volList  = e->GetVolumeNodes();

            tags.clear();

            for (int j = 0; j < nodeList.size(); ++j)
            {
                tags.push_back(nodeList[j]->m_id);
            }

            // Process edge-interior points
            for (int j = 0; j < edgeList.size(); ++j)
            {
                nodeList = edgeList[j]->m_edgeNodes;

                if (e->GetEdgeOrient(j, edgeList[j]) == StdRegions::eForwards)
                {
                    for (int k = 0; k < nodeList.size(); ++k)
                    {
                        tags.push_back(nodeList[k]->m_id);
                    }
                }
                else
                {
                    for (int k = nodeList.size() - 1; k >= 0; --k)
                    {
                        tags.push_back(nodeList[k]->m_id);
                    }
                }
            }

            // Process face-interior points
            for (int j = 0; j < faceList.size(); ++j)
            {
                nodeList = faceList[j]->m_faceNodes;
                int nFaceVerts = faceList[j]->m_vertexList.size();
                vector<int> faceIds(nFaceVerts), volFaceIds(nFaceVerts);

                for (int k = 0; k < nFaceVerts; ++k)
                {
                    faceIds   [k] = faceList[j]->m_vertexList[k]->m_id;
                    volFaceIds[k] =
                        e->GetVertexList()[e->GetFaceVertex(j, k)]->m_id;
                }

                if (nFaceVerts == 3)
                {
                    HOTriangle<NodeSharedPtr> hoTri(faceIds, nodeList);
                    hoTri.Align(volFaceIds);
                    for (int k = 0; k < hoTri.surfVerts.size(); ++k)
                    {
                        tags.push_back(hoTri.surfVerts[k]->m_id);
                    }
                }
                else
                {
                    HOQuadrilateral<NodeSharedPtr> hoQuad(faceIds, nodeList);
                    hoQuad.Align(volFaceIds);

                    for (int k = 0; k < hoQuad.surfVerts.size(); ++k)
                    {
                        tags.push_back(hoQuad.surfVerts[k]->m_id);
                    }
                }
            }

            // Process volume nodes
            for (int j = 0; j < volList.size(); ++j)
            {
                tags.push_back(volList[j]->m_id);
            }

            // Construct inverse of input reordering. First try to find it in
            // our cache.
            auto oIt = orderingMap.find(elmtType);

            // If it's not created, then create it.
            if (oIt == orderingMap.end())
            {
                vector<int> reordering = InputGmsh::CreateReordering(elmtType);
                vector<int> inv(tags.size());

                ASSERTL1(tags.size() == reordering.size(),
                         "Reordering map size not equal to element tags 1.");

                for (int j = 0; j < tags.size(); ++j)
                {
                    inv[reordering[j]] = j;
                }

                oIt = orderingMap.insert(make_pair(elmtType, inv)).first;
            }

            ASSERTL1(tags.size() == oIt->second.size(),
                     "Reordering map size not equal to element tags 2.");

            // Finally write element nodes.
            for (int j = 0; j < tags.size(); ++j)
            {
                m_mshFile << tags[oIt->second[j]] + 1 << " ";
            }

            m_mshFile << endl;
        }
    }
    m_mshFile << "$EndElements" << endl;
}

Member Data Documentation

className

ModuleKey Nektar::Utilities::OutputGmsh::className

static

Initial value:

=
    GetModuleFactory().RegisterCreatorFunction(ModuleKey(eOutputModule, "msh"),
                                               OutputGmsh::create,
                                               "Writes Gmsh msh file.")

Definition at line 73 of file OutputGmsh.h.

elmMap

std::unordered_map<NekMeshUtils::ElmtConfig, unsigned int, ElmtConfigHash> Nektar::Utilities::OutputGmsh::elmMap

private

Definition at line 82 of file OutputGmsh.h.

Referenced by OutputGmsh(), and Process().