Nektar::Utilities::OutputGmsh Class Reference

Converter for Gmsh files. More...

#include <OutputGmsh.h>

Inheritance diagram for Nektar::Utilities::OutputGmsh:

Collaboration diagram for Nektar::Utilities::OutputGmsh:

Public Member Functions
	OutputGmsh (MeshSharedPtr m)
virtual	~OutputGmsh ()
virtual void	Process ()
	Write mesh to output file. More...
Public Member Functions inherited from Nektar::Utilities::OutputModule
	OutputModule (FieldSharedPtr p_f)
void	OpenStream ()
	Open a file for output. More...
	OutputModule (MeshSharedPtr p_m)
void	OpenStream ()
Public Member Functions inherited from Nektar::Utilities::Module
	Module (FieldSharedPtr p_f)
virtual void	Process (po::variables_map &vm)=0
void	RegisterConfig (string key, string value)
	Register a configuration option with a module. More...
void	PrintConfig ()
	Print out all configuration options for a module. More...
void	SetDefaults ()
	Sets default configuration options for those which have not been set. More...
bool	GetRequireEquiSpaced (void)
void	SetRequireEquiSpaced (bool pVal)
void	EvaluateTriFieldAtEquiSpacedPts (LocalRegions::ExpansionSharedPtr &exp, const Array< OneD, const NekDouble > &infield, Array< OneD, NekDouble > &outfield)
	Module (MeshSharedPtr p_m)
void	RegisterConfig (string key, string value)
void	PrintConfig ()
void	SetDefaults ()
MeshSharedPtr	GetMesh ()
virtual void	ProcessVertices ()
	Extract element vertices. More...
virtual void	ProcessEdges (bool ReprocessEdges=true)
	Extract element edges. More...
virtual void	ProcessFaces (bool ReprocessFaces=true)
	Extract element faces. More...
virtual void	ProcessElements ()
	Generate element IDs. More...
virtual void	ProcessComposites ()
	Generate composites. More...
virtual void	ClearElementLinks ()

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

Static Public Attributes
static ModuleKey	className

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

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

Detailed Description

Converter for Gmsh files.

Definition at line 70 of file OutputGmsh.h.

Constructor & Destructor Documentation

Nektar::Utilities::OutputGmsh::OutputGmsh

(

MeshSharedPtr

m

)

Definition at line 54 of file OutputGmsh.cpp.

References elmMap, Nektar::Utilities::InputGmsh::GenElmMap(), and Nektar::iterator.

                                      : OutputModule(m)
{
    map<unsigned int, ElmtConfig> igelmap = InputGmsh::GenElmMap();

    map<unsigned int, ElmtConfig>::iterator it;

    // Populate #InputGmsh::elmMap and use this to construct an
    // inverse mapping from %ElmtConfig to Gmsh ID.
    for (it = igelmap.begin(); it != igelmap.end(); ++it)
    {
        elmMap[it->second] = it->first;
    }
}

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

virtual

Definition at line 68 of file OutputGmsh.cpp.

{
}

Member Function Documentation

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

inlinestatic

Creates an instance of this class.

Definition at line 74 of file OutputGmsh.h.

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

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

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::Utilities::Module.

Definition at line 82 of file OutputGmsh.cpp.

References elmMap, Nektar::LibUtilities::ePrism, Nektar::LibUtilities::eTetrahedron, Nektar::iterator, Nektar::Utilities::Module::m_mesh, Nektar::Utilities::OutputModule::m_mshFile, and Nektar::Utilities::OutputModule::OpenStream().

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

    // 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 maxOrder = -1;

    // 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() > maxOrder)
        {
            maxOrder = e->GetMaxOrder();
        }
    }

    // maxOrder = 2;
    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];
            if ((e->GetConf().m_order <= 1 && maxOrder > 1) ||
                (e->GetConf().m_order == maxOrder &&
                 e->GetConf().m_faceNodes == false))
            {
                toComplete.push_back(e);
            }
            // Generate geometry information for this element. This will
            // be stored locally inside each element.
            SpatialDomains::GeometrySharedPtr geom =
                m_mesh->m_element[d][i]->GetGeom(m_mesh->m_spaceDim);
        }
    }

    // Complete these elements.
    for (int i = 0; i < toComplete.size(); ++i)
    {
        toComplete[i]->Complete(maxOrder);
    }

    // Do second pass over elements to enumerate high-order vertices.
    for (int d = 1; d <= 3; ++d)
    {
        for (int i = 0; i < m_mesh->m_element[d].size(); ++i)
        {
            // Keep track of faces and edges to ensure that high-order
            // nodes are only added once on common faces/edges.
            boost::unordered_set<int> edgesDone;
            boost::unordered_set<int> facesDone;
            ElementSharedPtr e = m_mesh->m_element[d][i];

            if (e->GetConf().m_order > 1)
            {
                vector<NodeSharedPtr> tmp;
                vector<EdgeSharedPtr> edgeList = e->GetEdgeList();
                vector<FaceSharedPtr> faceList = e->GetFaceList();
                vector<NodeSharedPtr> volList  = e->GetVolumeNodes();

                for (int j = 0; j < edgeList.size(); ++j)
                {
                    boost::unordered_set<int>::iterator it =
                        edgesDone.find(edgeList[j]->m_id);
                    if (it == edgesDone.end() || d != 3)
                    {
                        tmp.insert(tmp.end(),
                                   edgeList[j]->m_edgeNodes.begin(),
                                   edgeList[j]->m_edgeNodes.end());
                        edgesDone.insert(edgeList[j]->m_id);
                    }
                }

                for (int j = 0; j < faceList.size(); ++j)
                {
                    boost::unordered_set<int>::iterator it =
                        facesDone.find(faceList[j]->m_id);
                    if (it == facesDone.end() || d != 3)
                    {
                        tmp.insert(tmp.end(),
                                   faceList[j]->m_faceNodes.begin(),
                                   faceList[j]->m_faceNodes.end());
                        facesDone.insert(faceList[j]->m_id);
                    }
                }

                tmp.insert(tmp.end(), volList.begin(), volList.end());

                // Even though faces/edges are at this point unique
                // across the mesh, still need to test inserts since
                // high-order nodes may already have been inserted into
                // the list from an adjoining element or a boundary
                // element.
                for (int j = 0; j < tmp.size(); ++j)
                {
                    pair<NodeSet::iterator, bool> testIns =
                        m_mesh->m_vertexSet.insert(tmp[j]);

                    if (testIns.second)
                    {
                        (*(testIns.first))->m_id = id++;
                    }
                    else
                    {
                        tmp[j]->m_id = (*(testIns.first))->m_id;
                    }
                }
            }
        }
    }

    // Create ordered set of nodes - not required but looks nicer.
    std::set<NodeSharedPtr>::iterator it;
    std::set<NodeSharedPtr> tmp(m_mesh->m_vertexSet.begin(),
                                m_mesh->m_vertexSet.end());

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

    for (it = tmp.begin(); it != tmp.end(); ++it)
    {
        m_mshFile << (*it)->m_id << " " << scientific << setprecision(10)
                  << (*it)->m_x << " " << (*it)->m_y << " " << (*it)->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 = 0;

    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.
            m_mshFile << id << " " << elmMap[e->GetConf()] << " ";

            // 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);
            }

            if (e->GetConf().m_order > 1)
            {
                for (int j = 0; j < edgeList.size(); ++j)
                {
                    nodeList = edgeList[j]->m_edgeNodes;
                    for (int k = 0; k < nodeList.size(); ++k)
                    {
                        tags.push_back(nodeList[k]->m_id);
                        // cout << "EDGENODE" << endl;
                    }
                }

                for (int j = 0; j < faceList.size(); ++j)
                {
                    nodeList = faceList[j]->m_faceNodes;
                    for (int k = 0; k < nodeList.size(); ++k)
                    {
                        // cout << "FACENODE" << endl;
                        tags.push_back(nodeList[k]->m_id);
                    }
                }

                for (int j = 0; j < volList.size(); ++j)
                {
                    // cout << "VOLNODE" << endl;
                    tags.push_back(volList[j]->m_id);
                }
            }

            // Re-order tetrahedral vertices.
            if (e->GetConf().m_e == LibUtilities::eTetrahedron)
            {
                int order = e->GetConf().m_order;
                if (order > 4)
                {
                    cerr << "Temporary error: Gmsh tets only supported "
                         << "up to 4th order - will fix soon!" << endl;
                    abort();
                }
                int pos = 4;
                // Swap edge 1->3 nodes with edge 2->3 nodes.
                pos = 4 + 4 * (order - 1);
                for (int j = 0; j < order - 1; ++j)
                {
                    swap(tags[j + pos], tags[j + pos + order - 1]);
                }
                // Reverse ordering of other vertical edge-interior
                // nodes.
                reverse(tags.begin() + 4 + 3 * (order - 1),
                        tags.begin() + 4 + 4 * (order - 1));
                reverse(tags.begin() + 4 + 4 * (order - 1),
                        tags.begin() + 4 + 5 * (order - 1));
                reverse(tags.begin() + 4 + 5 * (order - 1),
                        tags.begin() + 4 + 6 * (order - 1));

                // Swap face 2 nodes with face 3.
                pos = 4 + 6 * (order - 1) + 2 * (order - 2) * (order - 1) / 2;
                for (int j = 0; j < (order - 2) * (order - 1) / 2; ++j)
                {
                    swap(tags[j + pos],
                         tags[j + pos + (order - 2) * (order - 1) / 2]);
                }

                // Re-order face points. Gmsh ordering (node->face) is:
                //
                // Face 0: 0->2->1
                // Face 1: 0->1->3
                // Face 2: 0->3->2
                // Face 3: 3->1->2
                //
                // Therefore need to reorder nodes for faces 0, 2 and
                // 3 to match nodal ordering.

                // Re-order face 0: transpose
                vector<int> tmp((order - 2) * (order - 1) / 2);
                int a = 0;
                pos = 4 + 6 * (order - 1);
                for (int j = 0; j < order - 2; ++j)
                {
                    for (int k = 0; k < order - 2 - j; ++k, ++a)
                    {
                        tmp[a] =
                            tags[pos + j + k * (2 * (order - 2) + 1 - k) / 2];
                    }
                }
                for (int j = 0; j < (order - 1) * (order - 2) / 2; ++j)
                {
                    tags[pos + j] = tmp[j];
                }

                // Re-order face 2: transpose
                pos = 4 + 6 * (order - 1) + 2 * (order - 2) * (order - 1) / 2;
                a = 0;
                for (int j = 0; j < order - 2; ++j)
                {
                    for (int k = 0; k < order - 2 - j; ++k, ++a)
                    {
                        tmp[a] =
                            tags[pos + j + k * (2 * (order - 2) + 1 - k) / 2];
                    }
                }
                for (int j = 0; j < (order - 1) * (order - 2) / 2; ++j)
                {
                    tags[pos + j] = tmp[j];
                }

                // Re-order face 3: reflect in y direction
                pos = 4 + 6 * (order - 1) + 3 * (order - 2) * (order - 1) / 2;
                a = 0;
                for (int j = 0; j < order - 2; ++j)
                {
                    for (int k = order - 3 - j; k >= 0; --k, ++a)
                    {
                        tmp[a] =
                            tags[pos + j + k * (2 * (order - 2) + 1 - k) / 2];
                    }
                }

                for (int j = 0; j < (order - 1) * (order - 2) / 2; ++j)
                {
                    tags[pos + j] = tmp[j];
                }
            }
            // Re-order prism vertices.
            else if (e->GetConf().m_e == LibUtilities::ePrism)
            {
                int order = e->GetConf().m_order;
                if (order > 2)
                {
                    cerr << "Temporary error: Gmsh prisms only "
                         << "supported up to 2nd order!" << endl;
                    abort();
                }

                // Swap nodes.
                vector<int> temp(18);
                temp[0]  = tags[0];
                temp[1]  = tags[1];
                temp[2]  = tags[4];
                temp[3]  = tags[3];
                temp[4]  = tags[2];
                temp[5]  = tags[5];
                temp[6]  = tags[6];
                temp[7]  = tags[10];
                temp[8]  = tags[9];
                temp[9]  = tags[11];
                temp[10] = tags[7];
                temp[11] = tags[14];
                temp[12] = tags[8];
                temp[13] = tags[13];
                temp[14] = tags[12];
                temp[15] = tags[15];
                temp[16] = tags[17];
                temp[17] = tags[16];
                for (int k = 0; k < 18; ++k)
                {
                    tags[k] = temp[k];
                }
            }

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

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

Member Data Documentation

ModuleKey Nektar::Utilities::OutputGmsh::className

static

Initial value:

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

Definition at line 77 of file OutputGmsh.h.

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

private

Definition at line 86 of file OutputGmsh.h.

Referenced by OutputGmsh(), and Process().