Nektar::Utilities::InputNekpp Class Reference

#include <InputNekpp.h>

Inheritance diagram for Nektar::Utilities::InputNekpp:

Collaboration diagram for Nektar::Utilities::InputNekpp:

Public Member Functions
	InputNekpp (MeshSharedPtr m)
	Set up InputNekpp object. More...
virtual	~InputNekpp ()
virtual void	Process ()
Public Member Functions inherited from Nektar::Utilities::InputModule
	InputModule (FieldSharedPtr p_m)
void	AddFile (string fileType, string fileName)
	InputModule (MeshSharedPtr p_m)
void	OpenStream ()
	Open a file for input. More...
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...

Static Public Member Functions
static ModuleSharedPtr	create (MeshSharedPtr m)
	Creates an instance of this class. More...

Static Public Attributes
static ModuleKey	className
	ModuleKey for class. More...

Additional Inherited Members
Protected Member Functions inherited from Nektar::Utilities::InputModule
void	PrintSummary ()
	Print summary of elements. More...
void	PrintSummary ()
	Print summary of elements. More...
Protected Member Functions inherited from Nektar::Utilities::Module
	Module ()
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...
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::InputModule
set< string >	m_allowedFiles
std::ifstream	m_mshFile
	Input 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 48 of file InputNekpp.h.

Constructor & Destructor Documentation

Nektar::Utilities::InputNekpp::InputNekpp

(

MeshSharedPtr

m

)

Set up InputNekpp object.

Definition at line 57 of file InputNekpp.cpp.

                                              : InputModule(m)
        {
            
        }

Nektar::Utilities::InputNekpp::~InputNekpp ( )

virtual

Definition at line 62 of file InputNekpp.cpp.

        {
            
        }

Member Function Documentation

static ModuleSharedPtr Nektar::Utilities::InputNekpp::create ( MeshSharedPtr  m )

inlinestatic

Creates an instance of this class.

Definition at line 56 of file InputNekpp.h.

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

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

void Nektar::Utilities::InputNekpp::Process ( )

virtual

Gmsh file contains a list of nodes and their coordinates, along with a list of elements and those nodes which define them. We read in and store the list of nodes in #m_node and store the list of elements in #m_element. Each new element is supplied with a list of entries from #m_node which defines the element. Finally some mesh statistics are printed.

Parameters

pFilename

Filename of Gmsh file to read.

Implements Nektar::Utilities::Module.

Definition at line 77 of file InputNekpp.cpp.

References ASSERTL1, Nektar::LibUtilities::SessionReader::CreateInstance(), Nektar::LibUtilities::eNodalTriElec, Nektar::LibUtilities::eNodalTriEvenlySpaced, Nektar::LibUtilities::eNodalTriFekete, Nektar::LibUtilities::ePolyEvenlySpaced, Nektar::Utilities::GetElementFactory(), Nektar::iterator, Nektar::Utilities::Module::m_config, Nektar::Utilities::Module::m_mesh, Nektar::Utilities::Module::ProcessComposites(), Nektar::Utilities::Module::ProcessEdges(), Nektar::Utilities::Module::ProcessFaces(), and Nektar::SpatialDomains::MeshGraph::Read().

        {
            vector<string> filename;
            filename.push_back(m_config["infile"].as<string>());
            
            LibUtilities::SessionReaderSharedPtr pSession =
                LibUtilities::SessionReader::CreateInstance(0, NULL, filename);
            SpatialDomains::MeshGraphSharedPtr graph =
                SpatialDomains::MeshGraph::Read(pSession);

            m_mesh->m_expDim   = graph->GetMeshDimension ();
            m_mesh->m_spaceDim = graph->GetSpaceDimension();

            // Copy vertices.
            map<int, NodeSharedPtr> vIdMap;
            int nVerts = graph->GetNvertices();
            for (int i = 0; i < nVerts; ++i)
            {
                SpatialDomains::PointGeomSharedPtr vert =
                    graph->GetVertex(i);
                NodeSharedPtr n(new Node(vert->GetVid(),
                    (*vert)(0), (*vert)(1), (*vert)(2)));
                m_mesh->m_vertexSet.insert(n);
                vIdMap[vert->GetVid()] = n;
            }

            map<int, EdgeSharedPtr> eIdMap;
            map<int, EdgeSharedPtr>::iterator itEmap;
            map<int, FaceSharedPtr> fIdMap;
            map<int, FaceSharedPtr>::iterator itFmap;

            // Load up all edges from graph
            {
                int nel = 0;
                SpatialDomains::SegGeomMap tmp = graph->GetAllSegGeoms();
                SpatialDomains::SegGeomMap::iterator it;
                pair<EdgeSet::iterator,bool> testIns;
                nel += tmp.size();

                for (it = tmp.begin(); it != tmp.end(); ++it)
                {
                    pair<int, SpatialDomains::GeometrySharedPtr> tmp2(
                            it->first, boost::dynamic_pointer_cast<
                            SpatialDomains::Geometry>(it->second));
                    
                    // load up edge set in order of SegGeomMap; 
                    vector<NodeSharedPtr> curve; // curved nodes if deformed
                    int id0 = it->second->GetVid(0);
                    int id1 = it->second->GetVid(1);
                    LibUtilities::PointsType ptype = it->second->GetPointsKeys()[0].GetPointsType();
                    EdgeSharedPtr ed = EdgeSharedPtr(new Edge(vIdMap[id0], vIdMap[id1],
                                                              curve, ptype));
                    
                    testIns = m_mesh->m_edgeSet.insert(ed);
                    (*(testIns.first))->m_id = it->second->GetEid();
                    eIdMap[it->second->GetEid()] = ed;
                }
            }


            // load up all faces from graph
            {
                int nel = 0;
                SpatialDomains::TriGeomMap tmp = graph->GetAllTriGeoms();
                SpatialDomains::TriGeomMap::iterator it;
                pair<FaceSet::iterator,bool> testIns;
                nel += tmp.size();

                for (it = tmp.begin(); it != tmp.end(); ++it)
                {
                    pair<int, SpatialDomains::GeometrySharedPtr> tmp2(
                            it->first, boost::dynamic_pointer_cast<
                            SpatialDomains::Geometry>(it->second));
                            
                    vector<NodeSharedPtr> faceVertices;
                    vector<EdgeSharedPtr> faceEdges;
                    vector<NodeSharedPtr> faceNodes;
                    
                    for(int i = 0; i < 3; ++i)
                    {
                        faceVertices.push_back(vIdMap[it->second->GetVid(i)]);
                        faceEdges.push_back(eIdMap[it->second->GetEid(i)]);
                    }
                    
                    FaceSharedPtr fac = FaceSharedPtr( new Face(faceVertices,faceNodes,faceEdges,
                                                                LibUtilities::ePolyEvenlySpaced));
                    testIns = m_mesh->m_faceSet.insert(fac);
                    (*(testIns.first))->m_id = it->second->GetFid();
                    fIdMap[it->second->GetFid()] = fac;
                }

                SpatialDomains::QuadGeomMap tmp3 = graph->GetAllQuadGeoms();
                SpatialDomains::QuadGeomMap::iterator it2;
                
                for (it2 = tmp3.begin(); it2 != tmp3.end(); ++it2)
                {
                    pair<int, SpatialDomains::GeometrySharedPtr> tmp2(
                            it2->first, boost::dynamic_pointer_cast<
                            SpatialDomains::Geometry>(it2->second));
                            
                    vector<NodeSharedPtr> faceVertices;
                    vector<EdgeSharedPtr> faceEdges;
                    vector<NodeSharedPtr> faceNodes;
                    
                    for(int i = 0; i < 4; ++i)
                    {
                        faceVertices.push_back(vIdMap[it2->second->GetVid(i)]);
                        faceEdges.push_back(eIdMap[it2->second->GetEid(i)]);
                    }
                    
                    FaceSharedPtr fac = FaceSharedPtr( new Face(faceVertices,faceNodes,faceEdges,
                                                                LibUtilities::ePolyEvenlySpaced));
                    testIns = m_mesh->m_faceSet.insert(fac);
                    (*(testIns.first))->m_id = it2->second->GetFid();
                    fIdMap[it2->second->GetFid()] = fac;
                }
            }

            // Set up curved information

            // Curved Edges
            SpatialDomains::CurveMap &curvedEdges = graph->GetCurvedEdges();
            SpatialDomains::CurveMap::iterator it;

            for (it = curvedEdges.begin(); it != curvedEdges.end(); ++it)
            {
                SpatialDomains::CurveSharedPtr curve = it->second;
                int id = curve->m_curveID;
                ASSERTL1(eIdMap.find(id) != eIdMap.end(),
                         "Failed to find curved edge");
                EdgeSharedPtr edg = eIdMap[id];
                edg->m_curveType = curve->m_ptype;
                for(int j = 0; j < curve->m_points.size()-2; ++j)
                {
                    NodeSharedPtr n(new Node(j, (*curve->m_points[j+1])(0),
                                             (*curve->m_points[j+1])(1),
                                             (*curve->m_points[j+1])(2)));
                    edg->m_edgeNodes.push_back(n);
                }
            }

            // Curved Faces
            SpatialDomains::CurveMap &curvedFaces = graph->GetCurvedFaces();
            for (it = curvedFaces.begin(); it != curvedFaces.end(); ++it)
            {
                SpatialDomains::CurveSharedPtr curve = it->second;
                int id = curve->m_curveID;
                ASSERTL1(fIdMap.find(id) != fIdMap.end(),
                         "Failed to find curved edge");
                FaceSharedPtr fac = fIdMap[id];
                fac->m_curveType = curve->m_ptype;
                int Ntot = curve->m_points.size();

                if (fac->m_curveType == LibUtilities::eNodalTriFekete       ||
                    fac->m_curveType == LibUtilities::eNodalTriEvenlySpaced ||
                    fac->m_curveType == LibUtilities::eNodalTriElec)
                {
                    int N    = ((int)sqrt(8.0*Ntot+1.0)-1)/2;
                    for(int j = 3+3*(N-2); j < Ntot; ++j)
                    {
                        NodeSharedPtr n(new Node(j, (*curve->m_points[j])(0),
                                                 (*curve->m_points[j])(1),
                                                 (*curve->m_points[j])(2)));
                        fac->m_faceNodes.push_back(n);
                    }
                }
                else // quad face.
                {
                    int N    = (int)sqrt((double)Ntot);
                    for(int j = 1; j < N-1; ++j)
                    {
                        for(int k = 1; k < N-1; ++k)
                        {
                            NodeSharedPtr n(new Node((j-1)*(N-2)+k-1,
                                                     (*curve->m_points[j*N+k])(0),
                                                     (*curve->m_points[j*N+k])(1),
                                                     (*curve->m_points[j*N+k])(2)));
                            fac->m_faceNodes.push_back(n);
                        }
                    }
                }
            }

            // Get hold of mesh composites and set up m_mesh->m_elements

            SpatialDomains::CompositeMap       GraphComps= graph->GetComposites();
            SpatialDomains::CompositeMapIter   compIt;
            SpatialDomains::GeometryVectorIter geomIt;


            // calculate the number of element of dimension
            // m_mesh->m_expDim in composite list so we can set up
            // element vector of this size to allow for
            // non-consecutive insertion to list (Might consider
            // setting element up as a map)?
            int nel = 0; 
            for(compIt = GraphComps.begin(); compIt != GraphComps.end(); ++compIt)
            {
                // Get hold of dimension
                int dim = (*compIt->second)[0]->GetShapeDim();
                
                if(dim == m_mesh->m_expDim) 
                {
                    nel += (*compIt->second).size();
                }
            }
            m_mesh->m_element[m_mesh->m_expDim].resize(nel);

            // loop over all composites and set up elements with edges and faces from the maps above. 
            for(compIt = GraphComps.begin(); compIt != GraphComps.end(); ++compIt)
            {
                // Get hold of dimension
                int dim = (*compIt->second)[0]->GetShapeDim();

                // compIt->second is a GeometryVector
                for(geomIt  = (*compIt->second).begin(); 
                    geomIt != (*compIt->second).end();
                        ++geomIt)
                {
                    ElmtConfig conf((*geomIt)->GetShapeType(),1,true,true);
                    
                    // Get hold of geometry
                    vector<NodeSharedPtr> nodeList;
                    for (int i = 0; i < (*geomIt)->GetNumVerts(); ++i)
                    {
                        nodeList.push_back(vIdMap[(*geomIt)->GetVid(i)]);
                    }
                
                    vector<int> tags;
                    tags.push_back(compIt->first);
                    
                    ElementSharedPtr E = GetElementFactory().
                        CreateInstance((*geomIt)->GetShapeType(),conf,nodeList,tags);
                    
                    E->SetId((*geomIt)->GetGlobalID());
                    
                    if(dim == m_mesh->m_expDim) // load mesh into location baded on globalID
                    {
                        m_mesh->m_element[dim][(*geomIt)->GetGlobalID()] = E;
                    }
                    else // push onto vector for later usage as composite region
                    {
                        m_mesh->m_element[dim].push_back(E);
                    }
                    
                    if(dim > 1)
                    {
                        // reset edges 
                        for (int i = 0; i < (*geomIt)->GetNumEdges(); ++i)
                        {
                            EdgeSharedPtr edg = eIdMap[(*geomIt)->GetEid(i)];
                            E->SetEdge(i,edg);
                            // set up link back to this element
                            edg->m_elLink.push_back(pair<ElementSharedPtr,int>(E,i));
                        }
                    }
                    
                    if(dim  == 3)
                    {
                        // reset faces 
                        for (int i = 0; i < (*geomIt)->GetNumFaces(); ++i)
                        {
                            FaceSharedPtr fac = fIdMap[(*geomIt)->GetFid(i)];
                            E->SetFace(i,fac);
                            // set up link back to this slement
                            fac->m_elLink.push_back(pair<ElementSharedPtr,int>(E,i));
                        }
                    }
                }                             
            }
            ProcessEdges(false); 
            ProcessFaces(false);
            ProcessComposites();
        }

Member Data Documentation

ModuleKey Nektar::Utilities::InputNekpp::className

static

Initial value:

= 
            GetModuleFactory().RegisterCreatorFunction(
                ModuleKey(eInputModule, "xml"), InputNekpp::create,
                "Reads Nektar++ xml file.")

ModuleKey for class.

Definition at line 60 of file InputNekpp.h.