#include <Module.h>

Inheritance diagram for Nektar::NekMeshUtils::Module:

Collaboration diagram for Nektar::NekMeshUtils::Module:

Public Member Functions
NEKMESHUTILS_EXPORT	Module (MeshSharedPtr p_m)

virtual NEKMESHUTILS_EXPORT void	Process ()=0

NEKMESHUTILS_EXPORT void	RegisterConfig (std::string key, std::string value)
	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 ()

Protected Member Functions
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
MeshSharedPtr	m_mesh
	Mesh object. More...

std::map< std::string, ConfigOption >	m_config
	List of configuration values. More...

Detailed Description

Abstract base class for mesh converter modules. Each subclass implements the Process() function, which in some way alters the mesh #m.

Definition at line 157 of file NekMeshUtils/Module/Module.h.

Constructor & Destructor Documentation

NEKMESHUTILS_EXPORT Nektar::NekMeshUtils::Module::Module ( MeshSharedPtr p_m )

inline

Definition at line 160 of file NekMeshUtils/Module/Module.h.

160 : m_mesh(p_m) {}

Nektar::NekMeshUtils::Module::m_mesh

MeshSharedPtr m_mesh

Mesh object.

Definition: NekMeshUtils/Module/Module.h:186

Member Function Documentation

void Nektar::NekMeshUtils::Module::ClearElementLinks ( )

virtual

clear all element link information from mesh entities to be able to reprocess new mesh

Definition at line 454 of file NekMeshUtils/Module/Module.cpp.

References Nektar::iterator, and m_mesh.

Referenced by Nektar::NekMeshUtils::VolumeMesh::Process(), Nektar::Utilities::ProcessOptiExtract::Process(), and Nektar::Utilities::ProcessLinkCheck::Process().

 {
     EdgeSet::iterator eit;
 
     for(eit = m_mesh->m_edgeSet.begin(); eit != m_mesh->m_edgeSet.end(); eit++)
     {
         (*eit)->m_elLink.clear();
     }
 
     FaceSet::iterator fit;
 
     for(fit = m_mesh->m_faceSet.begin(); fit != m_mesh->m_faceSet.end(); fit++)
     {
         (*fit)->m_elLink.clear();
     }
 }

NEKMESHUTILS_EXPORT MeshSharedPtr Nektar::NekMeshUtils::Module::GetMesh ( )

inline

Definition at line 166 of file NekMeshUtils/Module/Module.h.

References m_mesh.

         {
             return m_mesh;
         }

void Nektar::NekMeshUtils::Module::PrintConfig ( )

Print out all configuration options for a module.

Definition at line 868 of file NekMeshUtils/Module/Module.cpp.

References Nektar::iterator, and m_config.

 {
     map<string, ConfigOption>::iterator it;
 
     if (m_config.size() == 0)
     {
         cerr << "No configuration options for this module." << endl;
         return;
     }
 
     for (it = m_config.begin(); it != m_config.end(); ++it)
     {
         cerr << setw(10) << it->first << ": " << it->second.desc
              << endl;
     }
 }

void Nektar::NekMeshUtils::Module::PrismLines	(	int	prism,
		PerMap &	perFaces,
		std::set< int > &	prismsDone,
		std::vector< ElementSharedPtr > &	line
	)

protected

Definition at line 789 of file NekMeshUtils/Module/Module.cpp.

References Nektar::iterator, and m_mesh.

Referenced by ReorderPrisms().

 {
     int                i;
     set<int>::iterator it = prismsDone.find(prism);
     PerMap::iterator   it2;
 
     if (it == prismsDone.end())
     {
         return;
     }
 
     // Remove this prism from the list.
     prismsDone.erase(it);
     line.push_back(m_mesh->m_element[3][prism]);
 
     // Now find prisms connected to this one through a triangular face.
     for (i = 1; i <= 3; i += 2)
     {
         FaceSharedPtr f = m_mesh->m_element[3][prism]->GetFace(i);
         int nextId;
 
         // See if this face is periodic.
         it2 = perFaces.find(f->m_id);
 
         if (it2 != perFaces.end())
         {
             int id2 = it2->second.first->m_id;
             nextId  = it2->second.first->m_elLink[0].first->GetId();
             perFaces.erase(it2);
             perFaces.erase(id2);
             PrismLines(nextId, perFaces, prismsDone, line);
         }
 
         // Nothing else connected to this face.
         if (f->m_elLink.size() == 1)
         {
             continue;
         }
 
         nextId = f->m_elLink[0].first->GetId();
         if (nextId == m_mesh->m_element[3][prism]->GetId())
         {
             nextId = f->m_elLink[1].first->GetId();
         }
 
         PrismLines(nextId, perFaces, prismsDone, line);
     }
 }

virtual NEKMESHUTILS_EXPORT void Nektar::NekMeshUtils::Module::Process ( )

pure virtual

void Nektar::NekMeshUtils::Module::ProcessComposites ( )

virtual

Generate composites.

Generate a list of composites (groups of elements) from tag IDs stored in mesh vertices/edges/faces/elements.

Each element is assigned to a composite ID by an input module. First we scan the element list and generate a list of composite IDs. We then generate the composite objects and populate them with a second scan through the element list.

Definition at line 404 of file NekMeshUtils/Module/Module.cpp.

References Nektar::iterator, and m_mesh.

 {
     m_mesh->m_composite.clear();
 
     // For each element, check to see if a composite has been
     // created. If not, create a new composite. Otherwise, add the
     // element to the composite.
     for (int d = 0; d <= m_mesh->m_expDim; ++d)
     {
         vector<ElementSharedPtr> &elmt = m_mesh->m_element[d];
 
         for (int i = 0; i < elmt.size(); ++i)
         {
             CompositeMap::iterator it;
             unsigned int tagid = elmt[i]->GetTagList()[0];
 
             it = m_mesh->m_composite.find(tagid);
 
             if (it == m_mesh->m_composite.end())
             {
                 CompositeSharedPtr tmp = boost::shared_ptr<Composite>(
                                                     new Composite());
                 pair<CompositeMap::iterator, bool> testIns;
                 tmp->m_id  = tagid;
                 tmp->m_tag = elmt[i]->GetTag();
                 if(m_mesh->m_faceLabels.count(tmp->m_id) != 0)
                 {
                     tmp->m_label =  m_mesh->m_faceLabels[tmp->m_id];
                 }
 
                 testIns  = m_mesh->m_composite.insert(
                     pair<unsigned int, CompositeSharedPtr>(tagid,tmp));
                 it       = testIns.first;
             }
 
             if (elmt[i]->GetTag() != it->second->m_tag)
             {
                 cout << "Different types of elements in same composite!" << endl;
                 cout << " -> Composite uses " << it->second->m_tag << endl;
                 cout << " -> Element uses   " << elmt[i]->GetTag() << endl;
                 cout << "Have you specified physical volumes and surfaces?" << endl;
             }
             it->second->m_items.push_back(elmt[i]);
         }
     }
 }

void Nektar::NekMeshUtils::Module::ProcessEdges ( bool ReprocessEdges = true )

virtual

Extract element edges.

Create a unique set of mesh edges from elements stored in Mesh::element.

All elements are first scanned and a list of unique, enumerated edges produced in #m_edgeSet. Since each element generated its edges independently, we must now ensure that each element only uses edge objects from the #m_edgeSet set This ensures there are no duplicate edge objects. Finally, we scan the list of elements for 1-D boundary elements which correspond to an edge in #m_edgeSet. For such elements, we set its edgeLink to reference the corresponding edge in #m_edgeSet.

This routine only proceeds if the expansion dimension is 2 or 3.

Definition at line 178 of file NekMeshUtils/Module/Module.cpp.

References Nektar::iterator, and m_mesh.

 {
     if (m_mesh->m_expDim < 2) return;
 
     if(ReprocessEdges)
     {
         vector<ElementSharedPtr> &elmt = m_mesh->m_element[m_mesh->m_expDim];
 
         m_mesh->m_edgeSet.clear();
 
         // Clear all edge links
 
         // Scan all elements and generate list of unique edges
         for (int i = 0, eid = 0; i < elmt.size(); ++i)
         {
             for (int j = 0; j < elmt[i]->GetEdgeCount(); ++j)
             {
                 pair<EdgeSet::iterator,bool> testIns;
                 EdgeSharedPtr ed = elmt[i]->GetEdge(j);
                 testIns = m_mesh->m_edgeSet.insert(ed);
 
                 if (testIns.second)
                 {
                     EdgeSharedPtr ed2 = *testIns.first;
                     ed2->m_id = eid++;
                     ed2->m_elLink.push_back(
                         pair<ElementSharedPtr,int>(elmt[i],j));
                 }
                 else
                 {
                     EdgeSharedPtr e2 = *(testIns.first);
                     elmt[i]->SetEdge(j, e2);
                     if (e2->m_edgeNodes.size() == 0 &&
                         ed->m_edgeNodes.size() > 0)
                     {
                         e2->m_curveType = ed->m_curveType;
                         e2->m_edgeNodes = ed->m_edgeNodes;
 
                         // Reverse nodes if appropriate.
                         if (e2->m_n1->m_id != ed->m_n1->m_id)
                         {
                             reverse(e2->m_edgeNodes.begin(),
                                     e2->m_edgeNodes.end());
                         }
                     }
 
                     e2->m_parentCAD = ed->m_parentCAD;
 
                     // Update edge to element map.
                     e2->m_elLink.push_back(
                         pair<ElementSharedPtr,int>(elmt[i],j));
                 }
             }
         }
     }
 
     // Create links for 1D elements
     for (int i = 0; i < m_mesh->m_element[1].size(); ++i)
     {
         ElementSharedPtr elmt = m_mesh->m_element[1][i];
         NodeSharedPtr v0 = elmt->GetVertex(0);
         NodeSharedPtr v1 = elmt->GetVertex(1);
         vector<NodeSharedPtr> edgeNodes;
         EdgeSharedPtr E = boost::shared_ptr<Edge>(
             new Edge(v0, v1, edgeNodes, elmt->GetConf().m_edgeCurveType));
 
         EdgeSet::iterator it = m_mesh->m_edgeSet.find(E);
         if (it == m_mesh->m_edgeSet.end())
         {
             cerr << "Cannot find corresponding element edge for "
                  << "1D element " << i << endl;
             abort();
         }
         elmt->SetEdgeLink(*it);
 
         // Update 2D element boundary map.
         pair<ElementSharedPtr, int> eMap = (*it)->m_elLink.at(0);
         eMap.first->SetBoundaryLink(eMap.second, i);
 
         // Update vertices
         elmt->SetVertex(0, (*it)->m_n1, false);
         elmt->SetVertex(1, (*it)->m_n2, false);
 
         // Copy curvature to edge.
         if ((*it)->m_edgeNodes.size() > 0)
         {
             ElementSharedPtr edge = elmt;
             if (edge->GetVertex(0) == (*it)->m_n1)
             {
                 edge->SetVolumeNodes((*it)->m_edgeNodes);
             }
             elmt->SetCurveType((*it)->m_curveType);
         }
     }
 }

void Nektar::NekMeshUtils::Module::ProcessElements ( )

virtual

Generate element IDs.

Enumerate elements stored in Mesh::element.

For all elements of equal dimension to the mesh dimension, we enumerate sequentially. All other elements in the list should be of lower dimension and have ID set by a corresponding edgeLink or faceLink (as set in ProcessEdges or ProcessFaces).

Definition at line 386 of file NekMeshUtils/Module/Module.cpp.

References m_mesh.

 {
     int cnt = 0;
     for (int i = 0; i < m_mesh->m_element[m_mesh->m_expDim].size(); ++i)
     {
         m_mesh->m_element[m_mesh->m_expDim][i]->SetId(cnt++);
     }
 }

void Nektar::NekMeshUtils::Module::ProcessFaces ( bool ReprocessFaces = true )

virtual

Extract element faces.

Create a unique set of mesh faces from elements stored in Mesh::element.

All elements are scanned and a unique list of enumerated faces is produced in #m_faceSet. Since elements created their own faces independently, we examine each element only uses face objects from #m_faceSet. Duplicate faces of those in #m_face are replaced with the corresponding entry in #m_faceSet. Finally, we scan the list of elements for 2-D boundary faces which correspond to faces in #m_faceSet. For such elements, we set its faceLink to reference the corresponding face in #m_faceSet.

This routine only proceeds if the expansion dimension is 3.

Definition at line 290 of file NekMeshUtils/Module/Module.cpp.

References Nektar::iterator, and m_mesh.

 {
     if (m_mesh->m_expDim < 3) return;
 
     if(ReprocessFaces)
     {
         vector<ElementSharedPtr> &elmt = m_mesh->m_element[m_mesh->m_expDim];
 
         m_mesh->m_faceSet.clear();
 
         // Scan all elements and generate list of unique faces
         for (int i = 0, fid = 0; i < elmt.size(); ++i)
         {
             for (int j = 0; j < elmt[i]->GetFaceCount(); ++j)
             {
                 pair<FaceSet::iterator,bool> testIns;
                 testIns = m_mesh->m_faceSet.insert(elmt[i]->GetFace(j));
 
                 if (testIns.second)
                 {
                     (*(testIns.first))->m_id = fid++;
                     (*(testIns.first))->m_elLink.push_back(
                         pair<ElementSharedPtr,int>(elmt[i],j));
                 }
                 else
                 {
                     elmt[i]->SetFace(j,*testIns.first);
                     // Update face to element map.
                     (*(testIns.first))->m_elLink.push_back(
                         pair<ElementSharedPtr,int>(elmt[i],j));
                 }
             }
         }
     }
 
     // Create links for 2D elements
     for (int i = 0; i < m_mesh->m_element[2].size(); ++i)
     {
         ElementSharedPtr elmt = m_mesh->m_element[2][i];
         vector<NodeSharedPtr> vertices = elmt->GetVertexList();
         vector<NodeSharedPtr> faceNodes;
         vector<EdgeSharedPtr> edgeList = elmt->GetEdgeList();
         FaceSharedPtr F = boost::shared_ptr<Face>(
             new Face(vertices, faceNodes, edgeList,
                      elmt->GetConf().m_faceCurveType));
 
         FaceSet::iterator it = m_mesh->m_faceSet.find(F);
         if (it == m_mesh->m_faceSet.end())
         {
             cout << "Cannot find corresponding element face for 2D "
                  << "element " << i << endl;
             abort();
         }
 
         elmt->SetFaceLink(*it);
 
         // Set edges/vertices
         for (int j = 0; j < elmt->GetVertexCount(); ++j)
         {
             elmt->SetVertex(j, (*it)->m_vertexList[j], false);
             elmt->SetEdge(j, (*it)->m_edgeList[j], false);
         }
 
         EdgeSet tmp(edgeList.begin(),edgeList.end());
 
         for (int j = 0; j < elmt->GetEdgeCount(); ++j)
         {
             EdgeSharedPtr e = elmt->GetEdge(j);
             EdgeSet::iterator f = tmp.find(e);
             if(f != tmp.end())
             {
                 e->m_parentCAD = (*f)->m_parentCAD;
             }
         }
 
         // Update 3D element boundary map.
         pair<ElementSharedPtr, int> eMap = (*it)->m_elLink.at(0);
         eMap.first->SetBoundaryLink(eMap.second, i);
 
         // Copy face curvature
         if ((*it)->m_faceNodes.size() > 0)
         {
             elmt->SetVolumeNodes((*it)->m_faceNodes);
             elmt->SetCurveType((*it)->m_curveType);
         }
     }
 }

void Nektar::NekMeshUtils::Module::ProcessVertices ( )

virtual

Extract element vertices.

Create a unique set of mesh vertices from elements stored in Mesh::element.

Each element is processed in turn and the vertices extracted and inserted into #m_vertexSet, which at the end of the routine contains all unique vertices in the mesh.

Definition at line 138 of file NekMeshUtils/Module/Module.cpp.

References m_mesh.

 {
     vector<ElementSharedPtr> &elmt = m_mesh->m_element[m_mesh->m_expDim];
 
     m_mesh->m_vertexSet.clear();
 
     for (int i = 0, vid = 0; i < elmt.size(); ++i)
     {
         for (int j = 0; j < elmt[i]->GetVertexCount(); ++j)
         {
             pair<NodeSet::iterator,bool> testIns =
                 m_mesh->m_vertexSet.insert(elmt[i]->GetVertex(j));
 
             if (testIns.second)
             {
                 (*(testIns.first))->m_id = vid++;
             }
             else
             {
                 elmt[i]->SetVertex(j,*testIns.first);
             }
         }
     }
 }

void Nektar::NekMeshUtils::Module::RegisterConfig	(	std::string	key,
		std::string	value
	)

Register a configuration option with a module.

Definition at line 844 of file NekMeshUtils/Module/Module.cpp.

References Nektar::iterator, and m_config.

 {
     map<string, ConfigOption>::iterator it = m_config.find(key);
     if (it == m_config.end())
     {
         cerr << "WARNING: Unrecognised config option " << key
              << ", proceeding anyway." << endl;
     }
 
     it->second.beenSet = true;
 
     if (it->second.isBool)
     {
         it->second.value = "1";
     }
     else
     {
         it->second.value = val;
     }
 }

void Nektar::NekMeshUtils::Module::ReorderPrisms ( PerMap & perFaces )

protected

Reorder node IDs so that prisms and tetrahedra are aligned correctly.

Orientation of prism lines (i.e. a large prism which has been split into subprisms) cannot be guaranteed when elements are created one-by-one, or when periodic boundary conditions are used. This routine uses the following strategy:

Destroy the existing node numbering.
Detect a line of prisms using the PrismLines routine.
For each line, renumber node IDs consistently so that highest ID per-element corresponds to the line of collapsed coordinate points.
Recreate each prism in the line using the new ordering, and apply the existing OrientPrism routine to orient nodes accordingly.
When all prism lines are processed, recreate all tetrahedra using the existing orientation code.
Finally renumber any other nodes (i.e. those belonging to hexahedra).

The last step is to eliminate duplicate edges/faces and reenumerate.

NOTE: This routine does not copy face-interior high-order information yet!

Definition at line 497 of file NekMeshUtils/Module/Module.cpp.

References ASSERTL0, ASSERTL1, Nektar::LibUtilities::NekFactory< tKey, tBase, >::CreateInstance(), Nektar::LibUtilities::ePrism, Nektar::LibUtilities::eTetrahedron, Nektar::NekMeshUtils::GetElementFactory(), Nektar::iterator, m_mesh, PrismLines(), ProcessEdges(), ProcessElements(), and ProcessFaces().

Referenced by Nektar::Utilities::ProcessPerAlign::Process().

 {
     // Loop over elements and extract any that are prisms.
     int i, j, k;
 
     if (m_mesh->m_expDim < 3)
     {
         return;
     }
 
     map<int, int>    lines;
     set<int>         prismsDone, tetsDone;
     PerMap::iterator pIt;
 
     // Compile list of prisms and tets.
     for (i = 0; i < m_mesh->m_element[3].size(); ++i)
     {
         ElementSharedPtr el = m_mesh->m_element[3][i];
 
         if (el->GetConf().m_e == LibUtilities::ePrism)
         {
             prismsDone.insert(i);
         }
         else if (el->GetConf().m_e == LibUtilities::eTetrahedron)
         {
             tetsDone.insert(i);
         }
     }
 
     // Destroy existing node numbering.
     NodeSet::iterator it;
     for (it = m_mesh->m_vertexSet.begin(); it != m_mesh->m_vertexSet.end(); ++it)
     {
         (*it)->m_id = -1;
     }
 
     // Counter for new node IDs.
     int nodeId = 0;
     int prismTris[2][3] = {{0,1,4}, {3,2,5}};
 
     // Warning flag for high-order curvature information.
     bool warnCurvature = false;
 
     // facesDone tracks face IDs inside prisms which have already been
     // aligned.
     boost::unordered_set<int> facesDone;
     boost::unordered_set<int>::iterator fIt[2], fIt2;
 
     // Loop over prisms until we've found all lines of prisms.
     while (prismsDone.size() > 0)
     {
         vector<ElementSharedPtr> line;
 
         // Call PrismLines to identify all prisms connected to
         // prismDone.begin() and place them in line[].
         PrismLines(*prismsDone.begin(), perFaces, prismsDone, line);
 
         // Loop over each prism, figure out which line of vertices
         // contains the vertex with highest ID.
         for (i = 0; i < line.size(); ++i)
         {
             // Copy tags and nodes from existing element.
             vector<int>           tags  = line[i]->GetTagList();
             vector<NodeSharedPtr> nodes = line[i]->GetVertexList();
 
             // See if either face of this prism has been renumbered
             // already.
             FaceSharedPtr f[2] = {
                 line[i]->GetFace(1), line[i]->GetFace(3)
             };
 
             fIt[0] = facesDone.find(f[0]->m_id);
             fIt[1] = facesDone.find(f[1]->m_id);
 
             // See if either of these faces is periodic. If it is, then
             // assign ids accordingly.
             for (j = 0; j < 2; ++j)
             {
                 pIt = perFaces.find(f[j]->m_id);
 
                 if (pIt == perFaces.end())
                 {
                     continue;
                 }
 
                 fIt2 = facesDone.find(pIt->second.first->m_id);
 
                 if (fIt[j] == facesDone.end() &&
                     fIt2   != facesDone.end())
                 {
                     fIt[j] = fIt2;
                 }
             }
 
             if (fIt[0] != facesDone.end() &&
                 fIt[1] != facesDone.end())
             {
                 // Should not be the case that both faces have already
                 // been renumbered.
                 ASSERTL0(false, "Renumbering error!");
             }
             else if (fIt[0] == facesDone.end() &&
                      fIt[1] == facesDone.end())
             {
                 // Renumber both faces.
                 for (j = 0; j < 2; ++j)
                 {
                     for (k = 0; k < 3; ++k)
                     {
                         NodeSharedPtr n = nodes[prismTris[j][k]];
                         if (n->m_id == -1)
                         {
                             n->m_id = nodeId++;
                         }
                     }
                 }
 
                 facesDone.insert(f[0]->m_id);
                 facesDone.insert(f[1]->m_id);
             }
             else
             {
                 // Renumber face. t identifies the face not yet
                 // numbered, o identifies the other face.
                 int t = fIt[0] == facesDone.end() ? 0 : 1;
                 int o = (t+1) % 2;
                 ASSERTL1(fIt[o] != facesDone.end(),"Renumbering error");
 
                 // Determine which of the three vertices on the 'other'
                 // face corresponds to the highest ID - this signifies
                 // the singular point of the line of prisms.
                 int tmp1[3] = {
                     nodes[prismTris[o][0]]->m_id,
                     nodes[prismTris[o][1]]->m_id,
                     nodes[prismTris[o][2]]->m_id
                 };
                 int tmp2[3] = {0,1,2};
 
                 if (tmp1[0] > tmp1[1])
                 {
                     swap(tmp1[0], tmp1[1]);
                     swap(tmp2[0], tmp2[1]);
                 }
 
                 if (tmp1[1] > tmp1[2])
                 {
                     swap(tmp1[1], tmp1[2]);
                     swap(tmp2[1], tmp2[2]);
                 }
 
                 if (tmp1[0] > tmp1[2])
                 {
                     swap(tmp1[0], tmp1[2]);
                     swap(tmp2[0], tmp2[2]);
                 }
 
                 // Renumber this face so that highest ID matches.
                 for (j = 0; j < 3; ++j)
                 {
                     NodeSharedPtr n = nodes[prismTris[t][tmp2[j]]];
                     if (n->m_id == -1)
                     {
                         n->m_id = nodeId++;
                     }
                 }
 
                 facesDone.insert(f[t]->m_id);
             }
 
             for (j = 0; j < 6; ++j)
             {
                 ASSERTL1(nodes[j]->m_id != -1, "Renumbering error");
             }
 
             // Recreate prism with the new ordering.
             ElmtConfig conf(LibUtilities::ePrism, 1, false, false, true);
             ElementSharedPtr el = GetElementFactory().CreateInstance(
                 LibUtilities::ePrism, conf, nodes, tags);
 
             // Now transfer high-order information back into
             // place. TODO: Face curvature.
             for (j = 0; j < 9; ++j)
             {
                 EdgeSharedPtr e1 = line[i]->GetEdge(j);
                 for (k = 0; k < 9; ++k)
                 {
                     EdgeSharedPtr e2 = el->GetEdge(k);
                     if (e1->m_n1 == e2->m_n1 && e1->m_n2 == e2->m_n2)
                     {
                         e2->m_edgeNodes = e1->m_edgeNodes;
                     }
                     else if (e1->m_n1 == e2->m_n1 && e1->m_n2 == e2->m_n2)
                     {
                         e2->m_edgeNodes = e1->m_edgeNodes;
                         std::reverse(e2->m_edgeNodes.begin(),
                                      e2->m_edgeNodes.end());
                     }
                 }
             }
 
             // Warn users that we're throwing away face curvature
             if (!warnCurvature)
             {
                 for (j = 0; j < 5; ++j)
                 {
                     if (line[i]->GetFace(j)->m_faceNodes.size() > 0)
                     {
                         warnCurvature = true;
                         break;
                     }
                 }
             }
 
             // Replace old prism.
             m_mesh->m_element[3][line[i]->GetId()] = el;
         }
     }
 
     if (warnCurvature)
     {
         cerr << "[ReorderPrisms] WARNING: Face curvature detected in "
              << "some prisms; this will be ignored in further module "
              << "evaluations."
              << endl;
     }
 
     // Loop over periodic faces, enumerate vertices.
     for (pIt = perFaces.begin(); pIt != perFaces.end(); ++pIt)
     {
         FaceSharedPtr f2       = pIt->second.first;
         FaceSharedPtr f1       = perFaces[f2->m_id].first;
         vector<int>   perVerts = pIt->second.second;
         int           nVerts   = perVerts.size();
 
         // Number periodic vertices first.
         for (j = 0; j < nVerts; ++j)
         {
             NodeSharedPtr n1 = f1->m_vertexList[j];
             NodeSharedPtr n2 = f2->m_vertexList[perVerts[j]];
 
             if (n1->m_id == -1 && n2->m_id == -1)
             {
                 n1->m_id = nodeId++;
                 n2->m_id = nodeId++;
             }
             else if (n1->m_id != -1 && n2->m_id != -1)
             {
                 continue;
             }
             else
             {
                 ASSERTL0(false, "Periodic face renumbering error");
             }
         }
     }
 
     // Recreate tets.
     set<int>::iterator it2;
     for (it2 = tetsDone.begin(); it2 != tetsDone.end(); ++it2)
     {
         ElementSharedPtr el = m_mesh->m_element[3][*it2];
         vector<NodeSharedPtr> nodes = el->GetVertexList();
         vector<int> tags = el->GetTagList();
 
         for (i = 0; i < 4; ++i)
         {
             if (nodes[i]->m_id == -1)
             {
                 nodes[i]->m_id = nodeId++;
             }
         }
 
         // Recreate tet.
         ElmtConfig conf(LibUtilities::eTetrahedron, 1, false, false, true);
         m_mesh->m_element[3][*it2] = GetElementFactory().CreateInstance(
             LibUtilities::eTetrahedron, conf, nodes, tags);
     }
 
     // Enumerate rest of vertices.
     for (it = m_mesh->m_vertexSet.begin(); it != m_mesh->m_vertexSet.end(); ++it)
     {
         if ((*it)->m_id == -1)
         {
             (*it)->m_id = nodeId++;
         }
     }
 
     ProcessEdges   ();
     ProcessFaces   ();
     ProcessElements();
 }

void Nektar::NekMeshUtils::Module::SetDefaults ( )

Sets default configuration options for those which have not been set.

Definition at line 889 of file NekMeshUtils/Module/Module.cpp.

References Nektar::iterator, and m_config.

 {
     map<string, ConfigOption>::iterator it;
 
     for (it = m_config.begin(); it != m_config.end(); ++it)
     {
         if (!it->second.beenSet)
         {
             it->second.value = it->second.defValue;
         }
     }
 }

Member Data Documentation

std::map<std::string, ConfigOption> Nektar::NekMeshUtils::Module::m_config

protected

List of configuration values.

Definition at line 188 of file NekMeshUtils/Module/Module.h.

MeshSharedPtr Nektar::NekMeshUtils::Module::m_mesh

protected

Mesh object.

Definition at line 186 of file NekMeshUtils/Module/Module.h.

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation