This processing module calculates the Jacobian of elements using SpatialDomains::GeomFactors and the Element::GetGeom method. For now it simply prints a list of elements which have negative Jacobian. More...

#include <ProcessExtractSurf.h>

Inheritance diagram for Nektar::Utilities::ProcessExtractSurf:

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Collaboration diagram for Nektar::Utilities::ProcessExtractSurf:

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Public Member Functions
	ProcessExtractSurf (MeshSharedPtr m)

virtual	~ProcessExtractSurf ()

virtual void	Process ()
	Write mesh to output file. More...

Public Member Functions inherited from Nektar::Utilities::ProcessModule
	ProcessModule ()

	ProcessModule (FieldSharedPtr p_f)

	ProcessModule (MeshSharedPtr p_m)

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 boost::shared_ptr< Module >	create (MeshSharedPtr m)
	Creates an instance of this class. More...

Static Public Attributes
static ModuleKey	className

Additional Inherited Members
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::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

This processing module calculates the Jacobian of elements using SpatialDomains::GeomFactors and the Element::GetGeom method. For now it simply prints a list of elements which have negative Jacobian.

Definition at line 51 of file ProcessExtractSurf.h.

Constructor & Destructor Documentation

Nektar::Utilities::ProcessExtractSurf::ProcessExtractSurf ( MeshSharedPtr m )

Definition at line 54 of file ProcessExtractSurf.cpp.

References Nektar::Utilities::Module::m_config.

                                                               : ProcessModule(m)
         {
             m_config["surf"] = ConfigOption(false, "-1",
                 "Tag identifying surface/composite to process.");
         }

Nektar::Utilities::ProcessExtractSurf::~ProcessExtractSurf ( )

virtual

Definition at line 60 of file ProcessExtractSurf.cpp.

61 {

62 }

Member Function Documentation

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

inlinestatic

Creates an instance of this class.

Definition at line 55 of file ProcessExtractSurf.h.

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

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

void Nektar::Utilities::ProcessExtractSurf::Process ( )

virtual

Write mesh to output file.

Implements Nektar::Utilities::Module.

Definition at line 64 of file ProcessExtractSurf.cpp.

References Nektar::ParseUtils::GenerateSeqVector(), Nektar::iterator, Nektar::Utilities::Module::m_config, and Nektar::Utilities::Module::m_mesh.

         {
             int i, j;
             string surf = m_config["surf"].as<string>();
 
             // Obtain vector of surface IDs from string.
             vector<unsigned int> surfs;
             ParseUtils::GenerateSeqVector(surf.c_str(), surfs);
             sort(surfs.begin(), surfs.end());
 
             // If we're running in verbose mode print out a list of surfaces.
             if (m_mesh->m_verbose)
             {
                 cout << "ProcessExtractSurf: extracting surface"
                      << (surfs.size() > 1 ? "s" : "") << " " << surf << endl;
             }
 
             // Make a copy of all existing elements of one dimension lower.
             vector<ElementSharedPtr> el = m_mesh->m_element[m_mesh->m_expDim-1];
 
             // Clear all elements.
             m_mesh->m_element[m_mesh->m_expDim]  .clear();
             m_mesh->m_element[m_mesh->m_expDim-1].clear();
 
             // Clear existing vertices, edges and faces.
             m_mesh->m_vertexSet.clear();
             m_mesh->m_edgeSet.clear();
             m_mesh->m_faceSet.clear();
 
             // Clear all edge -> element links.
             for (i = 0; i < el.size(); ++i)
             {
                 vector<EdgeSharedPtr> edges = el[i]->GetEdgeList();
                 for (j = 0; j < edges.size(); ++j)
                 {
                     edges[j]->m_elLink.clear();
                 }
 
                 FaceSharedPtr f = el[i]->GetFaceLink();
                 if (f)
                 {
                     for (j = 0; j < f->m_edgeList.size(); ++j)
                     {
                         f->m_edgeList[j]->m_elLink.clear();
                     }
                 }
             }
 
             // keptIds stores IDs of elements we processed earlier.
             boost::unordered_set<int> keptIds;
 
             // Iterate over list of surface elements.
             for (i = 0; i < el.size(); ++i)
             {
                 // Work out whether this lies on our surface of interest.
                 vector<int> inter, tags = el[i]->GetTagList();
 
                 sort(tags.begin(), tags.end());
                 set_intersection(surfs.begin(), surfs.end(),
                                  tags .begin(), tags .end(),
                                  back_inserter(inter));
                 
                 // It doesn't continue to next element.
                 if (inter.size() != 1)
                 {
                     continue;
                 }
 
                 // Get list of element vertices and edges.
                 ElementSharedPtr      elmt  = el[i];
                 vector<NodeSharedPtr> verts = elmt->GetVertexList();
                 vector<EdgeSharedPtr> edges = elmt->GetEdgeList();
 
                 // Insert surface vertices.
                 for (j = 0; j < verts.size(); ++j)
                 {
                     m_mesh->m_vertexSet.insert(verts[j]);
                 }
 
                 // Problem: edges and element IDs aren't enumerated with
                 // geometry IDs by some input modules/the Module ProcessEdges
                 // function. Get around this by replacing everything in the
                 // edge/face with information from edge/face link.
                 EdgeSharedPtr e = elmt->GetEdgeLink();
                 FaceSharedPtr f = elmt->GetFaceLink();
                 if (e)
                 {
                     elmt->SetId(e->m_id);
                 }
                 else if (f)
                 {
                     for (j = 0; j < edges.size(); ++j)
                     {
                         m_mesh->m_edgeSet.insert(f->m_edgeList[j]);
                         elmt->SetEdge(j, f->m_edgeList[j]);
                         f->m_edgeList[j]->m_elLink.push_back(
                             std::make_pair(elmt, j));
                     }
                     elmt->SetId(f->m_id);
                 }
                 else
                 {
                     for (j = 0; j < edges.size(); ++j)
                     {
                         m_mesh->m_edgeSet.insert(edges[j]);
                     }
                 }
 
                 // Nullify edge/face links to get correct tag
                 elmt->SetFaceLink(FaceSharedPtr());
                 elmt->SetEdgeLink(EdgeSharedPtr());
                 keptIds.insert(elmt->GetId());
 
                 // Push element back into the list.
                 m_mesh->m_element[m_mesh->m_expDim-1].push_back(elmt);
             }
 
             // Decrement the expansion dimension to get manifold embedding.
             m_mesh->m_expDim--;
 
             // Now process composites. This is necessary because 2D surfaces may
             // contain both quadrilaterals and triangles and so need to be split
             // up.
             CompositeMap tmp = m_mesh->m_composite;
             CompositeMap::iterator it;
             
             m_mesh->m_composite.clear();
             int maxId = -1;
 
             // Loop over composites for first time to determine any composites
             // which don't have elements of the correct dimension.
             for (it = tmp.begin(); it != tmp.end(); ++it)
             {
                 if (it->second->m_items[0]->GetDim() != m_mesh->m_expDim)
                 {
                     continue;
                 }
 
                 vector<ElementSharedPtr> el = it->second->m_items;
                 it->second->m_items.clear();
 
                 for (i = 0; i < el.size(); ++i)
                 {
                     if (keptIds.count(el[i]->GetId()) > 0)
                     {
                         it->second->m_items.push_back(el[i]);
                     }
                 }
 
                 if (it->second->m_items.size() == 0)
                 {
                     continue;
                 }
 
                 m_mesh->m_composite.insert(*it);
 
                 // Figure out the maximum ID so if we need to create new
                 // composites we can give them a unique ID.
                 maxId = (std::max)(maxId, (int)it->second->m_id) + 1;
             }
 
             tmp = m_mesh->m_composite;
             m_mesh->m_composite.clear();
             map<string, CompositeSharedPtr>::iterator it2;
 
             // Now do another loop over the composites to remove composites
             // which don't contain any elements in the new mesh.
             for (it = tmp.begin(); it != tmp.end(); ++it)
             {
                 CompositeSharedPtr c = it->second;
                 vector<ElementSharedPtr> el = c->m_items;
 
                 // Remove all but the first element from this composite.
                 string initialTag = el[0]->GetTag();
                 c->m_items.resize(1);
                 c->m_tag = initialTag;
 
                 // newComps stores the new composites. The key is the composite
                 // type (e.g. Q for quad) and value is the composite.
                 map<string, CompositeSharedPtr> newComps;
                 newComps[initialTag] = c;
 
                 // Loop over remaining elements in composite and figure out
                 // whether it needs to be split up.
                 for (i = 1; i < el.size(); ++i)
                 {
                     // See if tag exists. If it does, we append this to the
                     // composite, otherwise we create a new composite and store
                     // it in newComps.
                     string tag = el[i]->GetTag();
                     it2 = newComps.find(tag);
                     if (it2 == newComps.end())
                     {
                         CompositeSharedPtr newComp(new Composite());
                         newComp->m_id  = maxId++;
                         newComp->m_tag = tag;
                         newComp->m_items.push_back(el[i]);
                         newComps[tag] = newComp;
                     }
                     else
                     {
                         it2->second->m_items.push_back(el[i]);
                     }
                 }
 
                 // Print out mapping information if we remapped composite IDs.
                 if (m_mesh->m_verbose && newComps.size() > 1)
                 {
                     cout << "- Mapping composite " << it->first << " ->";
                 }
 
                 // Insert new composites.
                 for (i = 0, it2 = newComps.begin(); it2 != newComps.end();
                      ++it2, ++i)
                 {
                     if (m_mesh->m_verbose && newComps.size() > 1)
                     {
                         cout << (i > 0 ? ", " : " ") << it2->second->m_id << "("
                              << it2->second->m_tag << ")";
                     }
                     m_mesh->m_composite[it2->second->m_id] = it2->second;
                 }
 
                 if (m_mesh->m_verbose && newComps.size() > 1)
                 {
                     cout << endl;
                 }
             }
         }

Member Data Documentation

ModuleKey Nektar::Utilities::ProcessExtractSurf::className

static

Initial value:

= 
            GetModuleFactory().RegisterCreatorFunction(
                ModuleKey(eProcessModule, "extract"), ProcessExtractSurf::create,
                "Process elements to extract a specified surface(s) or composites(s).")

Definition at line 58 of file ProcessExtractSurf.h.

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation