Nektar::Utilities::ProcessExtractSurf Class Reference

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:

Collaboration diagram for Nektar::Utilities::ProcessExtractSurf:

Public Member Functions
	ProcessExtractSurf (MeshSharedPtr m)
virtual	~ProcessExtractSurf ()
virtual void	Process ()
	Write mesh to output file.
Public Member Functions inherited from Nektar::Utilities::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.
void	PrintConfig ()
	Print out all configuration options for a module.
void	SetDefaults ()
	Sets default configuration options for those which have not been set.
bool	GetRequireEquiSpaced (void)
void	SetRequireEquiSpaced (bool pVal)
	Module (MeshSharedPtr p_m)
void	RegisterConfig (string key, string value)
void	PrintConfig ()
void	SetDefaults ()
MeshSharedPtr	GetMesh ()
virtual void	ProcessVertices ()
	Extract element vertices.

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

Static Public Attributes
static ModuleKey	className

Additional Inherited Members
Protected Member Functions inherited from Nektar::Utilities::Module
virtual void	ProcessEdges (bool ReprocessEdges=true)
	Extract element edges.
virtual void	ProcessFaces (bool ReprocessFaces=true)
	Extract element faces.
virtual void	ProcessElements ()
	Generate element IDs.
virtual void	ProcessComposites ()
	Generate composites.
void	ReorderPrisms (PerMap &perFaces)
	Reorder node IDs so that prisms and tetrahedra are aligned correctly.
void	PrismLines (int prism, PerMap &perFaces, set< int > &prismsDone, vector< ElementSharedPtr > &line)
Protected Attributes inherited from Nektar::Utilities::Module
FieldSharedPtr	m_f
	Field object.
map< string, ConfigOption >	m_config
	List of configuration values.
bool	m_requireEquiSpaced
MeshSharedPtr	m_mesh
	Mesh object.

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.

        {
        }

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.

                                                                   {
                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.