ExpandMeshByRotation.cpp File Reference

#include <LibUtilities/BasicConst/NektarUnivTypeDefs.hpp>
#include <LibUtilities/BasicUtils/ParseUtils.hpp>
#include <LibUtilities/BasicUtils/SessionReader.h>
#include <SpatialDomains/MeshGraph.h>
#include <cstdio>
#include <cstdlib>
#include <sstream>
#include <map>
#include <iomanip>
#include <tinyxml.h>

Include dependency graph for ExpandMeshByRotation.cpp:

Go to the source code of this file.

Functions
void	ExpandVertices (TiXmlElement *mesh, map< int, int > jointVerts, map< int, int > &fullVerts)
void	ExpandEdges (TiXmlElement *mesh, map< int, int > &newVerts, map< int, int > jointEdges, map< int, int > &newEdges)
void	ExpandElmts (TiXmlElement *mesh, map< int, int > &newEdges, int &nOrigElmts)
void	ExpandComposites (TiXmlElement *mesh, map< int, int > fullEdges, int nOrigElmts)
int	main (int argc, char *argv[])
string	GetXmlString (char tag, vector< unsigned int > &ids)

Function Documentation

void ExpandComposites	(	TiXmlElement *	mesh,
		map< int, int >	fullEdges,
		int	nOrigElmts
	)

All elements are of the form: "<C ID = "N"> ... </C>". Read the ID field first.

Parse out the element components corresponding to type of element.

Keep looking

Definition at line 473 of file ExpandMeshByRotation.cpp.

References ASSERTL0, ErrorUtil::efatal, GetXmlString(), Nektar::iterator, and NEKERROR.

Referenced by main().

{
    TiXmlElement* field = mesh->FirstChildElement("COMPOSITE");
    ASSERTL0(field, "Unable to find COMPOSITE tag in file.");

    int nextCompositeNumber = -1;

    /// All elements are of the form: "<C ID = "N"> ... </C>".
    /// Read the ID field first.
    TiXmlElement *composite = field->FirstChildElement("C");

    while (composite)
    {
        nextCompositeNumber++;
        
        int indx;
        int err = composite->QueryIntAttribute("ID", &indx);
        ASSERTL0(err == TIXML_SUCCESS, "Unable to read attribute ID.");
        
        TiXmlNode* compositeChild = composite->FirstChild();
        // This is primarily to skip comments that may be present.
        // Comments appear as nodes just like elements.
        // We are specifically looking for text in the body
        // of the definition.
        while(compositeChild && compositeChild->Type() != TiXmlNode::TINYXML_TEXT)
        {
            compositeChild = compositeChild->NextSibling();
        }
        
        ASSERTL0(compositeChild, "Unable to read composite definition body.");
        std::string compositeStr = compositeChild->ToText()->ValueStr();
        
        /// Parse out the element components corresponding to type of element.
        std::istringstream compositeDataStrm(compositeStr.c_str());


        try
        {

            std::string compositeElementStr;
            compositeDataStrm >> compositeElementStr;
            
            std::istringstream tokenStream(compositeElementStr);
            char type;
            
            tokenStream >> type;
            
            // in what follows we are assuming there is only one block of data 
            std::string::size_type indxBeg = compositeElementStr.find_first_of('[') + 1;
            std::string::size_type indxEnd = compositeElementStr.find_last_of(']') - 1;
        
            ASSERTL0(indxBeg <= indxEnd, (std::string("Error reading index definition:") +  compositeElementStr).c_str());
            
            std::string indxStr = compositeElementStr.substr(indxBeg, indxEnd - indxBeg + 1);
            std::vector<unsigned int> seqVector;
            std::vector<unsigned int>::iterator seqIter;
            
            bool err = ParseUtils::GenerateSeqVector(indxStr.c_str(), seqVector);
            
            ASSERTL0(err, (std::string("Error reading composite elements: ") + indxStr).c_str());
            
            switch(type)
            {
            case 'E':   // Expand edges using newEdges map and known values
                {
                    int seqlen = seqVector.size();
                    int nedges = newEdges.size();
                    
                    map<unsigned int, unsigned int> seqMap;
                    
                    for(int i =0; i < seqlen; ++i) // set up a map of defined edges
                    {
                        seqMap[seqVector[i]] = 1;
                    }
                         
                    // if edge does not exist in composite add it to the list 
                    for(int i =0; i < seqlen; ++i)
                    {
                        if(seqMap.count(newEdges[seqVector[i]+nedges]) == 0)
                        {
                            seqVector.push_back(newEdges[seqVector[i]+nedges]);
                        }                        
                    }
                }
                break;
                
                case 'T':  case 'Q':  // Expand Triangles & Quads with new elements
                {
                    int seqlen = seqVector.size();
                    
                    for(int i = 0; i < seqlen; ++i)
                    {
                        seqVector.push_back(seqVector[i]+nOrigElmts);
                    }
                    
                    break;
                }
            default:
                NEKERROR(ErrorUtil::efatal, (std::string("Unrecognized composite token: ") + compositeElementStr).c_str());
            }
            
            // now redefine string in composite
            
            
            composite->ReplaceChild(compositeChild, TiXmlText(GetXmlString(type,seqVector)));
            

        }
        catch(...)
        {
            NEKERROR(ErrorUtil::efatal,
                     (std::string("Unable to read COMPOSITE data for composite: ") + compositeStr).c_str());
        }
        
        /// Keep looking
        composite = composite->NextSiblingElement("C");
    }
}

void ExpandEdges	(	TiXmlElement *	mesh,
		map< int, int > &	newVerts,
		map< int, int >	jointEdges,
		map< int, int > &	newEdges
	)

Look for elements in ELEMENT block.

All elements are of the form: "<E ID="#"> ... </E>", with ? being the element type. Read the ID field first.

Since all edge data is one big text block, we need to accumulate all TINYXML_TEXT data and then parse it. This approach effectively skips all comments or other node types since we only care about the edge list. We cannot handle missing edge numbers as we could with missing element numbers due to the text block format.

Now parse out the edges, three fields at a time.

Definition at line 210 of file ExpandMeshByRotation.cpp.

References ASSERTL0, ErrorUtil::efatal, and NEKERROR.

Referenced by main().

{
    /// Look for elements in ELEMENT block.
    TiXmlElement* field = mesh->FirstChildElement("EDGE");
    
    ASSERTL0(field, "Unable to find EDGE tag in file.");
    
    /// All elements are of the form: "<E ID="#"> ... </E>", with
    /// ? being the element type.
    /// Read the ID field first.
    TiXmlElement *edge = field->FirstChildElement("E");
    
    /// Since all edge data is one big text block, we need to
    /// accumulate all TINYXML_TEXT data and then parse it.  This
    /// approach effectively skips all comments or other node
    /// types since we only care about the edge list.  We
    /// cannot handle missing edge numbers as we could with
    /// missing element numbers due to the text block format.
    std::string edgeStr;
    int indx;
    int nextEdgeNumber = -1;

    map<int,int> edgeVert0,edgeVert1;
    while(edge)
    {
        nextEdgeNumber++;
        
        int err = edge->QueryIntAttribute("ID",&indx);
        ASSERTL0(err == TIXML_SUCCESS, "Unable to read edge attribute ID.");
        
        TiXmlNode *child = edge->FirstChild();
        edgeStr.clear();
        if (child->Type() == TiXmlNode::TINYXML_TEXT)
        {
            edgeStr += child->ToText()->ValueStr();
        }
        
        /// Now parse out the edges, three fields at a time.
        int vertex1, vertex2;
        std::istringstream edgeDataStrm(edgeStr.c_str());
        
        try
        {
            while (!edgeDataStrm.fail())
            {
                edgeDataStrm >> vertex1 >> vertex2;                
            }
            edgeVert0[indx] = vertex1;
            edgeVert1[indx] = vertex2;
        }
        catch(...)
        {
            NEKERROR(ErrorUtil::efatal, (std::string("Unable to read edge data: ") + edgeStr).c_str());
        }
        edge = edge->NextSiblingElement("E");
    }

    int nedges = edgeVert0.size();
    int cnt    = nedges;
    int cnt1   = nedges;
    int norigverts = newVerts.size();

    for(int i = 0; i < nedges; ++i)
    {
        if(jointEdges.count(i) == 0)
        {
            stringstream s;
            
            s << setw(5) << newVerts[edgeVert0[i]+norigverts] << "  "
              << newVerts[edgeVert1[i]+norigverts] << "   ";
            TiXmlElement * e = new TiXmlElement( "E" );
            e->SetAttribute("ID",cnt1);
            e->LinkEndChild( new TiXmlText(s.str()) );
            field->LinkEndChild(e);
            newEdges[cnt++] = cnt1++;
        }
        else
        {
            newEdges[cnt++] = jointEdges[i];
        }   
    }
}

void ExpandElmts	(	TiXmlElement *	mesh,
		map< int, int > &	newEdges,
		int &	nOrigElmts
	)

All elements are of the form: "<? ID="#"> ... </?>", with ? being the element type.

These should be ordered.

Read id attribute.

Read text element description.

Parse out the element components corresponding to type of element.

Keep looking

Definition at line 293 of file ExpandMeshByRotation.cpp.

References ASSERTL0, ErrorUtil::efatal, and NEKERROR.

Referenced by main().

{

    TiXmlElement* field = mesh->FirstChildElement("ELEMENT");

    ASSERTL0(field, "Unable to find ELEMENT tag in file.");
    
    int nextElementNumber = -1;
    
    /// All elements are of the form: "<? ID="#"> ... </?>", with
    /// ? being the element type.
    
    TiXmlElement *element = field->FirstChildElement();

    map<int,vector<int> > ElmtEdges;
    
    while (element)
    {
        std::string elementType(element->ValueStr());
        
        ASSERTL0(elementType == "Q" || elementType == "T",
                 (std::string("Unknown 2D element type: ") + elementType).c_str());
        
        /// These should be ordered.
        nextElementNumber++;
        
        /// Read id attribute.
        int indx;
        int err = element->QueryIntAttribute("ID", &indx);
        ASSERTL0(err == TIXML_SUCCESS, "Unable to read element attribute ID.");
        
        /// Read text element description.
        TiXmlNode* elementChild = element->FirstChild();
        std::string elementStr;
        while(elementChild)
        {
            if (elementChild->Type() == TiXmlNode::TINYXML_TEXT)
            {
                elementStr += elementChild->ToText()->ValueStr();
            }
            elementChild = elementChild->NextSibling();
        }

        ASSERTL0(!elementStr.empty(), "Unable to read element description body.");
        
        /// Parse out the element components corresponding to type of element.
        if (elementType == "T")
        {
            // Read three edge numbers
            int edge1, edge2, edge3;
            std::istringstream elementDataStrm(elementStr.c_str());
            
            try
            {
                elementDataStrm >> edge1;
                elementDataStrm >> edge2;
                elementDataStrm >> edge3;
                
                ASSERTL0(!elementDataStrm.fail(), (std::string("Unable to read element data for TRIANGLE: ") + elementStr).c_str());
                
                vector<int> edges;
                edges.push_back(edge1);
                edges.push_back(edge2);
                edges.push_back(edge3);

                ElmtEdges[indx] = edges;
            }
            catch(...)
            {
                NEKERROR(ErrorUtil::efatal, (std::string("Unable to read element data for TRIANGLE: ") + elementStr).c_str());
            }
        }
        else if (elementType == "Q")
        {
            // Read four edge numbers
            int edge1, edge2, edge3, edge4;
            std::istringstream elementDataStrm(elementStr.c_str());
            
            try
            {
                elementDataStrm >> edge1;
                elementDataStrm >> edge2;
                elementDataStrm >> edge3;
                elementDataStrm >> edge4;
                
                ASSERTL0(!elementDataStrm.fail(), (std::string("Unable to read element data for QUAD: ") + elementStr).c_str());

                vector<int> edges;
                edges.push_back(edge1);
                edges.push_back(edge2);
                edges.push_back(edge3);
                edges.push_back(edge4);

                ElmtEdges[indx] = edges;
                
            }
            catch(...)
            {
                NEKERROR(ErrorUtil::efatal,(std::string("Unable to read element data for QUAD: ") + elementStr).c_str());
            }
        }
        
        /// Keep looking
        element = element->NextSiblingElement();
    }
    
    nelmts = ElmtEdges.size();
    int nedges = newEdges.size();
    
    for(int i = 0; i < ElmtEdges.size(); ++i)
    {
        stringstream s;
        
        for(int j = 0; j < ElmtEdges[i].size() ; ++j)
        {
            s << setw(10) << newEdges[ElmtEdges[i][j]+nedges];
        }
        
        TiXmlElement * f;
        switch(ElmtEdges[i].size())
        {
        case 3:
            f = new TiXmlElement("T");
                break;
        case 4:
            f = new TiXmlElement("Q");
            break;
        default:
            abort();
        }
        f->SetAttribute("ID", i+nelmts);
        f->LinkEndChild( new TiXmlText(s.str()));
        field->LinkEndChild(f);
    }
}

void ExpandVertices	(	TiXmlElement *	mesh,
		map< int, int >	jointVerts,
		map< int, int > &	fullVerts
	)

Error value returned by TinyXML.

Definition at line 115 of file ExpandMeshByRotation.cpp.

References ASSERTL0, npts, and Vmath::Vmax().

Referenced by main().

{
    
    TiXmlElement* element = mesh->FirstChildElement("VERTEX");
    ASSERTL0(element, "Unable to find mesh VERTEX tag in file.");
    
    TiXmlElement *vertex = element->FirstChildElement("V");
    
    int indx;
    int nextVertexNumber = -1;
    int err;    /// Error value returned by TinyXML.
    
    vector<NekDouble> xpts,ypts,zpts;
    NekDouble xval, yval, zval;
        
    NekDouble yoffset = 0.0;
    while (vertex)
    {
        nextVertexNumber++;
        
        TiXmlAttribute *vertexAttr = vertex->FirstAttribute();
        std::string attrName(vertexAttr->Name());

        ASSERTL0(attrName == "ID", (std::string("Unknown attribute name: ") + attrName).c_str());
        
        err = vertexAttr->QueryIntValue(&indx);
        ASSERTL0(err == TIXML_SUCCESS, "Unable to read attribute ID.");
        
        // Now read body of vertex
        std::string vertexBodyStr;
        
        TiXmlNode *vertexBody = vertex->FirstChild();

        while (vertexBody)
        {
            // Accumulate all non-comment body data.
            if (vertexBody->Type() == TiXmlNode::TINYXML_TEXT)
            {
                vertexBodyStr += vertexBody->ToText()->Value();
                vertexBodyStr += " ";
            }
            
            vertexBody = vertexBody->NextSibling();
        }

        ASSERTL0(!vertexBodyStr.empty(), "Vertex definitions must contain vertex data.");

        // Get vertex data from the data string.
        std::istringstream vertexDataStrm(vertexBodyStr.c_str());

        try
        {
            while(!vertexDataStrm.fail())
            {
                vertexDataStrm >> xval >> yval >> zval;                
            }
            xpts.push_back(xval);
            ypts.push_back(yval +yoffset);
            zpts.push_back(zval);
        }
        catch(...)
        {
            ASSERTL0(false, "Unable to read VERTEX data.");
        }   
        vertex = vertex->NextSiblingElement("V");
    }

    // Add in newvertices
    int npts = xpts.size();
    NekDouble xmax = Vmath::Vmax(npts,&xpts[0],1);
    int cnt = npts;
    int cnt1 = npts;

    for(int i = 0; i < npts; ++i)
    {
        if(jointVerts.count(i) == 0)
        {
            stringstream s;
            xval = xmax - xpts[i];
            yval = -ypts[i];
            s << scientific << setprecision(8) 
              << xval << " " << yval << " " << zpts[i];
            TiXmlElement * v = new TiXmlElement( "V" );
            v->SetAttribute("ID",cnt1);
            v->LinkEndChild(new TiXmlText(s.str()));
            element->LinkEndChild(v);
            newVerts[cnt++] = cnt1++;
        }
        else
        {
            newVerts[cnt++] = jointVerts[i];
        }
    }       
}

string GetXmlString	(	char	tag,
		vector< unsigned int > &	ids
	)

Definition at line 430 of file ExpandMeshByRotation.cpp.

References Nektar::iterator.

Referenced by ExpandComposites(), and Nektar::Utilities::OutputNekpp::WriteXmlElements().

{
    stringstream st;
    vector<unsigned int>::iterator it;
    bool range = false;
    int vId = ids[0];
    int prevId = vId;
    
    st << " " << tag << "[" << vId;
    
    for (it = ids.begin()+1; it != ids.end(); ++it){
        // store previous element ID and get current one
        prevId = vId;
        vId = (*it);
        
        // continue an already started range
        if (prevId > -1 && vId == prevId + 1)
        {
            range = true;
            // if this is the last element, it's the end of a range, so write
            if (*it == ids.back())
            {
                st << "-" << vId;
            }
            continue;
        }
        
        // terminate a range, if present
        if (range)
        {
            st << "-" << prevId;
            range = false;
        }
        
        // write what will be either a single entry or start of new range
        st << "," << vId;
    }
    // terminate
    st << "] ";
    return st.str();
}

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 60 of file ExpandMeshByRotation.cpp.

References ExpandComposites(), ExpandEdges(), ExpandElmts(), and ExpandVertices().

{
    int i;
    
    if(argc !=3)
    {
        fprintf(stderr,"Usage: ./ExpandMeshByRotation meshfile  outfile\n");
        exit(1);
    }
    
    //------------------------------------------------------------
    // Create Session file which also reads meshfile. 
    LibUtilities::SessionReaderSharedPtr vSession
        = LibUtilities::SessionReader::CreateInstance(argc-1, argv);
    //-----------------------------------------------------------
    
    //-------------------------------------------------------------
    // Read in mesh from input file
    string meshfile(argv[argc-2]);
    SpatialDomains::MeshGraphSharedPtr graphShPt=SpatialDomains::MeshGraph::Read(vSession);
    SpatialDomains::Composite composite;
    composite = graphShPt->GetComposite(300);
    std::map<int,int> jointEdges, jointVerts, newVerts, newEdges; 
    int compsize = composite->size();
    for(i = 0; i < compsize; ++i)
    {
        SpatialDomains::Geometry1DSharedPtr tmp1 = boost::dynamic_pointer_cast<SpatialDomains::Geometry1D>((*composite)[i]);
        SpatialDomains::Geometry1DSharedPtr tmp2 = boost::dynamic_pointer_cast<SpatialDomains::Geometry1D>((*composite)[compsize-1-i]);
        jointEdges[tmp1->GetEid() ] = tmp2->GetEid();
        jointVerts[tmp1->GetVid(0)] = tmp2->GetVid(1);
        jointVerts[tmp1->GetVid(1)] = tmp2->GetVid(0);
    }


   //------------------------------------------------------------
    TiXmlDocument& meshdoc = vSession->GetDocument();

    TiXmlHandle docHandle(&meshdoc);
    TiXmlElement* mesh = docHandle.FirstChildElement("NEKTAR").FirstChildElement("GEOMETRY").Element();
    
    int nOrigElmts;
    //------------------------------------------------------------
    // Expand Mesh
    ExpandVertices(mesh,jointVerts,newVerts);

    ExpandEdges(mesh,newVerts,jointEdges,newEdges);
    
    ExpandElmts(mesh, newEdges,nOrigElmts);
    
    ExpandComposites( mesh, newEdges, nOrigElmts);

    meshdoc.SaveFile(argv[argc-1]);
    
}