Nektar::Utilities::OutputVtk Class Reference

Converter from fld to vtk. More...

#include <OutputVtk.h>

Inheritance diagram for Nektar::Utilities::OutputVtk:

Collaboration diagram for Nektar::Utilities::OutputVtk:

Public Member Functions
	OutputVtk (FieldSharedPtr f)
virtual	~OutputVtk ()
virtual void	Process (po::variables_map &vm)
	Write fld to output file. More...
virtual std::string	GetModuleName ()
	OutputVtk (MeshSharedPtr m)
virtual	~OutputVtk ()
virtual void	Process ()
	Write mesh to output file. More...
Public Member Functions inherited from Nektar::Utilities::OutputModule
	OutputModule (FieldSharedPtr p_f)
void	OpenStream ()
	Open a file for output. More...
	OutputModule (MeshSharedPtr p_m)
void	OpenStream ()
Public Member Functions inherited from Nektar::Utilities::Module
	Module (FieldSharedPtr p_f)
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 (std::string key, std::string value)
void	PrintConfig ()
void	SetDefaults ()
MeshSharedPtr	GetMesh ()
virtual void	ProcessVertices ()
	Extract element vertices. More...
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...
virtual void	ClearElementLinks ()

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

Static Public Attributes
static ModuleKey	m_className
static ModuleKey	className

Additional Inherited Members
Protected Member Functions inherited from Nektar::Utilities::Module
	Module ()
void	ReorderPrisms (PerMap &perFaces)
	Reorder node IDs so that prisms and tetrahedra are aligned correctly. More...
void	PrismLines (int prism, PerMap &perFaces, std::set< int > &prismsDone, std::vector< ElementSharedPtr > &line)
Protected Attributes inherited from Nektar::Utilities::OutputModule
ofstream	m_fldFile
	Output stream. More...
std::ofstream	m_mshFile
	Output 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...
std::map< std::string, ConfigOption >	m_config
	List of configuration values. More...

Detailed Description

Converter from fld to vtk.

Converter for Gmsh files.

Definition at line 48 of file FieldConvert/OutputModules/OutputVtk.h.

Constructor & Destructor Documentation

Nektar::Utilities::OutputVtk::OutputVtk

(

FieldSharedPtr

f

)

Definition at line 55 of file FieldConvert/OutputModules/OutputVtk.cpp.

References Nektar::Utilities::Module::m_requireEquiSpaced.

                                     : OutputModule(f)
{
    m_requireEquiSpaced = true;
}

Nektar::Utilities::OutputVtk::~OutputVtk ( )

virtual

Definition at line 60 of file FieldConvert/OutputModules/OutputVtk.cpp.

{
}

Nektar::Utilities::OutputVtk::OutputVtk

(

MeshSharedPtr

m

)

Definition at line 56 of file NekMesh/OutputModules/OutputVtk.cpp.

                                    : OutputModule(m)
{
}

virtual Nektar::Utilities::OutputVtk::~OutputVtk ( )

virtual

Member Function Documentation

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

inlinestatic

Creates an instance of this class.

Definition at line 51 of file NekMesh/OutputModules/OutputVtk.h.

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

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

static boost::shared_ptr<Module> Nektar::Utilities::OutputVtk::create ( FieldSharedPtr  f )

inlinestatic

Creates an instance of this class.

Definition at line 52 of file FieldConvert/OutputModules/OutputVtk.h.

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

                                                                {
            return MemoryManager<OutputVtk>::AllocateSharedPtr(f);
        }

virtual std::string Nektar::Utilities::OutputVtk::GetModuleName ( )

inlinevirtual

Implements Nektar::Utilities::Module.

Definition at line 63 of file FieldConvert/OutputModules/OutputVtk.h.

        {
            return "OutputVtk";
        }

void Nektar::Utilities::OutputVtk::Process ( po::variables_map &  vm )

virtual

Write fld to output file.

Implements Nektar::Utilities::Module.

Definition at line 64 of file FieldConvert/OutputModules/OutputVtk.cpp.

References ASSERTL0, ASSERTL1, Nektar::LibUtilities::ePtsFile, Nektar::LibUtilities::ePtsLine, Nektar::LibUtilities::ePtsPlane, Nektar::LibUtilities::ePtsTetBlock, Nektar::LibUtilities::ePtsTriBlock, Nektar::Utilities::Module::m_config, Nektar::Utilities::Module::m_f, Nektar::LibUtilities::NullPtsField, and Nektar::LibUtilities::PortablePath().

{
    LibUtilities::PtsFieldSharedPtr fPts = m_f->m_fieldPts;

    // Do nothing if no expansion defined
    if (fPts == LibUtilities::NullPtsField && !m_f->m_exp.size())
    {
        return;
    }

    int i, j;
    if (m_f->m_verbose)
    {
        if(m_f->m_comm->TreatAsRankZero())
        {
            cout << "OutputVtk: Writing file..." << endl;
        }
    }

    // Extract the output filename and extension
    string filename = m_config["outfile"].as<string>();
    string path;
    
    // amend for parallel output if required
    if(m_f->m_session->GetComm()->GetSize() != 1)
    {
        int    dot = filename.find_last_of('.');
        string ext = filename.substr(dot,filename.length()-dot);
        string start = filename.substr(0,dot);
        path = start + "_vtu"; 
        
        boost::format pad("P%1$07d.vtu");
        pad % m_f->m_session->GetComm()->GetRank();
        filename = pad.str();

        fs::path poutfile(filename.c_str());
        fs::path specPath(path.c_str());
        
        if(m_f->m_comm->TreatAsRankZero())
        {
            try
            {
                fs::create_directory(specPath);
            }
            catch (fs::filesystem_error& e)
            {
                ASSERTL0(false, "Filesystem error: " + string(e.what()));
            }
            cout << "Writing files to directory: " << specPath << endl;
        }   
        
        fs::path fulloutname = specPath / poutfile;
        filename =  LibUtilities::PortablePath(fulloutname);
        m_f->m_comm->Block();
    }
    else
    {
        fs::path specPath(filename.c_str());
        cout << "Writing: " << specPath << endl;
        filename =  LibUtilities::PortablePath(specPath);
    }

    // Write solution.
    ofstream outfile(filename.c_str());
    m_f->m_exp[0]->WriteVtkHeader(outfile);
    int nfields = 0;
    int dim = 0; 

    vector<string> fieldname;
    if(fPts == LibUtilities::NullPtsField) // standard output in collapsed coordinates 
    {
       dim =  m_f->m_exp[0]->GetExp(0)->GetCoordim();
    
       int nstrips;
       if (m_f->m_fielddef.size() == 0)
       {
           nfields = 0;
       }
       else
       {
           nfields = m_f->m_fielddef[0]->m_fields.size();
       }
       m_f->m_session->LoadParameter("Strip_Z", nstrips, 1);
       
       // Homogeneous strip variant
       for(int s = 0; s < nstrips; ++s)
       {
           // For each field write out field data for each expansion.
           for (i = 0; i < m_f->m_exp[0]->GetNumElmts(); ++i)
           {
               m_f->m_exp[0]->WriteVtkPieceHeader(outfile,i,s);
               
               // For this expansion write out each field.
               for (j = 0; j < nfields; ++j)
               {
                   m_f->m_exp[s*nfields+j]->WriteVtkPieceData(
                                    outfile, i, m_f->m_fielddef[0]->m_fields[j]);
               }
               m_f->m_exp[0]->WriteVtkPieceFooter(outfile, i);
           }
       }
       
       // save field names for parallel output 
       for(i = 0; i < nfields; ++i)
       {
           fieldname.push_back(m_f->m_fielddef[0]->m_fields[i]);
       }
   }
   else  // write out data stored in fPts (for example if equispaced output is called). 
   {
        int i   = 0;
        int j   = 0;

        dim = fPts->GetDim();

        if(fPts->GetNpoints() == 0)
        {
            return;
        }

        int nvert, vtktype; 
        switch(fPts->GetPtsType())
        {
            case LibUtilities::ePtsFile:
            case LibUtilities::ePtsLine:
            {
                ASSERTL0(false,"VTK output needs settig up for PtsFile or Pts Line");
                break;
            }
            case LibUtilities::ePtsPlane:
            {
                ASSERTL0(false,"VTK output needs settig up for PtsPlane");
                break;
            }
            case LibUtilities::ePtsTriBlock:
            {
                nvert = 3;
                vtktype = 5;
                break;
            }
            case LibUtilities::ePtsTetBlock:
            {
                nvert = 4;
                vtktype = 10;
                break;
            }
            default:
                ASSERTL0(false, "ptsType not supported yet.");
        }

        vector<Array<OneD, int> > ptsConn;
        fPts->GetConnectivity(ptsConn);

        nfields = fPts->GetNFields();
        
        int nPts    = fPts->GetNpoints();
        int numBlocks = 0;
        for(i = 0; i < ptsConn.size(); ++i)
        {
            numBlocks += ptsConn[i].num_elements()/nvert;
        }
        
        // write out pieces of data. 
        outfile << "    <Piece NumberOfPoints=\""
                << nPts << "\" NumberOfCells=\""
                << numBlocks << "\">" << endl;
        outfile << "      <Points>" << endl;
        outfile << "        <DataArray type=\"Float64\" "
                << "NumberOfComponents=\""<<3<<"\" format=\"ascii\">" << endl;
        for(i = 0; i < nPts; ++i)
        {
            for(j = 0; j < dim; ++j)
            {
                outfile << "          "  << setprecision(8)     << scientific 
                        <<  fPts->GetPointVal(j, i) << " ";
            }
            for(j = dim; j < 3; ++j) // pack to 3D since paraview does not seem to handle 2D
            {
                outfile  <<  "          0.000000" ; 
            }
            outfile << endl;
        }
        outfile << "        </DataArray>" << endl;
        outfile << "      </Points>" << endl;
        outfile << "      <Cells>" << endl;
        outfile << "        <DataArray type=\"Int32\" "
                << "Name=\"connectivity\" format=\"ascii\">" << endl;
        
        // dump connectivity data if it exists
        outfile << "          ";
        int cnt = 1; 
        for(i = 0; i < ptsConn.size();++i)
        {
            for(j = 0; j < ptsConn[i].num_elements(); ++j)
            {
                outfile << ptsConn[i][j] << " ";
                if( (!(cnt % nvert)) && cnt )
                {
                    outfile << std::endl;
                    outfile << "          ";
                }
                cnt ++;
            }
        }
        outfile << "        </DataArray>" << endl;
        outfile << "        <DataArray type=\"Int32\" "
                << "Name=\"offsets\" format=\"ascii\">" << endl;

        outfile << "          ";
                for (i = 0; i < numBlocks; ++i)
        {
            outfile << i*nvert+nvert << " ";
        }
        outfile << endl;
        outfile << "        </DataArray>" << endl;
        outfile << "        <DataArray type=\"UInt8\" "
                << "Name=\"types\" format=\"ascii\">" << endl;
        outfile << "          ";
        for (i = 0; i < numBlocks; ++i)
        {
            outfile << vtktype <<" ";
        }
        outfile << endl;
        outfile << "        </DataArray>" << endl;
        outfile << "      </Cells>" << endl;
        outfile << "      <PointData>" << endl;
        
        // printing the fields
        for(j = 0; j < nfields; ++j)
        {
            fieldname.push_back(fPts->GetFieldName(j));
            outfile << "        <DataArray type=\"Float64\" Name=\""
                    << fPts->GetFieldName(j) << "\">" << endl;
            outfile << "          ";
            for(i = 0; i < fPts->GetNpoints(); ++i)
            {
                outfile <<  fPts->GetPointVal(dim+j, i) << " ";
            }
            outfile << endl;
            outfile << "        </DataArray>" << endl;
        }
        
        outfile << "      </PointData>" << endl;
        outfile << "    </Piece>" << endl;
   }

   m_f->m_exp[0]->WriteVtkFooter(outfile);
   cout << "Written file: " << filename << endl;

    // output parallel outline info if necessary
    if(m_f->m_comm->GetRank() == 0)
    {
        ASSERTL1(fieldname.size() == nfields, "fieldname not the same size as nfields");
        int nprocs = m_f->m_comm->GetSize();
        if(nprocs != 1)
        {
            filename = m_config["outfile"].as<string>();
            int    dot = filename.find_last_of('.');
            string body = filename.substr(0,dot);
            filename = body + ".pvtu";

            ofstream outfile(filename.c_str());

            outfile << "<?xml version=\"1.0\"?>" << endl;
            outfile << "<VTKFile type=\"PUnstructuredGrid\" version=\"0.1\" "
                    << "byte_order=\"LittleEndian\">" << endl;
            outfile << "<PUnstructuredGrid GhostLevel=\"0\">" << endl;
            outfile << "<PPoints> " << endl;
            outfile << "<PDataArray type=\"Float64\" NumberOfComponents=\""
                    <<  3 << "\"/> " << endl; 
            outfile << "</PPoints>" << endl;
            outfile << "<PCells>" << endl;
            outfile << "<PDataArray type=\"Int32\" Name=\"connectivity\" NumberOfComponents=\"1\"/>" << endl; 
            outfile << "<PDataArray type=\"Int32\" Name=\"offsets\"      NumberOfComponents=\"1\"/>" << endl;
            outfile << "<PDataArray type=\"UInt8\" Name=\"types\"        NumberOfComponents=\"1\"/>" << endl;
            outfile << "</PCells>" << endl;
            outfile << "<PPointData Scalars=\"Material\">" << endl;
            for(int i = 0; i < nfields; ++i)
            {
                outfile << "<PDataArray type=\"Float64\" Name=\"" <<
                    fieldname[i]  << "\"/>" << endl;
            }
            outfile << "</PPointData>" << endl;

            for(int i = 0; i < nprocs; ++i)
            {
                boost::format pad("P%1$07d.vtu");
                pad % i; 
                outfile << "<Piece Source=\"" << path << "/" << pad.str() << "\"/>" <<endl;
            }
            outfile << "</PUnstructuredGrid>"  << endl;
            outfile << "</VTKFile>" << endl;
            cout << "Written file: " << filename << endl;
        }
    }
}

void Nektar::Utilities::OutputVtk::Process ( )

virtual

Write mesh to output file.

Implements Nektar::Utilities::Module.

Definition at line 64 of file NekMesh/OutputModules/OutputVtk.cpp.

References Nektar::iterator, Nektar::Utilities::Module::m_config, and Nektar::Utilities::Module::m_mesh.

{
    if (m_mesh->m_verbose)
    {
        cout << "OutputVtk: Writing file..." << endl;
    }

    vtkPolyData *vtkMesh   = vtkPolyData::New();
    vtkPoints *vtkPoints   = vtkPoints::New();
    vtkCellArray *vtkPolys = vtkCellArray::New();

    std::set<NodeSharedPtr>::iterator it;

    std::set<NodeSharedPtr> tmp(m_mesh->m_vertexSet.begin(),
                                m_mesh->m_vertexSet.end());

    for (it = tmp.begin(); it != tmp.end(); ++it)
    {
        NodeSharedPtr n = *it;
        vtkPoints->InsertPoint(n->m_id, n->m_x, n->m_y, n->m_z);
    }

    vtkIdType p[8];
    vector<ElementSharedPtr> &elmt = m_mesh->m_element[m_mesh->m_expDim];
    for (int i = 0; i < elmt.size(); ++i)
    {
        int vertexCount = elmt[i]->GetVertexCount();
        for (int j = 0; j < vertexCount; ++j)
        {
            p[j] = elmt[i]->GetVertex(j)->m_id;
        }
        vtkPolys->InsertNextCell(vertexCount, &p[0]);
    }

    vtkMesh->SetPoints(vtkPoints);
    vtkMesh->SetPolys(vtkPolys);

    // Write out the new mesh
    vtkPolyDataWriter *vtkMeshWriter = vtkPolyDataWriter::New();
    vtkMeshWriter->SetFileName(m_config["outfile"].as<string>().c_str());
#if VTK_MAJOR_VERSION <= 5
    vtkMeshWriter->SetInput(vtkMesh);
#else
    vtkMeshWriter->SetInputData(vtkMesh);
#endif
    vtkMeshWriter->Update();
}

Member Data Documentation

ModuleKey Nektar::Utilities::OutputVtk::className

static

Initial value:

= GetModuleFactory().RegisterCreatorFunction(
    ModuleKey(eOutputModule, "vtk"), OutputVtk::create, "Writes a VTK file.")

Definition at line 55 of file NekMesh/OutputModules/OutputVtk.h.

ModuleKey Nektar::Utilities::OutputVtk::m_className

static

Initial value:

=
    GetModuleFactory().RegisterCreatorFunction(
        ModuleKey(eOutputModule, "vtu"), OutputVtk::create,
        "Writes a VTU file.")

Definition at line 55 of file FieldConvert/OutputModules/OutputVtk.h.