Nektar::FieldUtils::OutputVtk Class Reference

Converter from fld to vtk. More...

#include <OutputVtk.h>

Inheritance diagram for Nektar::FieldUtils::OutputVtk:

Public Member Functions
	OutputVtk (FieldSharedPtr f)
virtual	~OutputVtk ()
virtual std::string	GetModuleName ()
Public Member Functions inherited from Nektar::FieldUtils::OutputFileBase
	OutputFileBase (FieldSharedPtr f)
virtual	~OutputFileBase ()
virtual void	Process (po::variables_map &vm)
	Write fld to output file. More...
virtual std::string	GetModuleDescription ()
virtual ModulePriority	GetModulePriority ()
Public Member Functions inherited from Nektar::FieldUtils::OutputModule
	OutputModule (FieldSharedPtr p_f)
FIELD_UTILS_EXPORT void	OpenStream ()
	Open a file for output. More...
Public Member Functions inherited from Nektar::FieldUtils::Module
FIELD_UTILS_EXPORT	Module (FieldSharedPtr p_f)
FIELD_UTILS_EXPORT void	RegisterConfig (std::string key, std::string value="")
	Register a configuration option with a module. More...
FIELD_UTILS_EXPORT void	PrintConfig ()
	Print out all configuration options for a module. More...
FIELD_UTILS_EXPORT void	SetDefaults ()
	Sets default configuration options for those which have not been set. More...
FIELD_UTILS_EXPORT void	EvaluateTriFieldAtEquiSpacedPts (LocalRegions::ExpansionSharedPtr &exp, const Array< OneD, const NekDouble > &infield, Array< OneD, NekDouble > &outfield)

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

Static Public Attributes
static ModuleKey	m_className

Protected Member Functions
virtual void	OutputFromPts (po::variables_map &vm)
	Write from pts to output file. More...
virtual void	OutputFromExp (po::variables_map &vm)
	Write from m_exp to output file. More...
virtual void	OutputFromData (po::variables_map &vm)
	Write from data to output file. More...
virtual fs::path	GetPath (std::string &filename, po::variables_map &vm)
virtual fs::path	GetFullOutName (std::string &filename, po::variables_map &vm)
Protected Member Functions inherited from Nektar::FieldUtils::Module
	Module ()

Private Member Functions
void	WriteVtkHeader (std::ostream &outfile)
void	WriteVtkFooter (std::ostream &outfile)
void	WriteEmptyVtkPiece (std::ofstream &outfile)
void	WritePVtu (po::variables_map &vm)
std::string	PrepareOutput (po::variables_map &vm)

Additional Inherited Members
Protected Attributes inherited from Nektar::FieldUtils::OutputFileBase
bool	m_requireEquiSpaced
Protected Attributes inherited from Nektar::FieldUtils::OutputModule
std::ofstream	m_fldFile
	Output stream. More...
Protected Attributes inherited from Nektar::FieldUtils::Module
FieldSharedPtr	m_f
	Field object. More...
std::map< std::string, ConfigOption >	m_config
	List of configuration values. More...

Detailed Description

Converter from fld to vtk.

Definition at line 47 of file library/FieldUtils/OutputModules/OutputVtk.h.

Constructor & Destructor Documentation

OutputVtk()

Nektar::FieldUtils::OutputVtk::OutputVtk

(

FieldSharedPtr

f

)

Definition at line 55 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

References Nektar::FieldUtils::OutputFileBase::m_requireEquiSpaced.

                                     : OutputFileBase(f)
{
    m_requireEquiSpaced = true;
}

~OutputVtk()

Nektar::FieldUtils::OutputVtk::~OutputVtk ( )

virtual

Definition at line 60 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

{
}

Member Function Documentation

create()

static std::shared_ptr<Module> Nektar::FieldUtils::OutputVtk::create ( FieldSharedPtr  f )

inlinestatic

Creates an instance of this class.

Definition at line 51 of file library/FieldUtils/OutputModules/OutputVtk.h.

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

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

GetFullOutName()

fs::path Nektar::FieldUtils::OutputVtk::GetFullOutName ( std::string &  filename, po::variables_map &  vm  )

protectedvirtual

Implements Nektar::FieldUtils::OutputFileBase.

Definition at line 305 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

References CellMLToNektar.pycml::format, GetPath(), and Nektar::FieldUtils::Module::m_f.

Referenced by GetModuleName(), and PrepareOutput().

{
    int nprocs = m_f->m_comm->GetSize();

    fs::path fulloutname;
    if (nprocs == 1)
    {
        fulloutname = filename;
    }
    else
    {
        // Guess at filename that might belong to this process.
        boost::format pad("P%1$07d.%2$s");
        pad % m_f->m_comm->GetRank() % "vtu";

        // Generate full path name
        fs::path specPath = GetPath(filename, vm);
        fs::path poutfile(pad.str());
        fulloutname = specPath / poutfile;
    }
    return   fulloutname;
}

GetModuleName()

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

inlinevirtual

Reimplemented from Nektar::FieldUtils::OutputFileBase.

Definition at line 60 of file library/FieldUtils/OutputModules/OutputVtk.h.

References GetFullOutName(), GetPath(), OutputFromData(), OutputFromExp(), OutputFromPts(), PrepareOutput(), WriteEmptyVtkPiece(), WritePVtu(), WriteVtkFooter(), and WriteVtkHeader().

    {
        return "OutputVtk";
    }

GetPath()

fs::path Nektar::FieldUtils::OutputVtk::GetPath ( std::string &  filename, po::variables_map &  vm  )

protectedvirtual

Implements Nektar::FieldUtils::OutputFileBase.

Definition at line 284 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

References Nektar::FieldUtils::Module::m_f.

Referenced by GetFullOutName(), GetModuleName(), PrepareOutput(), and WritePVtu().

{
    boost::ignore_unused(vm);

    int nprocs = m_f->m_comm->GetSize();
    fs::path specPath;
    if (nprocs == 1)
    {
        specPath = fs::path(filename);
    }
    else
    {
        // replace .vtu by _vtu
        int    dot  = filename.find_last_of('.');
        string path = filename.substr(0, dot) + "_vtu";
        specPath = fs::path(path);
    }
    return   fs::path(specPath);
}

OutputFromData()

void Nektar::FieldUtils::OutputVtk::OutputFromData ( po::variables_map &  vm )

protectedvirtual

Write from data to output file.

Implements Nektar::FieldUtils::OutputFileBase.

Definition at line 278 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

References Nektar::ErrorUtil::efatal, and NEKERROR.

Referenced by GetModuleName().

{
    boost::ignore_unused(vm);
    NEKERROR(ErrorUtil::efatal, "OutputVtk can't write using only FieldData.");
}

OutputFromExp()

void Nektar::FieldUtils::OutputVtk::OutputFromExp ( po::variables_map &  vm )

protectedvirtual

Write from m_exp to output file.

Implements Nektar::FieldUtils::OutputFileBase.

Definition at line 230 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

References Nektar::FieldUtils::Module::m_f, PrepareOutput(), WriteEmptyVtkPiece(), WritePVtu(), WriteVtkFooter(), and WriteVtkHeader().

Referenced by GetModuleName().

{
    int i,j;
    // Extract the output filename and extension
    string filename = PrepareOutput(vm);

    // Write solution.
    ofstream outfile(filename.c_str());
    WriteVtkHeader(outfile);
    int nfields = m_f->m_variables.size();

    int nstrips;
    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_variables[j]);
            }
            m_f->m_exp[0]->WriteVtkPieceFooter(outfile, i);
        }
    }

    if (m_f->m_exp[0]->GetNumElmts() == 0)
    {
        WriteEmptyVtkPiece(outfile);
    }

    WriteVtkFooter(outfile);
    cout << "Written file: " << filename << endl;

    // output parallel outline info if necessary
    if ( (m_f->m_comm->GetRank() == 0) &&
         (m_f->m_comm->GetSize() != 1))
    {
        WritePVtu(vm);
    }
}

OutputFromPts()

void Nektar::FieldUtils::OutputVtk::OutputFromPts ( po::variables_map &  vm )

protectedvirtual

Write from pts to output file.

Implements Nektar::FieldUtils::OutputFileBase.

Definition at line 64 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

References Nektar::ErrorUtil::efatal, Nektar::LibUtilities::ePtsBox, Nektar::LibUtilities::ePtsFile, Nektar::LibUtilities::ePtsLine, Nektar::LibUtilities::ePtsPlane, Nektar::LibUtilities::ePtsSegBlock, Nektar::LibUtilities::ePtsTetBlock, Nektar::LibUtilities::ePtsTriBlock, Nektar::FieldUtils::Module::m_f, NEKERROR, PrepareOutput(), WritePVtu(), WriteVtkFooter(), and WriteVtkHeader().

Referenced by GetModuleName().

{
    int i, j;
    LibUtilities::PtsFieldSharedPtr fPts = m_f->m_fieldPts;

    // Extract the output filename and extension
    string filename = PrepareOutput(vm);

    // Write solution.
    ofstream outfile(filename.c_str());
    WriteVtkHeader(outfile);
    int nfields = 0;
    int dim     = fPts->GetDim();

    int nvert   = 1;
    int vtktype = 1;
    switch (fPts->GetPtsType())
    {
        case LibUtilities::ePtsFile:
        case LibUtilities::ePtsLine:
        {
            NEKERROR(ErrorUtil::efatal,
                     "VTK output needs setting up for ePtsFile and ePtsLine");
            break;
        }
        case LibUtilities::ePtsPlane:
        {
            NEKERROR(ErrorUtil::efatal,
                     "VTK output needs setting up for PtsPlane");
            break;
        }
        case LibUtilities::ePtsBox:
        {
            NEKERROR(ErrorUtil::efatal,
                     "VTK output needs setting up for PtsBox");
            break;
        }
        case LibUtilities::ePtsSegBlock:
        {
            nvert = 2;
            vtktype = 3;
            break;
        }
        case LibUtilities::ePtsTriBlock:
        {
            nvert   = 3;
            vtktype = 5;
            break;
        }
        case LibUtilities::ePtsTetBlock:
        {
            nvert   = 4;
            vtktype = 10;
            break;
        }
        default:
            NEKERROR(ErrorUtil::efatal, "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)
    {
        outfile << "        <DataArray type=\"Float64\" Name=\""
                << m_f->m_variables[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;

    WriteVtkFooter(outfile);
    cout << "Written file: " << filename << endl;

    // output parallel outline info if necessary
    if ( (m_f->m_comm->GetRank() == 0) &&
         (m_f->m_comm->GetSize() != 1))
    {
        WritePVtu(vm);
        cout << "Written file: " << filename << endl;
    }
}

PrepareOutput()

std::string Nektar::FieldUtils::OutputVtk::PrepareOutput ( po::variables_map &  vm )

private

Definition at line 427 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

References ASSERTL0, GetFullOutName(), GetPath(), Nektar::FieldUtils::Module::m_config, Nektar::FieldUtils::Module::m_f, and Nektar::LibUtilities::PortablePath().

Referenced by GetModuleName(), OutputFromExp(), and OutputFromPts().

{
    // Extract the output filename and extension
    string filename = m_config["outfile"].as<string>();

    fs::path specPath    = GetPath(filename,vm);
    fs::path fulloutname = GetFullOutName(filename,vm);
    filename = LibUtilities::PortablePath(fulloutname);

    if (m_f->m_comm->GetSize() != 1)
    {
        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;
        }
        m_f->m_comm->Block();
    }
    else
    {
        cout << "Writing: " << specPath << endl;
    }
    return filename;
}

WriteEmptyVtkPiece()

void Nektar::FieldUtils::OutputVtk::WriteEmptyVtkPiece ( std::ofstream &  outfile )

private

Definition at line 343 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

Referenced by GetModuleName(), and OutputFromExp().

{
    // write out empty piece of data.
    outfile << "    <Piece NumberOfPoints=\"" << 0 << "\" NumberOfCells=\"" << 0
            << "\">" << endl;
    outfile << "      <Points>" << endl;
    outfile << "        <DataArray type=\"Float64\" "
            << "NumberOfComponents=\"" << 3 << "\" format=\"ascii\">" << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "      </Points>" << endl;
    outfile << "      <Cells>" << endl;
    outfile << "        <DataArray type=\"Int32\" "
            << "Name=\"connectivity\" format=\"ascii\">" << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "        <DataArray type=\"Int32\" "
            << "Name=\"offsets\" format=\"ascii\">" << endl;

    outfile << "          ";
    outfile << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "        <DataArray type=\"UInt8\" "
            << "Name=\"types\" format=\"ascii\">" << endl;
    outfile << "          ";
    outfile << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "      </Cells>" << endl;
    outfile << "      <PointData>" << endl;

    outfile << "      </PointData>" << endl;
    outfile << "    </Piece>" << endl;
}

WritePVtu()

void Nektar::FieldUtils::OutputVtk::WritePVtu ( po::variables_map &  vm )

private

Definition at line 375 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

References CellMLToNektar.pycml::format, GetPath(), Nektar::FieldUtils::Module::m_config, Nektar::FieldUtils::Module::m_f, and Nektar::LibUtilities::PortablePath().

Referenced by GetModuleName(), OutputFromExp(), and OutputFromPts().

{
    string 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());

    int nprocs  = m_f->m_comm->GetSize();
    string path = LibUtilities::PortablePath(GetPath(filename,vm));

    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 < m_f->m_variables.size(); ++i)
    {
        outfile << "<PDataArray type=\"Float64\" Name=\""
                << m_f->m_variables[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;
}

WriteVtkFooter()

void Nektar::FieldUtils::OutputVtk::WriteVtkFooter ( std::ostream &  outfile )

private

Definition at line 337 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

Referenced by GetModuleName(), OutputFromExp(), and OutputFromPts().

{
    outfile << "  </UnstructuredGrid>" << endl;
    outfile << "</VTKFile>" << endl;
}

WriteVtkHeader()

void Nektar::FieldUtils::OutputVtk::WriteVtkHeader ( std::ostream &  outfile )

private

Definition at line 329 of file library/FieldUtils/OutputModules/OutputVtk.cpp.

Referenced by GetModuleName(), OutputFromExp(), and OutputFromPts().

{
    outfile << "<?xml version=\"1.0\"?>" << endl;
    outfile << "<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" "
            << "byte_order=\"LittleEndian\">" << endl;
    outfile << "  <UnstructuredGrid>" << endl;
}

Member Data Documentation

m_className

ModuleKey Nektar::FieldUtils::OutputVtk::m_className

static

Initial value:

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

Definition at line 55 of file library/FieldUtils/OutputModules/OutputVtk.h.