Nektar::FieldUtils::OutputVtkBase Class Reference

Converter from fld to vtk. More...

#include <OutputVtkBase.h>

Inheritance diagram for Nektar::FieldUtils::OutputVtkBase:

Public Member Functions
	OutputVtkBase (FieldSharedPtr f)
	~OutputVtkBase () override
Public Member Functions inherited from Nektar::FieldUtils::OutputFileBase
	OutputFileBase (FieldSharedPtr f)
	~OutputFileBase () override
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)
virtual	~Module ()=default
void	Process (po::variables_map &vm)
std::string	GetModuleName ()
std::string	GetModuleDescription ()
const ConfigOption &	GetConfigOption (const std::string &key) const
ModulePriority	GetModulePriority ()
std::vector< ModuleKey >	GetModulePrerequisites ()
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	AddFile (std::string fileType, std::string fileName)
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
std::string	v_GetModuleName () override
void	v_OutputFromPts (po::variables_map &vm) override
	Write from pts to output file. More...
void	v_OutputFromExp (po::variables_map &vm) override
	Write from m_exp to output file. More...
void	v_OutputFromData (po::variables_map &vm) override
	Write from data to output file. More...
fs::path	v_GetPath (std::string &filename, po::variables_map &vm) override
fs::path	v_GetFullOutName (std::string &filename, po::variables_map &vm) override
std::string	PrepareOutput (po::variables_map &vm)
Protected Member Functions inherited from Nektar::FieldUtils::OutputFileBase
void	v_Process (po::variables_map &vm) override
	Write fld to output file. More...
std::string	v_GetModuleName () override
std::string	v_GetModuleDescription () override
ModulePriority	v_GetModulePriority () override
virtual void	v_OutputFromPts (po::variables_map &vm)=0
	Write from pts to output file. More...
virtual void	v_OutputFromExp (po::variables_map &vm)=0
	Write from m_exp to output file. More...
virtual void	v_OutputFromData (po::variables_map &vm)=0
	Write from data to output file. More...
virtual fs::path	v_GetPath (std::string &filename, po::variables_map &vm)
fs::path	GetPath (std::string &filename, po::variables_map &vm)
virtual fs::path	v_GetFullOutName (std::string &filename, po::variables_map &vm)
fs::path	GetFullOutName (std::string &filename, po::variables_map &vm)
Protected Member Functions inherited from Nektar::FieldUtils::Module
	Module ()
virtual void	v_Process (po::variables_map &vm)
virtual std::string	v_GetModuleName ()
virtual std::string	v_GetModuleDescription ()
virtual ModulePriority	v_GetModulePriority ()
virtual std::vector< ModuleKey >	v_GetModulePrerequisites ()

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

Additional Inherited Members
Public Attributes inherited from Nektar::FieldUtils::Module
FieldSharedPtr	m_f
	Field object. More...
Protected Attributes inherited from Nektar::FieldUtils::OutputFileBase
bool	m_requireEquiSpaced
bool	m_prohibitWrite = false
bool	m_equispacedSetup = false
Protected Attributes inherited from Nektar::FieldUtils::OutputModule
std::ofstream	m_fldFile
	Output stream. More...
Protected Attributes inherited from Nektar::FieldUtils::Module
std::map< std::string, ConfigOption >	m_config
	List of configuration values. More...
std::set< std::string >	m_allowedFiles
	List of allowed file formats. More...

Detailed Description

Converter from fld to vtk.

Definition at line 45 of file OutputVtkBase.h.

Constructor & Destructor Documentation

OutputVtkBase()

Nektar::FieldUtils::OutputVtkBase::OutputVtkBase

(

FieldSharedPtr

f

)

Definition at line 58 of file OutputVtkBase.cpp.

                                             : OutputFileBase(f)
{
    m_requireEquiSpaced = true;
}

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

~OutputVtkBase()

Nektar::FieldUtils::OutputVtkBase::~OutputVtkBase ( )

override

Definition at line 63 of file OutputVtkBase.cpp.

{
}

Member Function Documentation

create()

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

inlinestatic

Creates an instance of this class.

Definition at line 49 of file OutputVtkBase.h.

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

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

PrepareOutput()

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

protected

Definition at line 428 of file OutputVtkBase.cpp.

{
    // Extract the output filename and extension
    string filename = m_config["outfile"].as<string>();
 
    ASSERTL0(filename != "", "Legacy VTK output requires a filename.");
 
    fs::path specPath    = GetPath(filename, vm);
    fs::path fulloutname = GetFullOutName(filename, vm);
    filename             = LibUtilities::PortablePath(fulloutname);
 
    if (m_f->m_comm->GetSpaceComm()->GetSize() != 1)
    {
        if (m_f->m_comm->GetSpaceComm()->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->GetSpaceComm()->Block();
    }
    else
    {
        cout << "Writing: " << specPath << endl;
    }
    return filename;
}

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

Referenced by Nektar::FieldUtils::OutputVtk::v_OutputFromExp(), v_OutputFromExp(), and v_OutputFromPts().

v_GetFullOutName()

fs::path Nektar::FieldUtils::OutputVtkBase::v_GetFullOutName ( std::string &  filename, po::variables_map &  vm  )

overrideprotectedvirtual

Reimplemented from Nektar::FieldUtils::OutputFileBase.

Definition at line 306 of file OutputVtkBase.cpp.

{
    int nprocs = m_f->m_comm->GetSpaceComm()->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->GetSpaceComm()->GetRank() % "vtu";
 
        // Generate full path name
        fs::path specPath = GetPath(filename, vm);
        fs::path poutfile(pad.str());
        fulloutname = specPath / poutfile;
    }
    return fulloutname;
}

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

v_GetModuleName()

std::string Nektar::FieldUtils::OutputVtkBase::v_GetModuleName ( )

inlineoverrideprotectedvirtual

Reimplemented from Nektar::FieldUtils::OutputFileBase.

Definition at line 59 of file OutputVtkBase.h.

    {
        return "OutputVtk";
    }

v_GetPath()

fs::path Nektar::FieldUtils::OutputVtkBase::v_GetPath ( std::string &  filename, po::variables_map &  vm  )

overrideprotectedvirtual

Reimplemented from Nektar::FieldUtils::OutputFileBase.

Definition at line 287 of file OutputVtkBase.cpp.

{
    int nprocs = m_f->m_comm->GetSpaceComm()->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);
}

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

Referenced by Nektar::FieldUtils::OutputVtk::WritePVtu().

v_OutputFromData()

void Nektar::FieldUtils::OutputVtkBase::v_OutputFromData ( po::variables_map &  vm )

overrideprotectedvirtual

Write from data to output file.

Implements Nektar::FieldUtils::OutputFileBase.

Definition at line 280 of file OutputVtkBase.cpp.

{
    NEKERROR(ErrorUtil::efatal,
             "OutputVtk can't write using only FieldData. You may need "
             "to add a mesh XML file to your input files.");
}

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

v_OutputFromExp()

void Nektar::FieldUtils::OutputVtkBase::v_OutputFromExp ( po::variables_map &  vm )

overrideprotectedvirtual

Write from m_exp to output file.

Implements Nektar::FieldUtils::OutputFileBase.

Definition at line 232 of file OutputVtkBase.cpp.

{
    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->GetSpaceComm()->GetRank() == 0) &&
        (m_f->m_comm->GetSpaceComm()->GetSize() != 1))
    {
        WritePVtu(vm);
    }
}

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

Referenced by Nektar::FieldUtils::OutputVtk::v_OutputFromExp().

v_OutputFromPts()

void Nektar::FieldUtils::OutputVtkBase::v_OutputFromPts ( po::variables_map &  vm )

overrideprotectedvirtual

Write from pts to output file.

Implements Nektar::FieldUtils::OutputFileBase.

Definition at line 67 of file OutputVtkBase.cpp.

{
    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].size() / nvert;
    }
 
    // write out pieces of data.
    outfile << "    <Piece NumberOfPoints=\"" << nPts << "\" NumberOfCells=\""
            << numBlocks << "\">" << endl;
    outfile << "      <Points>" << endl;
    outfile << "        <DataArray type=\"Float64\" "
            << "NumberOfComponents=\"" << 3 << R"(" 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\" "
            << R"(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].size(); ++j)
        {
            outfile << ptsConn[i][j] << " ";
            if ((!(cnt % nvert)) && cnt)
            {
                outfile << std::endl;
                outfile << "          ";
            }
            cnt++;
        }
    }
    outfile << "        </DataArray>" << endl;
    outfile << "        <DataArray type=\"Int32\" "
            << R"(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\" "
            << R"(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 << R"(        <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->GetSpaceComm()->GetRank() == 0) &&
        (m_f->m_comm->GetSpaceComm()->GetSize() != 1))
    {
        WritePVtu(vm);
        cout << "Written file: " << filename << endl;
    }
}

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 Nektar::FieldUtils::OutputVtk::v_OutputFromPts().

WriteEmptyVtkPiece()

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

private

Definition at line 344 of file OutputVtkBase.cpp.

{
    // write out empty piece of data.
    outfile << "    <Piece NumberOfPoints=\"" << 0 << "\" NumberOfCells=\"" << 0
            << "\">" << endl;
    outfile << "      <Points>" << endl;
    outfile << "        <DataArray type=\"Float64\" "
            << "NumberOfComponents=\"" << 3 << R"(" format="ascii">)" << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "      </Points>" << endl;
    outfile << "      <Cells>" << endl;
    outfile << "        <DataArray type=\"Int32\" "
            << R"(Name="connectivity" format="ascii">)" << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "        <DataArray type=\"Int32\" "
            << R"(Name="offsets" format="ascii">)" << endl;
 
    outfile << "          ";
    outfile << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "        <DataArray type=\"UInt8\" "
            << R"(Name="types" format="ascii">)" << endl;
    outfile << "          ";
    outfile << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "      </Cells>" << endl;
    outfile << "      <PointData>" << endl;
 
    outfile << "      </PointData>" << endl;
    outfile << "    </Piece>" << endl;
}

Referenced by v_OutputFromExp().

WritePVtu()

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

private

Definition at line 376 of file OutputVtkBase.cpp.

{
    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->GetSpaceComm()->GetSize();
    string path = LibUtilities::PortablePath(GetPath(filename, vm));
 
    outfile << "<?xml version=\"1.0\"?>" << endl;
    outfile << R"(<VTKFile type="PUnstructuredGrid" version="0.1" )"
            << "byte_order=\"LittleEndian\">" << endl;
    outfile << "<PUnstructuredGrid GhostLevel=\"0\">" << endl;
    outfile << "<PPoints> " << endl;
    outfile << R"(<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 << R"(<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;
}

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

Referenced by v_OutputFromExp(), and v_OutputFromPts().

WriteVtkFooter()

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

private

Definition at line 338 of file OutputVtkBase.cpp.

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

Referenced by v_OutputFromExp(), and v_OutputFromPts().

WriteVtkHeader()

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

private

Definition at line 330 of file OutputVtkBase.cpp.

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

Referenced by v_OutputFromExp(), and v_OutputFromPts().

Member Data Documentation

m_className

ModuleKey Nektar::FieldUtils::OutputVtkBase::m_className

static

Initial value:

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

Definition at line 53 of file OutputVtkBase.h.