Converter from fld to vtk. More...

#include <OutputFileBase.h>

Inheritance diagram for Nektar::FieldUtils::OutputFileBase:

Public Member Functions
	OutputFileBase (FieldSharedPtr f)

virtual	~OutputFileBase ()

virtual void	Process (po::variables_map &vm)
	Write fld to output file. More...

virtual std::string	GetModuleName ()

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)

virtual	~Module ()=default

const ConfigOption &	GetConfigOption (const std::string &key) const

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)

Protected Member Functions
virtual void	OutputFromPts (po::variables_map &vm)=0
	Write from pts to output file. More...

virtual void	OutputFromExp (po::variables_map &vm)=0
	Write from m_exp to output file. More...

virtual void	OutputFromData (po::variables_map &vm)=0
	Write from data to output file. More...

virtual fs::path	GetPath (std::string &filename, po::variables_map &vm)=0

virtual fs::path	GetFullOutName (std::string &filename, po::variables_map &vm)=0

Protected Member Functions inherited from Nektar::FieldUtils::Module
	Module ()

Protected Attributes
bool	m_requireEquiSpaced

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...

Private Member Functions
bool	WriteFile (std::string &filename, po::variables_map &vm)

void	ConvertExpToEquispaced (po::variables_map &vm)

void	PrintErrorFromPts ()

void	PrintErrorFromExp ()

Additional Inherited Members
Public Attributes inherited from Nektar::FieldUtils::Module
FieldSharedPtr	m_f
	Field object. More...

Detailed Description

Converter from fld to vtk.

Definition at line 47 of file OutputFileBase.h.

Constructor & Destructor Documentation

◆ OutputFileBase()

Nektar::FieldUtils::OutputFileBase::OutputFileBase ( FieldSharedPtr f )

Definition at line 49 of file OutputFileBase.cpp.

                                                : OutputModule(f)
 {
     m_requireEquiSpaced            = false;
     m_config["writemultiplefiles"] = ConfigOption(
         true, "0",
         "Write multiple files in parallel or when using nparts option");
 }

References Nektar::FieldUtils::Module::m_config, and m_requireEquiSpaced.

◆ ~OutputFileBase()

Nektar::FieldUtils::OutputFileBase::~OutputFileBase ( )

virtual

Definition at line 57 of file OutputFileBase.cpp.

58 {

59 }

Member Function Documentation

◆ ConvertExpToEquispaced()

void Nektar::FieldUtils::OutputFileBase::ConvertExpToEquispaced ( po::variables_map & vm )

private

Definition at line 302 of file OutputFileBase.cpp.

 {
     // Information to create new expansion
     int numFields   = m_f->m_exp.size();
     m_f->m_fielddef = m_f->m_exp[0]->GetFieldDefinitions();
  
     // Set points to equispaced
     int nPointsNew = 0;
     if (vm.count("output-points"))
     {
         nPointsNew = vm["output-points"].as<int>();
     }
     m_f->m_graph->SetExpansionInfoToEvenlySpacedPoints(nPointsNew);
  
     // Save original expansion
     vector<MultiRegions::ExpListSharedPtr> expOld = m_f->m_exp;
     // Create new expansion
     m_f->m_exp[0] = m_f->SetUpFirstExpList(m_f->m_numHomogeneousDir, true);
     for (int i = 1; i < numFields; ++i)
     {
         m_f->m_exp[i] = m_f->AppendExpList(m_f->m_numHomogeneousDir);
     }
     // Extract result to new expansion
     for (int i = 0; i < numFields; ++i)
     {
         m_f->m_exp[i]->ExtractCoeffsToCoeffs(expOld[i], expOld[i]->GetCoeffs(),
                                              m_f->m_exp[i]->UpdateCoeffs());
         m_f->m_exp[i]->BwdTrans(m_f->m_exp[i]->GetCoeffs(),
                                 m_f->m_exp[i]->UpdatePhys());
     }
     // Extract boundary expansion if needed
     if (m_f->m_writeBndFld)
     {
         Array<OneD, const MultiRegions::ExpListSharedPtr> BndExpOld;
         MultiRegions::ExpListSharedPtr BndExp;
         for (int i = 0; i < numFields; ++i)
         {
             BndExpOld = expOld[i]->GetBndCondExpansions();
             for (int j = 0; j < BndExpOld.size(); ++j)
             {
                 BndExp = m_f->m_exp[i]->UpdateBndCondExpansion(j);
  
                 BndExp->ExtractCoeffsToCoeffs(BndExpOld[j],
                                               BndExpOld[j]->GetCoeffs(),
                                               BndExp->UpdateCoeffs());
             }
         }
     }
     m_f->m_fielddef = std::vector<LibUtilities::FieldDefinitionsSharedPtr>();
 }

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

Referenced by Process().

◆ GetFullOutName()

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

protectedpure virtual

Implemented in Nektar::FieldUtils::OutputVtk, Nektar::FieldUtils::OutputTecplot, Nektar::FieldUtils::OutputPts, and Nektar::FieldUtils::OutputFld.

Referenced by WriteFile().

◆ GetModuleDescription()

virtual std::string Nektar::FieldUtils::OutputFileBase::GetModuleDescription ( )

inlinevirtual

Reimplemented from Nektar::FieldUtils::Module.

Definition at line 61 of file OutputFileBase.h.

     {
         return "Writing file";
     }

◆ GetModuleName()

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

inlinevirtual

Implements Nektar::FieldUtils::Module.

Reimplemented in Nektar::FieldUtils::OutputVtk, Nektar::FieldUtils::OutputTecplot, Nektar::FieldUtils::OutputPts, and Nektar::FieldUtils::OutputFld.

Definition at line 56 of file OutputFileBase.h.

     {
         return "OutputFileBase";
     }

Referenced by Process().

◆ GetModulePriority()

virtual ModulePriority Nektar::FieldUtils::OutputFileBase::GetModulePriority ( )

inlinevirtual

Implements Nektar::FieldUtils::Module.

Definition at line 66 of file OutputFileBase.h.

     {
         return eOutput;
     }

References Nektar::FieldUtils::eOutput.

◆ GetPath()

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

protectedpure virtual

Implemented in Nektar::FieldUtils::OutputVtk, Nektar::FieldUtils::OutputTecplot, Nektar::FieldUtils::OutputPts, and Nektar::FieldUtils::OutputFld.

Referenced by WriteFile().

◆ OutputFromData()

virtual void Nektar::FieldUtils::OutputFileBase::OutputFromData ( po::variables_map & vm )

protectedpure virtual

Write from data to output file.

Implemented in Nektar::FieldUtils::OutputVtk, Nektar::FieldUtils::OutputTecplot, Nektar::FieldUtils::OutputPts, and Nektar::FieldUtils::OutputFld.

Referenced by Process().

◆ OutputFromExp()

virtual void Nektar::FieldUtils::OutputFileBase::OutputFromExp ( po::variables_map & vm )

protectedpure virtual

Write from m_exp to output file.

Implemented in Nektar::FieldUtils::OutputVtk, Nektar::FieldUtils::OutputTecplot, Nektar::FieldUtils::OutputPts, and Nektar::FieldUtils::OutputFld.

Referenced by Process().

◆ OutputFromPts()

virtual void Nektar::FieldUtils::OutputFileBase::OutputFromPts ( po::variables_map & vm )

protectedpure virtual

Write from pts to output file.

Implemented in Nektar::FieldUtils::OutputVtk, Nektar::FieldUtils::OutputTecplot, Nektar::FieldUtils::OutputPts, and Nektar::FieldUtils::OutputFld.

Referenced by Process().

◆ PrintErrorFromExp()

void Nektar::FieldUtils::OutputFileBase::PrintErrorFromExp ( )

private

Definition at line 397 of file OutputFileBase.cpp.

 {
     int coordim =
         m_f->m_exp[0]->GetExp(0)->GetCoordim() + m_f->m_numHomogeneousDir;
     int totpoints           = m_f->m_exp[0]->GetTotPoints();
     std::string coordVars[] = {"x", "y", "z"};
  
     // Set up storage for coordinates
     Array<OneD, Array<OneD, NekDouble>> coords(coordim);
     for (int i = 0; i < coordim; ++i)
     {
         coords[i] = Array<OneD, NekDouble>(totpoints);
     }
  
     // Get coordinates
     if (coordim == 1)
     {
         m_f->m_exp[0]->GetCoords(coords[0]);
     }
     else if (coordim == 2)
     {
         m_f->m_exp[0]->GetCoords(coords[0], coords[1]);
     }
     else
     {
         m_f->m_exp[0]->GetCoords(coords[0], coords[1], coords[2]);
     }
  
     for (int j = 0; j < coordim; ++j)
     {
         NekDouble l2err   = m_f->m_exp[0]->L2(coords[j]);
         NekDouble linferr = m_f->m_exp[0]->Linf(coords[j]);
  
         if (m_f->m_comm->TreatAsRankZero())
         {
             cout << "L 2 error (variable " << coordVars[j] << ") : " << l2err
                  << endl;
  
             cout << "L inf error (variable " << coordVars[j]
                  << ") : " << linferr << endl;
         }
     }
  
     for (int j = 0; j < m_f->m_exp.size(); ++j)
     {
         NekDouble l2err   = m_f->m_exp[j]->L2(m_f->m_exp[j]->GetPhys());
         NekDouble linferr = m_f->m_exp[j]->Linf(m_f->m_exp[j]->GetPhys());
  
         if (m_f->m_comm->TreatAsRankZero() && m_f->m_variables.size() > 0)
         {
             cout << "L 2 error (variable " << m_f->m_variables[j]
                  << ") : " << l2err << endl;
  
             cout << "L inf error (variable " << m_f->m_variables[j]
                  << ") : " << linferr << endl;
         }
     }
 }

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

Referenced by Process().

◆ PrintErrorFromPts()

void Nektar::FieldUtils::OutputFileBase::PrintErrorFromPts ( )

private

Definition at line 353 of file OutputFileBase.cpp.

 {
     int coordim             = m_f->m_fieldPts->GetDim();
     std::string coordVars[] = {"x", "y", "z"};
  
     vector<string> variables = m_f->m_variables;
     variables.insert(variables.begin(), coordVars, coordVars + coordim);
     // Get fields and coordinates
     Array<OneD, Array<OneD, NekDouble>> fields(variables.size());
  
     // We can just grab everything from points. This should be a
     // reference, not a copy.
     m_f->m_fieldPts->GetPts(fields);
     for (int i = 0; i < fields.size(); ++i)
     {
         // calculate L2 and Linf value
         int npts = fields[i].size();
  
         NekDouble l2err   = 0.0;
         NekDouble linferr = 0.0;
         for (int j = 0; j < npts; ++j)
         {
             l2err += fields[i][j] * fields[i][j];
             linferr = max(linferr, fabs(fields[i][j]));
         }
  
         m_f->m_comm->AllReduce(l2err, LibUtilities::ReduceSum);
         m_f->m_comm->AllReduce(npts, LibUtilities::ReduceSum);
         m_f->m_comm->AllReduce(linferr, LibUtilities::ReduceMax);
  
         l2err /= npts;
         l2err = sqrt(l2err);
  
         if (m_f->m_comm->TreatAsRankZero())
         {
             cout << "L 2 error (variable " << variables[i] << ") : " << l2err
                  << endl;
  
             cout << "L inf error (variable " << variables[i]
                  << ") : " << linferr << endl;
         }
     }
 }

References Nektar::FieldUtils::Module::m_f, Nektar::LibUtilities::ReduceMax, Nektar::LibUtilities::ReduceSum, and tinysimd::sqrt().

Referenced by Process().

◆ Process()

void Nektar::FieldUtils::OutputFileBase::Process ( po::variables_map & vm )

virtual

Write fld to output file.

Implements Nektar::FieldUtils::Module.

Reimplemented in Nektar::FieldUtils::OutputTecplot.

Definition at line 61 of file OutputFileBase.cpp.

 {
     m_f->SetUpExp(vm);
  
     string filename = m_config["outfile"].as<string>();
  
     if (m_f->m_fieldPts != LibUtilities::NullPtsField)
     {
         ASSERTL0(!m_f->m_writeBndFld, "Boundary can't be obtained from pts.");
         if (WriteFile(filename, vm))
         {
             OutputFromPts(vm);
  
             if (vm.count("error"))
             {
                 PrintErrorFromPts();
             }
         }
     }
     else if (m_f->m_exp.size())
     {
         // reset expansion definition to use equispaced points if required.
         if (m_requireEquiSpaced && (vm.count("noequispaced") == 0) &&
             m_f->m_exp[0]->GetNumElmts() != 0)
         {
             ConvertExpToEquispaced(vm);
         }
         if (m_f->m_writeBndFld)
         {
             if (m_f->m_verbose && m_f->m_comm->TreatAsRankZero())
             {
                 cout << "\t" << GetModuleName()
                      << ": Writing boundary file(s): ";
                 for (int i = 0; i < m_f->m_bndRegionsToWrite.size(); ++i)
                 {
                     cout << m_f->m_bndRegionsToWrite[i];
                     if (i < m_f->m_bndRegionsToWrite.size() - 1)
                     {
                         cout << ", ";
                     }
                 }
                 cout << endl;
             }
  
             int nfields = m_f->m_variables.size();
             int normdim = m_f->m_graph->GetMeshDimension();
  
             // Prepare for normals output
             if (m_f->m_addNormals)
             {
                 // Prepare for creating expansions for normals
                 m_f->m_exp.resize(nfields + normdim);
                 ;
  
                 // Include normal name in m_variables
                 string normstr[3] = {"Norm_x", "Norm_y", "Norm_z"};
                 for (int j = 0; j < normdim; ++j)
                 {
                     m_f->m_exp[nfields + j] =
                         m_f->AppendExpList(m_f->m_numHomogeneousDir);
                     m_f->m_variables.push_back(normstr[j]);
                 }
             }
  
             // Move m_exp to a new expansion vector
             vector<MultiRegions::ExpListSharedPtr> exp(m_f->m_exp.size());
             exp.swap(m_f->m_exp);
  
             Array<OneD, Array<OneD, const MultiRegions::ExpListSharedPtr>>
                 BndExp(exp.size());
             for (int i = 0; i < exp.size(); ++i)
             {
                 BndExp[i] = exp[i]->GetBndCondExpansions();
             }
  
             // get hold of partition boundary regions so we can match it to
             // desired region extraction
             SpatialDomains::BoundaryConditions bcs(m_f->m_session,
                                                    exp[0]->GetGraph());
             const SpatialDomains::BoundaryRegionCollection bregions =
                 bcs.GetBoundaryRegions();
             map<int, int> BndRegionMap;
             map<int, LibUtilities::CommSharedPtr> BndRegionComm;
             int cnt = 0;
             for (auto &breg_it : bregions)
             {
                 BndRegionMap[breg_it.first] = cnt++;
                 BndRegionComm[breg_it.first] =
                     bcs.GetBoundaryCommunicators()[breg_it.first];
             }
  
             // find ending of output file and insert _b1, _b2
             int dot     = filename.find_last_of('.') + 1;
             string ext  = filename.substr(dot, filename.length() - dot);
             string name = filename.substr(0, dot - 1);
  
             // Store temporary communicator
             LibUtilities::CommSharedPtr tmpComm = m_f->m_comm;
  
             for (int i = 0; i < m_f->m_bndRegionsToWrite.size(); ++i)
             {
                 string outname =
                     name + "_b" +
                     boost::lexical_cast<string>(m_f->m_bndRegionsToWrite[i]) +
                     "." + ext;
  
                 if (!WriteFile(outname, vm))
                 {
                     continue;
                 }
                 RegisterConfig("outfile", outname);
  
                 if (BndRegionMap.count(m_f->m_bndRegionsToWrite[i]) == 1)
                 {
                     m_f->m_comm = BndRegionComm[m_f->m_bndRegionsToWrite[i]];
  
                     int Border = BndRegionMap[m_f->m_bndRegionsToWrite[i]];
  
                     for (int j = 0; j < exp.size(); ++j)
                     {
                         m_f->m_exp[j] = BndExp[j][Border];
                         m_f->m_exp[j]->BwdTrans(m_f->m_exp[j]->GetCoeffs(),
                                                 m_f->m_exp[j]->UpdatePhys());
                     }
  
                     if (m_f->m_addNormals)
                     {
                         // Get normals
                         Array<OneD, Array<OneD, NekDouble>> NormPhys;
                         exp[0]->GetBoundaryNormals(Border, NormPhys);
  
                         // add normal coefficients to expansions
                         for (int j = 0; j < normdim; ++j)
                         {
                             m_f->m_exp[nfields + j] =
                                 BndExp[nfields + j][Border];
                             Vmath::Vcopy(
                                 m_f->m_exp[nfields + j]->GetTotPoints(),
                                 NormPhys[j], 1,
                                 m_f->m_exp[nfields + j]->UpdatePhys(), 1);
                             m_f->m_exp[nfields + j]->FwdTrans_IterPerExp(
                                 m_f->m_exp[nfields + j]->GetPhys(),
                                 m_f->m_exp[nfields + j]->UpdateCoeffs());
                         }
                     }
                     OutputFromExp(vm);
                     // output error for regression checking.
                     if (vm.count("error"))
                     {
                         PrintErrorFromExp();
                     }
  
                     // Reset communicator
                     m_f->m_comm = tmpComm;
                 }
  
                 // put outfile back to filename in case of nparts option
                 RegisterConfig("outfile", filename);
             }
             // Restore m_exp
             exp.swap(m_f->m_exp);
         }
         else
         {
             if (WriteFile(filename, vm))
             {
                 OutputFromExp(vm);
                 // output error for regression checking.
                 if (vm.count("error"))
                 {
                     PrintErrorFromExp();
                 }
             }
         }
     }
     else if (m_f->m_data.size())
     {
         ASSERTL0(!m_f->m_writeBndFld, "Boundary extraction requires xml file.");
         if (WriteFile(filename, vm))
         {
             OutputFromData(vm);
         }
     }
 }

References ASSERTL0, ConvertExpToEquispaced(), Nektar::SpatialDomains::BoundaryConditions::GetBoundaryCommunicators(), Nektar::SpatialDomains::BoundaryConditions::GetBoundaryRegions(), GetModuleName(), Nektar::FieldUtils::Module::m_config, Nektar::FieldUtils::Module::m_f, m_requireEquiSpaced, CellMLToNektar.pycml::name, Nektar::LibUtilities::NullPtsField, OutputFromData(), OutputFromExp(), OutputFromPts(), PrintErrorFromExp(), PrintErrorFromPts(), Nektar::FieldUtils::Module::RegisterConfig(), Vmath::Vcopy(), and WriteFile().

Referenced by Nektar::FieldUtils::OutputTecplot::Process().

◆ WriteFile()

bool Nektar::FieldUtils::OutputFileBase::WriteFile	(	std::string &	filename,
		po::variables_map &	vm
	)

private

Definition at line 246 of file OutputFileBase.cpp.

 {
     // Get path to file. If procid was defined, get the full name
     //     to avoid checking files from other partitions
     fs::path outFile;
     if (vm.count("nparts"))
     {
         outFile = GetFullOutName(filename, vm);
     }
     else
     {
         outFile = GetPath(filename, vm);
     }
  
     LibUtilities::CommSharedPtr comm;
     if (m_f->m_comm)
     {
         comm = m_f->m_comm;
     }
     else
     {
         comm = LibUtilities::GetCommFactory().CreateInstance("Serial", 0, 0);
     }
  
     int count = fs::exists(outFile) ? 1 : 0;
     comm->AllReduce(count, LibUtilities::ReduceSum);
  
     int writeFile = 1;
     if (count && (vm.count("forceoutput") == 0))
     {
         if (vm.count("nparts") == 0) // do not do check if --nparts is enabled.
         {
  
             writeFile = 0; // set to zero for reduce all to be correct.
  
             if (comm->TreatAsRankZero())
             {
                 string answer;
                 cout << "Did you wish to overwrite " << outFile << " (y/n)? ";
                 getline(cin, answer);
                 if (answer.compare("y") == 0)
                 {
                     writeFile = 1;
                 }
                 else
                 {
                     cout << "Not writing file " << filename
                          << " because it already exists" << endl;
                 }
             }
             comm->AllReduce(writeFile, LibUtilities::ReduceSum);
         }
     }
     return (writeFile == 0) ? false : true;
 }

References CellMLToNektar.enum::answer, Nektar::LibUtilities::NekFactory< tKey, tBase, tParam >::CreateInstance(), Nektar::LibUtilities::GetCommFactory(), GetFullOutName(), GetPath(), Nektar::FieldUtils::Module::m_f, and Nektar::LibUtilities::ReduceSum.

Referenced by Process().

Member Data Documentation

◆ m_requireEquiSpaced

bool Nektar::FieldUtils::OutputFileBase::m_requireEquiSpaced

protected

Definition at line 87 of file OutputFileBase.h.

Referenced by OutputFileBase(), Nektar::FieldUtils::OutputTecplot::OutputTecplot(), Nektar::FieldUtils::OutputVtk::OutputVtk(), and Process().

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ OutputFileBase()

◆ ~OutputFileBase()

Member Function Documentation

◆ ConvertExpToEquispaced()

◆ GetFullOutName()

◆ GetModuleDescription()

◆ GetModuleName()

◆ GetModulePriority()

◆ GetPath()

◆ OutputFromData()

◆ OutputFromExp()

◆ OutputFromPts()

◆ PrintErrorFromExp()

◆ PrintErrorFromPts()

◆ Process()

◆ WriteFile()

Member Data Documentation

◆ m_requireEquiSpaced