Nektar::FieldUtils::OutputFld Class Reference

Converter from fld to vtk. More...

#include <OutputFld.h>

Inheritance diagram for Nektar::FieldUtils::OutputFld:

Collaboration diagram for Nektar::FieldUtils::OutputFld:

Public Member Functions
	OutputFld (FieldSharedPtr f)
virtual	~OutputFld ()
virtual void	Process (po::variables_map &vm)
	Write fld to output file. More...
virtual std::string	GetModuleName ()
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 (string key, 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 bool	GetRequireEquiSpaced (void)
FIELD_UTILS_EXPORT void	SetRequireEquiSpaced (bool pVal)
FIELD_UTILS_EXPORT void	EvaluateTriFieldAtEquiSpacedPts (LocalRegions::ExpansionSharedPtr &exp, const Array< OneD, const NekDouble > &infield, Array< OneD, NekDouble > &outfield)

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

Static Public Attributes
static ModuleKey	m_className []

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

Detailed Description

Converter from fld to vtk.

Definition at line 48 of file OutputFld.h.

Constructor & Destructor Documentation

Nektar::FieldUtils::OutputFld::OutputFld

(

FieldSharedPtr

f

)

Definition at line 57 of file OutputFld.cpp.

References Nektar::FieldUtils::Module::m_config.

                                     : OutputModule(f)
{
    m_config["format"] = ConfigOption(
        false, "Xml", "Output format of field file");
}

Nektar::FieldUtils::OutputFld::~OutputFld ( )

virtual

Definition at line 63 of file OutputFld.cpp.

{
}

Member Function Documentation

static boost::shared_ptr<Module> Nektar::FieldUtils::OutputFld::create ( FieldSharedPtr  f )

inlinestatic

Creates an instance of this class.

Definition at line 52 of file OutputFld.h.

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

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

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

inlinevirtual

Implements Nektar::FieldUtils::Module.

Definition at line 64 of file OutputFld.h.

    {
        return "OutputFld";
    }

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

virtual

Write fld to output file.

Implements Nektar::FieldUtils::Module.

Definition at line 67 of file OutputFld.cpp.

References CellMLToNektar.enum::answer, Nektar::LibUtilities::NekFactory< tKey, tBase, >::CreateInstance(), Nektar::SpatialDomains::BoundaryConditions::GetBoundaryRegions(), Nektar::LibUtilities::GetCommFactory(), Nektar::LibUtilities::GetFieldIOFactory(), Nektar::FieldUtils::Module::m_config, Nektar::FieldUtils::Module::m_f, Nektar::LibUtilities::ReduceSum, and CellMLToNektar.CellMLToNektar::writefile().

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

    // Get IO format
    std::string iofmt("Xml");
    if(m_f->m_session)
    {
        if (m_f->m_session->DefinesSolverInfo("IOFormat"))
        {
            iofmt = m_f->m_session->GetSolverInfo("IOFormat");
        }
        if (m_f->m_session->DefinesCmdLineArgument("io-format"))
        {
            iofmt =
                m_f->m_session->GetCmdLineArgument<std::string>("io-format");
        }
    }
    if(m_config["format"].m_beenSet)
    {
        iofmt = m_config["format"].as<string>();
    }

    // Set up communicator and FieldIO object.
    LibUtilities::CommSharedPtr c = m_f->m_session ? m_f->m_session->GetComm() :
        LibUtilities::GetCommFactory().CreateInstance("Serial", 0, 0);
    LibUtilities::FieldIOSharedPtr fld =
        LibUtilities::GetFieldIOFactory().CreateInstance(iofmt, c, true);

    if (m_f->m_writeBndFld)
    {
        ModuleKey module;

        if (m_f->m_verbose)
        {
            if (m_f->m_comm->TreatAsRankZero())
            {
                cout << "OutputFld: 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;
            }
        }

        // Extract data to boundaryconditions
        if (m_f->m_fldToBnd)
        {
            for (int i = 0; i < m_f->m_exp.size(); ++i)
            {
                m_f->m_exp[i]->FillBndCondFromField();
            }
        }

        int nfields = m_f->m_exp.size();
        Array<OneD, Array<OneD, const MultiRegions::ExpListSharedPtr> > BndExp(
            nfields);
        for (int i = 0; i < nfields; ++i)
        {
            BndExp[i] = m_f->m_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,
                                               m_f->m_exp[0]->GetGraph());
        const SpatialDomains::BoundaryRegionCollection bregions =
            bcs.GetBoundaryRegions();
        SpatialDomains::BoundaryRegionCollection::const_iterator breg_it;
        map<int, int> BndRegionMap;
        int cnt = 0;
        for (breg_it = bregions.begin(); breg_it != bregions.end();
             ++breg_it, ++cnt)
        {
            BndRegionMap[breg_it->first] = cnt;
        }

        // 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);

        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;

            std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
            std::vector<std::vector<NekDouble> > FieldData;

            if (BndRegionMap.count(m_f->m_bndRegionsToWrite[i]) == 1)
            {
                int Border = BndRegionMap[m_f->m_bndRegionsToWrite[i]];

                FieldDef = BndExp[0][Border]->GetFieldDefinitions();
                FieldData.resize(FieldDef.size());

                for (int j = 0; j < nfields; ++j)
                {
                    for (int k = 0; k < FieldDef.size(); ++k)
                    {
                        BndExp[j][Border]->AppendFieldData(FieldDef[k],
                                                           FieldData[k]);

                        if (m_f->m_fielddef.size() > 0)
                        {
                            FieldDef[k]->m_fields.push_back(
                                m_f->m_fielddef[0]->m_fields[j]);
                        }
                        else
                        {
                            FieldDef[k]->m_fields.push_back(
                                m_f->m_session->GetVariable(j));
                        }
                    }
                }

                if (m_f->m_addNormals)
                {
                    int normdim       = m_f->m_graph->GetMeshDimension();
                    string normstr[3] = {"Norm_x", "Norm_y", "Norm_z"};

                    // Get normals
                    Array<OneD, Array<OneD, NekDouble> > NormPhys;
                    m_f->m_exp[0]->GetBoundaryNormals(Border, NormPhys);

                    // add normal coefficients to list to be dumped
                    for (int j = 0; j < normdim; ++j)
                    {
                        BndExp[0][Border]->FwdTrans(
                            NormPhys[j], BndExp[0][Border]->UpdateCoeffs());

                        for (int k = 0; k < FieldDef.size(); ++k)
                        {
                            BndExp[0][Border]->AppendFieldData(FieldDef[k],
                                                               FieldData[k]);
                            FieldDef[k]->m_fields.push_back(normstr[j]);
                        }
                    }
                }

                // output error for regression checking.
                if (vm.count("error"))
                {
                    int rank = m_f->m_session->GetComm()->GetRank();

                    for (int j = 0; j < nfields; ++j)
                    {
                        BndExp[j][Border]->BwdTrans(
                            BndExp[j][Border]->GetCoeffs(),
                            BndExp[j][Border]->UpdatePhys());

                        // Note currently these calls will
                        // hange since not all partitions will
                        // call error.
                        NekDouble l2err =
                            BndExp[j][Border]->L2(BndExp[j][Border]->GetPhys());

                        NekDouble linferr = BndExp[j][Border]->Linf(
                            BndExp[j][Border]->GetPhys());

                        if (rank == 0)
                        {
                            cout << "L 2 error (variable "
                                 << FieldDef[0]->m_fields[j] << ") : " << l2err
                                 << endl;

                            cout << "L inf error (variable "
                                 << FieldDef[0]->m_fields[j]
                                 << ") : " << linferr << endl;
                        }
                    }
                }
            }

            fld->Write(outname, FieldDef, FieldData, m_f->m_fieldMetaDataMap);
        }
    }
    else
    {
        if (m_f->m_verbose)
        {
            if (m_f->m_comm->TreatAsRankZero())
            {
                cout << "OutputFld: Writing file..." << endl;
            }
        }

        fs::path writefile(filename);
        int writefld = 1;
        if (fs::exists(writefile) && (vm.count("forceoutput") == 0))
        {
            int rank = 0;
            LibUtilities::CommSharedPtr comm;

            if (m_f->m_session)
            {
                comm = m_f->m_session->GetComm();
                rank = comm->GetRank();
            }
            else
            {
                comm = LibUtilities::GetCommFactory().CreateInstance(
                    "Serial", 0, 0);
            }

            writefld = 0; // set to zero for reduce all to be correct.

            if (rank == 0)
            {
                string answer;
                cout << "Did you wish to overwrite " << filename << " (y/n)? ";
                getline(cin, answer);
                if (answer.compare("y") == 0)
                {
                    writefld = 1;
                }
                else
                {
                    cout << "Not writing file " << filename
                         << " because it already exists" << endl;
                }
            }

            comm->AllReduce(writefld, LibUtilities::ReduceSum);
        }

        if (writefld)
        {
            fld->Write(filename, m_f->m_fielddef, m_f->m_data,
                       m_f->m_fieldMetaDataMap);
        }

        // output error for regression checking.
        if (vm.count("error"))
        {
            int rank = m_f->m_session->GetComm()->GetRank();

            for (int j = 0; j < m_f->m_exp.size(); ++j)
            {
                if (m_f->m_exp[j]->GetPhysState() == false)
                {
                    m_f->m_exp[j]->BwdTrans(m_f->m_exp[j]->GetCoeffs(),
                                            m_f->m_exp[j]->UpdatePhys());
                }

                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 (rank == 0)
                {
                    cout << "L 2 error (variable "
                         << m_f->m_fielddef[0]->m_fields[j] << ") : " << l2err
                         << endl;

                    cout << "L inf error (variable "
                         << m_f->m_fielddef[0]->m_fields[j] << ") : " << linferr
                         << endl;
                }
            }
        }
    }
}

Member Data Documentation

ModuleKey Nektar::FieldUtils::OutputFld::m_className

static

Initial value:

= {
    GetModuleFactory().RegisterCreatorFunction(ModuleKey(eOutputModule, "fld"),
                                               OutputFld::create,
                                               "Writes a Fld file."),
    GetModuleFactory().RegisterCreatorFunction(ModuleKey(eOutputModule, "chk"),
                                               OutputFld::create,
                                               "Writes a Fld file."),
}

Definition at line 56 of file OutputFld.h.