Nektar::SolverUtils::FileFieldInterpolator Class Reference

#include <FileSolution.h>

Public Member Functions
void	InitObject (const std::string functionName, LibUtilities::SessionReaderSharedPtr pSession, const Array< OneD, const MultiRegions::ExpListSharedPtr > pFields, std::set< std::string > &variables, std::map< std::string, int > &series, std::map< std::string, NekDouble > &time)
void	InterpolateField (const std::string variable, Array< OneD, NekDouble > &outarray, NekDouble time)
void	InterpolateField (const int v, Array< OneD, NekDouble > &outarray, const NekDouble time)
NekDouble	GetStartTime ()

Protected Member Functions
DNekBlkMatSharedPtr	GetFloquetBlockMatrix (int nexp)
	FileFieldInterpolator ()
	~FileFieldInterpolator ()
void	DFT (const std::string file, const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const bool timefromfile)
void	ImportFldBase (std::string pInfile, const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, int slice, std::map< std::string, NekDouble > &params)
	Import Base flow. More...

Protected Attributes
LibUtilities::SessionReaderSharedPtr	m_session
int	m_start
	number of slices More...
int	m_skip
int	m_slices
NekDouble	m_timeStart
	period length More...
NekDouble	m_period
int	m_isperiodic
int	m_interporder
std::map< int, Array< OneD, NekDouble > >	m_interp
	interpolation vector More...
std::map< std::string, int >	m_variableMap
	variables More...

Friends
class	MemoryManager< FileFieldInterpolator >

Detailed Description

Definition at line 52 of file FileSolution.h.

Constructor & Destructor Documentation

FileFieldInterpolator()

Nektar::SolverUtils::FileFieldInterpolator::FileFieldInterpolator ( )

protected

Definition at line 451 of file FileSolution.cpp.

{
}

~FileFieldInterpolator()

Nektar::SolverUtils::FileFieldInterpolator::~FileFieldInterpolator ( )

protected

Definition at line 447 of file FileSolution.cpp.

{
}

Member Function Documentation

DFT()

void Nektar::SolverUtils::FileFieldInterpolator::DFT ( const std::string  file, const Array< OneD, const MultiRegions::ExpListSharedPtr > &  pFields, const bool  timefromfile  )

protected

Definition at line 656 of file FileSolution.cpp.

{
    for (auto it : m_variableMap)
    {
        int ncoeffs         = pFields[it.second]->GetNcoeffs();
        m_interp[it.second] = Array<OneD, NekDouble>(ncoeffs * m_slices, 0.0);
    }
 
    // Import the slides into auxiliary vector
    // The base flow should be stored in the form "filename_%d.ext"
    // A subdirectory can also be included, such as "dir/filename_%d.ext"
    size_t found = file.find("%d");
    std::map<std::string, NekDouble> params;
    if (found != string::npos)
    {
        ASSERTL0(file.find("%d", found + 1) == string::npos,
                 "There are more than one '%d'.");
        int nstart = m_start;
        std::vector<NekDouble> times;
        for (int i = 0; i < m_slices; ++i)
        {
            int filen = nstart + i * m_skip;
            auto fmt  = boost::format(file) % filen;
            ImportFldBase(fmt.str(), pFields, i, params);
            if (m_session->GetComm()->GetRank() == 0)
            {
                cout << "read base flow file " << fmt.str() << endl;
            }
            if (timefromfile && params.count("time"))
            {
                times.push_back(params["time"]);
            }
        }
        if (timefromfile && times.size() == m_slices && m_slices > 1)
        {
            m_timeStart = times[0];
            if (m_interporder < 1)
            {
                m_period = m_slices * (times[m_slices - 1] - times[0]) /
                           (m_slices - 1.);
            }
            else
            {
                m_period = times[m_slices - 1] - times[0];
            }
        }
    }
    else if (m_slices == 1)
    {
        ImportFldBase(file.c_str(), pFields, 0, params);
    }
    else
    {
        ASSERTL0(
            false,
            "Since N_slices is specified, the filename provided for function "
            "'BaseFlow' must include exactly one instance of the format "
            "specifier '%d', to index the time-slices.");
    }
 
    if (!m_isperiodic || m_slices == 1)
    {
        return;
    }
 
    // Discrete Fourier Transform of the fields
    for (auto it : m_interp)
    {
        int npoints = pFields[it.first]->GetNcoeffs();
#ifdef NEKTAR_USING_FFTW
 
        // Discrete Fourier Transform using FFTW
        Array<OneD, NekDouble> fft_in(npoints * m_slices);
        Array<OneD, NekDouble> fft_out(npoints * m_slices);
 
        Array<OneD, NekDouble> m_tmpIN(m_slices);
        Array<OneD, NekDouble> m_tmpOUT(m_slices);
 
        // Shuffle the data
        for (int j = 0; j < m_slices; ++j)
        {
            Vmath::Vcopy(npoints, &(it.second)[j * npoints], 1, &(fft_in[j]),
                         m_slices);
        }
 
        m_FFT = LibUtilities::GetNektarFFTFactory().CreateInstance("NekFFTW",
                                                                   m_slices);
 
        // FFT Transform
        for (int i = 0; i < npoints; i++)
        {
            m_FFT->FFTFwdTrans(m_tmpIN  = fft_in + i * m_slices,
                               m_tmpOUT = fft_out + i * m_slices);
        }
 
        // Reshuffle data
        for (int s = 0; s < m_slices; ++s)
        {
            Vmath::Vcopy(npoints, &fft_out[s], m_slices,
                         &(it.second)[s * npoints], 1);
        }
 
        Vmath::Zero(fft_in.size(), &fft_in[0], 1);
        Vmath::Zero(fft_out.size(), &fft_out[0], 1);
#else
        // Discrete Fourier Transform using MVM
        DNekBlkMatSharedPtr blkmat;
        blkmat = GetFloquetBlockMatrix(npoints);
 
        int nrows = blkmat->GetRows();
        int ncols = blkmat->GetColumns();
 
        Array<OneD, NekDouble> sortedinarray(ncols);
        Array<OneD, NekDouble> sortedoutarray(nrows);
 
        // Shuffle the data
        for (int j = 0; j < m_slices; ++j)
        {
            Vmath::Vcopy(npoints, &(it.second)[j * npoints], 1,
                         &(sortedinarray[j]), m_slices);
        }
 
        // Create NekVectors from the given data arrays
        NekVector<NekDouble> in(ncols, sortedinarray, eWrapper);
        NekVector<NekDouble> out(nrows, sortedoutarray, eWrapper);
 
        // Perform matrix-vector multiply.
        out = (*blkmat) * in;
 
        // Reshuffle data
        for (int s = 0; s < m_slices; ++s)
        {
            Vmath::Vcopy(npoints, &sortedoutarray[s], m_slices,
                         &(it.second)[s * npoints], 1);
        }
 
        for (int r = 0; r < sortedinarray.size(); ++r)
        {
            sortedinarray[0]  = 0;
            sortedoutarray[0] = 0;
        }
 
#endif
    }
}

References ASSERTL0, Nektar::LibUtilities::NekFactory< tKey, tBase, tParam >::CreateInstance(), Nektar::eWrapper, CellMLToNektar.pycml::format, GetFloquetBlockMatrix(), Nektar::LibUtilities::GetNektarFFTFactory(), ImportFldBase(), m_interp, m_interporder, m_isperiodic, m_period, m_session, m_skip, m_slices, m_start, m_timeStart, m_variableMap, Vmath::Vcopy(), and Vmath::Zero().

Referenced by InitObject().

GetFloquetBlockMatrix()

DNekBlkMatSharedPtr Nektar::SolverUtils::FileFieldInterpolator::GetFloquetBlockMatrix ( int  nexp )

protected

Definition at line 621 of file FileSolution.cpp.

{
    DNekMatSharedPtr loc_mat;
    DNekBlkMatSharedPtr BlkMatrix;
 
    Array<OneD, unsigned int> nrows(nexp);
    Array<OneD, unsigned int> ncols(nexp);
 
    nrows = Array<OneD, unsigned int>(nexp, m_slices);
    ncols = Array<OneD, unsigned int>(nexp, m_slices);
 
    MatrixStorage blkmatStorage = eDIAGONAL;
    BlkMatrix = MemoryManager<DNekBlkMat>::AllocateSharedPtr(nrows, ncols,
                                                             blkmatStorage);
 
    const LibUtilities::PointsKey Pkey(m_slices,
                                       LibUtilities::eFourierEvenlySpaced);
    const LibUtilities::BasisKey BK(LibUtilities::eFourier, m_slices, Pkey);
    StdRegions::StdSegExp StdSeg(BK);
 
    StdRegions::StdMatrixKey matkey(StdRegions::eFwdTrans,
                                    StdSeg.DetShapeType(), StdSeg);
 
    loc_mat = StdSeg.GetStdMatrix(matkey);
 
    // set up array of block matrices.
    for (int i = 0; i < nexp; ++i)
    {
        BlkMatrix->SetBlock(i, i, loc_mat);
    }
 
    return BlkMatrix;
}

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), Nektar::StdRegions::StdExpansion::DetShapeType(), Nektar::eDIAGONAL, Nektar::LibUtilities::eFourier, Nektar::LibUtilities::eFourierEvenlySpaced, Nektar::StdRegions::eFwdTrans, Nektar::StdRegions::StdExpansion::GetStdMatrix(), and m_slices.

Referenced by DFT().

GetStartTime()

NekDouble Nektar::SolverUtils::FileFieldInterpolator::GetStartTime

(

)

Definition at line 805 of file FileSolution.cpp.

{
    return m_timeStart;
}

References m_timeStart.

ImportFldBase()

void Nektar::SolverUtils::FileFieldInterpolator::ImportFldBase ( std::string  pInfile, const Array< OneD, const MultiRegions::ExpListSharedPtr > &  pFields, int  pSlice, std::map< std::string, NekDouble > &  params  )

protected

Import Base flow.

Import field from infile and load into m_fields. This routine will also perform a BwdTrans to ensure data is in both the physical and coefficient storage.

Parameters

pInFile	Filename to read.
pFields	Array of expansion lists

Definition at line 462 of file FileSolution.cpp.

{
    std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
    std::vector<std::vector<NekDouble>> FieldData;
 
    int numexp = pFields[0]->GetExpSize();
    Array<OneD, int> ElementGIDs(numexp);
 
    // Define list of global element ids
    for (int i = 0; i < numexp; ++i)
    {
        ElementGIDs[i] = pFields[0]->GetExp(i)->GetGeom()->GetGlobalID();
    }
 
    // Get Homogeneous
    LibUtilities::FieldIOSharedPtr fld =
        LibUtilities::FieldIO::CreateForFile(m_session, pInfile);
    fld->Import(pInfile, FieldDef, FieldData,
                LibUtilities::NullFieldMetaDataMap, ElementGIDs);
 
    int nFileVar = FieldDef[0]->m_fields.size();
    for (int j = 0; j < nFileVar; ++j)
    {
        std::string var = FieldDef[0]->m_fields[j];
        if (!m_variableMap.count(var))
        {
            continue;
        }
        int ncoeffs = pFields[m_variableMap[var]]->GetNcoeffs();
        Array<OneD, NekDouble> tmp_coeff(ncoeffs, 0.);
        for (int i = 0; i < FieldDef.size(); ++i)
        {
            pFields[m_variableMap[var]]->ExtractDataToCoeffs(
                FieldDef[i], FieldData[i], FieldDef[i]->m_fields[j], tmp_coeff);
        }
        Vmath::Vcopy(ncoeffs, &tmp_coeff[0], 1,
                     &m_interp[m_variableMap[var]][pSlice * ncoeffs], 1);
    }
 
    LibUtilities::FieldMetaDataMap fieldMetaDataMap;
    fld->ImportFieldMetaData(pInfile, fieldMetaDataMap);
    // check to see if time defined
    if (fieldMetaDataMap != LibUtilities::NullFieldMetaDataMap)
    {
        auto iter = fieldMetaDataMap.find("Time");
        if (iter != fieldMetaDataMap.end())
        {
            params["time"] = boost::lexical_cast<NekDouble>(iter->second);
        }
    }
}

References Nektar::LibUtilities::FieldIO::CreateForFile(), m_interp, m_session, m_variableMap, Nektar::LibUtilities::NullFieldMetaDataMap, and Vmath::Vcopy().

Referenced by DFT().

InitObject()

void Nektar::SolverUtils::FileFieldInterpolator::InitObject	(	const std::string	functionName,
		LibUtilities::SessionReaderSharedPtr	pSession,
		const Array< OneD, const MultiRegions::ExpListSharedPtr >	pFields,
		std::set< std::string > &	variables,
		std::map< std::string, int > &	series,
		std::map< std::string, NekDouble > &	time
	)

Definition at line 341 of file FileSolution.cpp.

{
    m_session = pSession;
    for (size_t i = 0; i < m_session->GetVariables().size(); ++i)
    {
        std::string var = m_session->GetVariable(i);
        if (variables.count(var))
        {
            ASSERTL0(m_session->DefinesFunction(functionName, var) &&
                         (m_session->GetFunctionType(functionName, var) ==
                          LibUtilities::eFunctionTypeFile),
                     functionName + "(" + var + ") is not defined as a file.");
            m_variableMap[var] = i;
        }
    }
 
    if (series.count("start"))
    {
        m_start = series["start"];
    }
    else
    {
        m_start = 0;
    }
 
    if (series.count("skip"))
    {
        m_skip = series["skip"];
    }
    else
    {
        m_skip = 1;
    }
 
    if (series.count("slices"))
    {
        m_slices = series["slices"];
    }
    else
    {
        m_slices = 1;
    }
 
    if (series.count("order"))
    {
        m_interporder = series["order"];
    }
    else
    {
        m_interporder = 0;
    }
 
    if (series.count("isperiodic"))
    {
        m_isperiodic = series["isperiodic"];
    }
    else
    {
        m_isperiodic = 1;
    }
 
    bool timefromfile = false;
    if (times.count("period"))
    {
        m_period = times["period"];
    }
    else if (m_slices > 1)
    {
        timefromfile = true;
    }
    if (times.count("start"))
    {
        m_timeStart = times["start"];
    }
    else
    {
        m_timeStart = 0.;
    }
 
    if (m_session->GetComm()->GetRank() == 0)
    {
        cout << "baseflow info : interpolation order " << m_interporder
             << ", period " << m_period << ", periodicity ";
        if (m_isperiodic)
        {
            cout << "yes\n";
        }
        else
        {
            cout << "no\n";
        }
        cout << "baseflow info : files from " << m_start << " to "
             << (m_start + (m_slices - 1) * m_skip) << " (skip " << m_skip
             << ") with " << (m_slices - (m_interporder > 1))
             << " time intervals" << endl;
    }
 
    string file = m_session->GetFunctionFilename("Solution", 0);
    DFT(file, pFields, timefromfile);
}

References ASSERTL0, DFT(), Nektar::LibUtilities::eFunctionTypeFile, m_interporder, m_isperiodic, m_period, m_session, m_skip, m_slices, m_start, m_timeStart, and m_variableMap.

InterpolateField() [1/2]

void Nektar::SolverUtils::FileFieldInterpolator::InterpolateField	(	const int	v,
		Array< OneD, NekDouble > &	outarray,
		const NekDouble	time
	)

Definition at line 528 of file FileSolution.cpp.

{
    // doesnot have this variable
    if (!m_interp.count(v))
    {
        return;
    }
    // one slice, steady solution
    int npoints = m_interp[v].size() / m_slices;
    if (m_slices == 1)
    {
        Vmath::Vcopy(npoints, &m_interp[v][0], 1, &outarray[0], 1);
        return;
    }
    // unsteady solution
    time -= m_timeStart;
    if (m_isperiodic && time > m_period)
    {
        time = fmod(time, m_period);
        if (time < 0.)
        {
            time += m_period;
        }
    }
    if (m_interporder < 1)
    {
        NekDouble BetaT = 2 * M_PI * fmod(time, m_period) / m_period;
        NekDouble phase;
        Array<OneD, NekDouble> auxiliary(npoints);
 
        Vmath::Vcopy(npoints, &m_interp[v][0], 1, &outarray[0], 1);
        Vmath::Svtvp(npoints, cos(0.5 * m_slices * BetaT),
                     &m_interp[v][npoints], 1, &outarray[0], 1, &outarray[0],
                     1);
 
        for (int i = 2; i < m_slices; i += 2)
        {
            phase = (i >> 1) * BetaT;
 
            Vmath::Svtvp(npoints, cos(phase), &m_interp[v][i * npoints], 1,
                         &outarray[0], 1, &outarray[0], 1);
            Vmath::Svtvp(npoints, -sin(phase), &m_interp[v][(i + 1) * npoints],
                         1, &outarray[0], 1, &outarray[0], 1);
        }
    }
    else
    {
        NekDouble x = time;
        x           = x / m_period * (m_slices - 1);
        int ix      = x;
        if (ix < 0)
        {
            ix = 0;
        }
        if (ix > m_slices - 2)
        {
            ix = m_slices - 2;
        }
        int padleft = max(0, m_interporder / 2 - 1);
        if (padleft > ix)
        {
            padleft = ix;
        }
        int padright = m_interporder - 1 - padleft;
        if (padright > m_slices - 1 - ix)
        {
            padright = m_slices - 1 - ix;
        }
        padleft = m_interporder - 1 - padright;
        Array<OneD, NekDouble> coeff(m_interporder, 1.);
        for (int i = 0; i < m_interporder; ++i)
        {
            for (int j = 0; j < m_interporder; ++j)
            {
                if (i != j)
                {
                    coeff[i] *= (x - ix + padleft - (NekDouble)j) /
                                ((NekDouble)i - (NekDouble)j);
                }
            }
        }
        Vmath::Zero(npoints, &outarray[0], 1);
        for (int i = ix - padleft; i < ix + padright + 1; ++i)
        {
            Vmath::Svtvp(npoints, coeff[i - ix + padleft],
                         &m_interp[v][i * npoints], 1, &outarray[0], 1,
                         &outarray[0], 1);
        }
    }
}

References m_interp, m_interporder, m_isperiodic, m_period, m_slices, m_timeStart, Vmath::Svtvp(), Vmath::Vcopy(), and Vmath::Zero().

InterpolateField() [2/2]

void Nektar::SolverUtils::FileFieldInterpolator::InterpolateField	(	const std::string	variable,
		Array< OneD, NekDouble > &	outarray,
		NekDouble	time
	)

Definition at line 517 of file FileSolution.cpp.

{
    if (!m_variableMap.count(variable))
    {
        return;
    }
    InterpolateField(m_variableMap[variable], outarray, time);
}

References InterpolateField(), and m_variableMap.

Referenced by InterpolateField().

Friends And Related Function Documentation

MemoryManager< FileFieldInterpolator >

friend class MemoryManager< FileFieldInterpolator >

friend

Definition at line 51 of file FileSolution.h.

Member Data Documentation

m_interp

std::map<int, Array<OneD, NekDouble> > Nektar::SolverUtils::FileFieldInterpolator::m_interp

protected

interpolation vector

Definition at line 83 of file FileSolution.h.

Referenced by DFT(), ImportFldBase(), and InterpolateField().

m_interporder

int Nektar::SolverUtils::FileFieldInterpolator::m_interporder

protected

Definition at line 81 of file FileSolution.h.

Referenced by DFT(), InitObject(), and InterpolateField().

m_isperiodic

int Nektar::SolverUtils::FileFieldInterpolator::m_isperiodic

protected

Definition at line 80 of file FileSolution.h.

Referenced by DFT(), InitObject(), and InterpolateField().

m_period

NekDouble Nektar::SolverUtils::FileFieldInterpolator::m_period

protected

Definition at line 79 of file FileSolution.h.

Referenced by DFT(), InitObject(), and InterpolateField().

m_session

LibUtilities::SessionReaderSharedPtr Nektar::SolverUtils::FileFieldInterpolator::m_session

protected

Definition at line 72 of file FileSolution.h.

Referenced by DFT(), ImportFldBase(), and InitObject().

m_skip

int Nektar::SolverUtils::FileFieldInterpolator::m_skip

protected

Definition at line 75 of file FileSolution.h.

Referenced by DFT(), and InitObject().

m_slices

int Nektar::SolverUtils::FileFieldInterpolator::m_slices

protected

Definition at line 76 of file FileSolution.h.

Referenced by DFT(), GetFloquetBlockMatrix(), InitObject(), and InterpolateField().

m_start

int Nektar::SolverUtils::FileFieldInterpolator::m_start

protected

number of slices

Definition at line 74 of file FileSolution.h.

Referenced by DFT(), and InitObject().

m_timeStart

NekDouble Nektar::SolverUtils::FileFieldInterpolator::m_timeStart

protected

period length

Definition at line 78 of file FileSolution.h.

Referenced by DFT(), GetStartTime(), InitObject(), and InterpolateField().

m_variableMap

std::map<std::string, int> Nektar::SolverUtils::FileFieldInterpolator::m_variableMap

protected

variables

Definition at line 85 of file FileSolution.h.

Referenced by DFT(), ImportFldBase(), InitObject(), and InterpolateField().