Nektar::LinearisedAdvection Class Reference

#include <LinearisedAdvection.h>

Inheritance diagram for Nektar::LinearisedAdvection:

Collaboration diagram for Nektar::LinearisedAdvection:

Static Public Member Functions
static SolverUtils::AdvectionSharedPtr	create (std::string)
	Creates an instance of this class. More...

Static Public Attributes
static std::string	className
	Name of class. More...

Protected Member Functions
DNekBlkMatSharedPtr	GetFloquetBlockMatrix (FloquetMatType mattype, bool UseContCoeffs=false) const
DNekBlkMatSharedPtr	GenFloquetBlockMatrix (FloquetMatType mattype, bool UseContCoeffs=false) const
	LinearisedAdvection ()
virtual	~LinearisedAdvection ()
virtual void	v_InitObject (LibUtilities::SessionReaderSharedPtr pSession, Array< OneD, MultiRegions::ExpListSharedPtr > pFields)
	Initialises the advection object. More...
virtual void	v_Advect (const int nConvectiveFields, const Array< OneD, MultiRegions::ExpListSharedPtr > &fields, const Array< OneD, Array< OneD, NekDouble > > &advVel, const Array< OneD, Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble &time)
	Advects a vector field. More...
virtual void	v_SetBaseFlow (const Array< OneD, Array< OneD, NekDouble > > &inarray)
	Overrides the base flow used during linearised advection. More...
void	UpdateBase (const NekDouble m_slices, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, const NekDouble m_time, const NekDouble m_period)
void	DFT (const string file, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields, const NekDouble m_slices)
void	ImportFldBase (std::string pInfile, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields, int slice)
	Import Base flow. More...

Protected Attributes
LibUtilities::SessionReaderSharedPtr	m_session
int	m_spacedim
int	m_expdim
Array< OneD, Array< OneD, NekDouble > >	m_baseflow
	Storage for base flow. More...
int	m_slices
	number of slices More...
NekDouble	m_period
	period length More...
Array< OneD, Array< OneD, NekDouble > >	m_interp
	interpolation vector More...
LibUtilities::NektarFFTSharedPtr	m_FFT
	auxiliary variables More...
Array< OneD, NekDouble >	m_tmpIN
Array< OneD, NekDouble >	m_tmpOUT
bool	m_useFFTW
bool	m_singleMode
	flag to determine if use single mode or not More...
bool	m_halfMode
	flag to determine if use half mode or not More...
bool	m_multipleModes
	flag to determine if use multiple mode or not More...
FloquetBlockMatrixMapShPtr	m_FloquetBlockMat
Protected Attributes inherited from Nektar::SolverUtils::Advection
AdvectionFluxVecCB	m_fluxVector
	Callback function to the flux vector (set when advection is in conservative form). More...
RiemannSolverSharedPtr	m_riemann
	Riemann solver for DG-type schemes. More...
int	m_spaceDim
	Storage for space dimension. Used for homogeneous extension. More...

Private Types
enum	FloquetMatType { eForwardsCoeff, eForwardsPhys }
enum	HomogeneousType { eHomogeneous1D, eHomogeneous2D, eHomogeneous3D, eNotHomogeneous }
	Parameter for homogeneous expansions. More...
typedef map< FloquetMatType, DNekBlkMatSharedPtr >	FloquetBlockMatrixMap
	A map between matrix keys and their associated block matrices. More...
typedef boost::shared_ptr < FloquetBlockMatrixMap >	FloquetBlockMatrixMapShPtr
	A shared pointer to a BlockMatrixMap. More...

Private Attributes
bool	m_useFFT
	flag to determine if use or not the FFT for transformations More...
enum HomogeneousType	m_HomogeneousType
NekDouble	m_LhomX
	physical length in X direction (if homogeneous) More...
NekDouble	m_LhomY
	physical length in Y direction (if homogeneous) More...
NekDouble	m_LhomZ
	physical length in Z direction (if homogeneous) More...
int	m_npointsX
	number of points in X direction (if homogeneous) More...
int	m_npointsY
	number of points in Y direction (if homogeneous) More...
int	m_npointsZ
	number of points in Z direction (if homogeneous) More...
int	m_HomoDirec
	number of homogenous directions More...
int	m_NumMode
	Mode to use in case of single mode analysis. More...
SpatialDomains::BoundaryConditionsSharedPtr	m_boundaryConditions

Friends
class	MemoryManager< LinearisedAdvection >

Additional Inherited Members
Public Member Functions inherited from Nektar::SolverUtils::Advection
SOLVER_UTILS_EXPORT void	InitObject (LibUtilities::SessionReaderSharedPtr pSession, Array< OneD, MultiRegions::ExpListSharedPtr > pFields)
	Interface function to initialise the advection object. More...
SOLVER_UTILS_EXPORT void	Advect (const int nConvectiveFields, const Array< OneD, MultiRegions::ExpListSharedPtr > &fields, const Array< OneD, Array< OneD, NekDouble > > &advVel, const Array< OneD, Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble &time)
	Interface function to advect the vector field. More...
template<typename FuncPointerT , typename ObjectPointerT >
void	SetFluxVector (FuncPointerT func, ObjectPointerT obj)
	Set the flux vector callback function. More...
void	SetRiemannSolver (RiemannSolverSharedPtr riemann)
	Set a Riemann solver object for this advection object. More...
void	SetFluxVector (AdvectionFluxVecCB fluxVector)
	Set the flux vector callback function. More...
void	SetBaseFlow (const Array< OneD, Array< OneD, NekDouble > > &inarray)
	Set the base flow used for linearised advection objects. More...

Detailed Description

Definition at line 47 of file LinearisedAdvection.h.

Member Typedef Documentation

typedef map< FloquetMatType, DNekBlkMatSharedPtr> Nektar::LinearisedAdvection::FloquetBlockMatrixMap

private

A map between matrix keys and their associated block matrices.

Definition at line 57 of file LinearisedAdvection.h.

typedef boost::shared_ptr<FloquetBlockMatrixMap> Nektar::LinearisedAdvection::FloquetBlockMatrixMapShPtr

private

A shared pointer to a BlockMatrixMap.

Definition at line 59 of file LinearisedAdvection.h.

Member Enumeration Documentation

enum Nektar::LinearisedAdvection::FloquetMatType

private

Enumerator
eForwardsCoeff
eForwardsPhys

Definition at line 49 of file LinearisedAdvection.h.

    {
        eForwardsCoeff,
        eForwardsPhys
    };

enum Nektar::LinearisedAdvection::HomogeneousType

private

Parameter for homogeneous expansions.

Enumerator
eHomogeneous1D
eHomogeneous2D
eHomogeneous3D
eNotHomogeneous

Definition at line 146 of file LinearisedAdvection.h.

    {
        eHomogeneous1D,
        eHomogeneous2D,
        eHomogeneous3D,
        eNotHomogeneous
    };

Constructor & Destructor Documentation

Nektar::LinearisedAdvection::LinearisedAdvection ( )

protected

Constructor. Creates ...

Parameters

param

Definition at line 64 of file LinearisedAdvection.cpp.

                                        :
    Advection()
{
}

Nektar::LinearisedAdvection::~LinearisedAdvection ( )

protectedvirtual

Definition at line 232 of file LinearisedAdvection.cpp.

{
}

Member Function Documentation

static SolverUtils::AdvectionSharedPtr Nektar::LinearisedAdvection::create ( std::string  )

inlinestatic

Creates an instance of this class.

Definition at line 65 of file LinearisedAdvection.h.

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

                                                           {
        return MemoryManager<LinearisedAdvection>::AllocateSharedPtr();
    }

void Nektar::LinearisedAdvection::DFT ( const string  file, Array< OneD, MultiRegions::ExpListSharedPtr > &  pFields, const NekDouble  m_slices  )

protected

Definition at line 767 of file LinearisedAdvection.cpp.

References ASSERTL0, Nektar::LibUtilities::NekFactory< tKey, tBase, >::CreateInstance(), eForwardsPhys, Nektar::eWrapper, GetFloquetBlockMatrix(), Nektar::LibUtilities::GetNektarFFTFactory(), ImportFldBase(), m_baseflow, m_FFT, m_interp, m_slices, m_tmpIN, m_tmpOUT, Vmath::Smul(), Vmath::Vcopy(), and Vmath::Zero().

Referenced by v_InitObject().

{
    int ConvectedFields = m_baseflow.num_elements()-1;
    int npoints         = m_baseflow[0].num_elements();
    m_interp            = Array<OneD, Array<OneD, NekDouble> > (ConvectedFields);

    for (int i = 0; i < ConvectedFields; ++i)
    {
        m_interp[i] = Array<OneD,NekDouble>(npoints*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");
    ASSERTL0(found != string::npos && file.find("%d", found+1) == string::npos,
             "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.");
    char* buffer = new char[file.length() + 8];
    for (int i = 0; i < m_slices; ++i)
    {
        sprintf(buffer, file.c_str(), i);
        ImportFldBase(buffer,pFields,i);
    }
    delete[] buffer;


    // Discrete Fourier Transform of the fields
    for(int k=0; k< ConvectedFields;++k)
    {
#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,&m_interp[k][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,&m_interp[k][s*npoints],1);

        }

        Vmath::Zero(fft_in.num_elements(),&fft_in[0],1);
        Vmath::Zero(fft_out.num_elements(),&fft_out[0],1);
#else
        //Discrete Fourier Transform using MVM
        DNekBlkMatSharedPtr blkmat;
        blkmat = GetFloquetBlockMatrix(eForwardsPhys);

        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,&m_interp[k][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,&m_interp[k][s*npoints],1);
        }

        for(int r=0; r<sortedinarray.num_elements();++r)
        {
            sortedinarray[0]=0;
            sortedoutarray[0]=0;
        }

#endif

        //scaling of the Fourier coefficients
        NekDouble j=-1;
        for (int i = 2; i < m_slices; i += 2)
        {
            Vmath::Smul(2*npoints,j,&m_interp[k][i*npoints],1,&m_interp[k][i*npoints],1);
            j=-j;

        }

    }

}

DNekBlkMatSharedPtr Nektar::LinearisedAdvection::GenFloquetBlockMatrix ( FloquetMatType  mattype, bool  UseContCoeffs = false  ) const

protected

DNekBlkMatSharedPtr Nektar::LinearisedAdvection::GetFloquetBlockMatrix ( FloquetMatType  mattype, bool  UseContCoeffs = false  ) const

protected

Definition at line 728 of file LinearisedAdvection.cpp.

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

Referenced by DFT().

{
    DNekMatSharedPtr    loc_mat;
    DNekBlkMatSharedPtr BlkMatrix;
    int n_exp = 0;

    n_exp = m_baseflow[0].num_elements(); // will operatore on m_phys

    Array<OneD,unsigned int> nrows(n_exp);
    Array<OneD,unsigned int> ncols(n_exp);

    nrows = Array<OneD, unsigned int>(n_exp,m_slices);
    ncols = Array<OneD, unsigned int>(n_exp,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 < n_exp; ++i)
    {
        BlkMatrix->SetBlock(i,i,loc_mat);
    }

    return BlkMatrix;
}

void Nektar::LinearisedAdvection::ImportFldBase ( std::string  pInfile, Array< OneD, MultiRegions::ExpListSharedPtr > &  pFields, int  slice  )

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

infile

Filename to read.

Definition at line 576 of file LinearisedAdvection.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, m_baseflow, m_halfMode, m_interp, m_multipleModes, m_npointsZ, m_session, m_singleMode, Nektar::LibUtilities::NullFieldMetaDataMap, Vmath::Vcopy(), and Vmath::Zero().

Referenced by DFT(), and v_InitObject().

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

    int nqtot = m_baseflow[0].num_elements();
    int nvar = m_session->GetVariables().size();
    int s;
    Array<OneD, NekDouble> tmp_coeff(pFields[0]->GetNcoeffs(), 0.0);

    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 =
    MemoryManager<LibUtilities::FieldIO>::AllocateSharedPtr(
                                                    m_session->GetComm());
    fld->Import(pInfile, FieldDef, FieldData,
                LibUtilities::NullFieldMetaDataMap,
                ElementGIDs);


    if(m_session->DefinesSolverInfo("HOMOGENEOUS"))
    {
        std::string HomoStr = m_session->GetSolverInfo("HOMOGENEOUS");
    }

    // copy FieldData into m_fields
    for(int j = 0; j < nvar; ++j)
    {
        for(int i = 0; i < FieldDef.size(); ++i)
        {
            if((m_session->DefinesSolverInfo("HOMOGENEOUS") &&
               (m_session->GetSolverInfo("HOMOGENEOUS")=="HOMOGENEOUS1D" ||
                m_session->GetSolverInfo("HOMOGENEOUS")=="1D" ||
                m_session->GetSolverInfo("HOMOGENEOUS")=="Homo1D")) &&
                 m_multipleModes==false)
            {
                // w-component must be ignored and set to zero.
                // SJS I do not believe this is always the case
                if (j != nvar - 2)
                {
                    // p component (it is 4th variable of the 3D and
                    // corresponds 3rd variable of 2D)
                    s = (j == nvar - 1) ? 2 : j;

                    //extraction of the 2D
                    pFields[j]->ExtractDataToCoeffs(
                                        FieldDef[i],
                                        FieldData[i],
                                        FieldDef[i]->m_fields[s],
                                        tmp_coeff);

                }

                //Zero higher modes than being considered in
                //multi-mode expansion
                if (m_npointsZ > 2)
                {
                    // @Chris not clear why this is being done. Seems
                    // to be zeroing all but the first two complex
                    // modes?
                    int ncplane = (pFields[0]->GetNcoeffs()) / m_npointsZ;
                    Vmath::Zero(ncplane*(m_npointsZ-2),
                                &tmp_coeff[2*ncplane], 1);
                }
            }
            // 2D cases
            else
            {
                bool flag = FieldDef[i]->m_fields[j] ==
                    m_session->GetVariable(j);

                ASSERTL0(flag, (std::string("Order of ") + pInfile
                                + std::string(" data and that defined in "
                                "m_boundaryconditions differs")).c_str());

                pFields[j]->ExtractDataToCoeffs(FieldDef[i], FieldData[i],
                                                FieldDef[i]->m_fields[j],
                                                tmp_coeff);
            }
        }

        if(m_singleMode || m_halfMode)
        {
            //pFields[j]->SetWaveSpace(true);

            pFields[j]->GetPlane(0)->BwdTrans(tmp_coeff, m_baseflow[j]);

            if(m_singleMode)
            {
                //copy the bwd trans into the second plane for single
                //Mode Analysis
                int ncplane=(pFields[0]->GetNpoints())/m_npointsZ;
                Vmath::Vcopy(ncplane,&m_baseflow[j][0],1,&m_baseflow[j][ncplane],1);
            }
        }
        else // fully 3D base flow - put in physical space.
        {
            bool oldwavespace = pFields[j]->GetWaveSpace();
            pFields[j]->SetWaveSpace(false);
            pFields[j]->BwdTrans(tmp_coeff, m_baseflow[j]);
            pFields[j]->SetWaveSpace(oldwavespace);
        }
    }

    if(m_session->DefinesParameter("N_slices"))
    {
        int nConvectiveFields = pFields.num_elements()-1;

        for(int i=0; i<nConvectiveFields;++i)
        {

            Vmath::Vcopy(nqtot, &m_baseflow[i][0], 1, &m_interp[i][slice*nqtot], 1);
        }

    }
}

void Nektar::LinearisedAdvection::UpdateBase ( const NekDouble  m_slices, const Array< OneD, const NekDouble > &  inarray, Array< OneD, NekDouble > &  outarray, const NekDouble  m_time, const NekDouble  m_period  )

protected

Definition at line 703 of file LinearisedAdvection.cpp.

References m_baseflow, m_period, m_slices, Vmath::Svtvp(), and Vmath::Vcopy().

Referenced by v_Advect().

{
    int npoints     = m_baseflow[0].num_elements();
    NekDouble BetaT = 2*M_PI*fmod (m_time, m_period) / m_period;
    NekDouble phase;
    Array<OneD, NekDouble> auxiliary(npoints);

    Vmath::Vcopy(npoints,&inarray[0],1,&outarray[0],1);
    Vmath::Svtvp(npoints, cos(0.5*m_slices*BetaT),&inarray[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),&inarray[i*npoints],1,&outarray[0],1,&outarray[0],1);
        Vmath::Svtvp(npoints, -sin(phase), &inarray[(i+1)*npoints], 1, &outarray[0], 1,&outarray[0],1);
    }

}

void Nektar::LinearisedAdvection::v_Advect ( const int  nConvectiveFields, const Array< OneD, MultiRegions::ExpListSharedPtr > &  fields, const Array< OneD, Array< OneD, NekDouble > > &  advVel, const Array< OneD, Array< OneD, NekDouble > > &  inarray, Array< OneD, Array< OneD, NekDouble > > &  outarray, const NekDouble &  time  )

protectedvirtual

Advects a vector field.

Implements Nektar::SolverUtils::Advection.

Definition at line 239 of file LinearisedAdvection.cpp.

References ASSERTL0, ASSERTL1, Nektar::LibUtilities::eFunctionTypeFile, m_baseflow, m_halfMode, m_interp, m_multipleModes, m_period, m_session, m_slices, Vmath::Neg(), UpdateBase(), Vmath::Vmul(), and Vmath::Vvtvp().

{
    ASSERTL1(nConvectiveFields == inarray.num_elements(),
             "Number of convective fields and Inarray are not compatible");

    int nPointsTot = fields[0]->GetNpoints();
    int ndim       = advVel.num_elements();

    Array<OneD, NekDouble > Deriv
                = Array<OneD, NekDouble> (nPointsTot*nConvectiveFields);

    Array<OneD, NekDouble> grad0,grad1,grad2;

    // Evaluation of the gradient of each component of the base flow
    // \nabla U
    Array<OneD, NekDouble> grad_base_u0,grad_base_u1,grad_base_u2;

    // \nabla V
    Array<OneD, NekDouble> grad_base_v0,grad_base_v1,grad_base_v2;

    // \nabla W
    Array<OneD, NekDouble> grad_base_w0,grad_base_w1,grad_base_w2;

    grad0        = Array<OneD, NekDouble> (nPointsTot);
    grad_base_u0 = Array<OneD, NekDouble> (nPointsTot);
    grad_base_v0 = Array<OneD, NekDouble> (nPointsTot);
    grad_base_w0 = Array<OneD, NekDouble> (nPointsTot);

    // Evaluation of the base flow for periodic cases
    if (m_slices > 1)
    {
        ASSERTL0(m_session->GetFunctionType("BaseFlow", 0)
                 == LibUtilities::eFunctionTypeFile,
                 "Base flow should be a sequence of files.");

        for (int i = 0; i < ndim; ++i)
        {
            UpdateBase(m_slices, m_interp[i], m_baseflow[i],
                       time, m_period);
        }
    }


    //Evaluate the linearised advection term
    switch(ndim)
    {
        case 1:         // 1D
            ASSERTL0(false,"Not set up for 1D");
            break;
        case 2:  //2D
        {
            grad1 = Array<OneD, NekDouble> (nPointsTot);
            grad_base_u1 = Array<OneD, NekDouble> (nPointsTot);
            grad_base_v1 = Array<OneD, NekDouble> (nPointsTot);

            //Derivates of the base flow
            fields[0]-> PhysDeriv(m_baseflow[0], grad_base_u0, grad_base_u1);
            fields[0]-> PhysDeriv(m_baseflow[1], grad_base_v0, grad_base_v1);

            //x-equation
            fields[0]->PhysDeriv(inarray[0],grad0,grad1);
            // Evaluate U du'/dx
            Vmath::Vmul (nPointsTot,grad0,1,m_baseflow[0],1,outarray[0],1);
            //Evaluate U du'/dx+ V du'/dy
            Vmath::Vvtvp(nPointsTot,grad1,1,m_baseflow[1],1,outarray[0],1,
                         outarray[0],1);
            //Evaluate (U du'/dx+ V du'/dy)+u' dU/dx
            Vmath::Vvtvp(nPointsTot,grad_base_u0,1,advVel[0],1,outarray[0],1,
                         outarray[0],1);
            //Evaluate (U du'/dx+ V du'/dy +u' dU/dx)+v' dU/dy
            Vmath::Vvtvp(nPointsTot,grad_base_u1,1,advVel[1],1,outarray[0],1,
                         outarray[0],1);
            Vmath::Neg(nPointsTot,outarray[0],1);

            //y-equation
            fields[0]->PhysDeriv(inarray[1],grad0,grad1);
            // Evaluate U dv'/dx
            Vmath::Vmul (nPointsTot,grad0,1,m_baseflow[0],1,outarray[1],1);
            //Evaluate U dv'/dx+ V dv'/dy
            Vmath::Vvtvp(nPointsTot,grad1,1,m_baseflow[1],1,outarray[1],1,
                         outarray[1],1);
            //Evaluate (U dv'/dx+ V dv'/dy)+u' dV/dx
            Vmath::Vvtvp(nPointsTot,grad_base_v0,1,advVel[0],1,outarray[1],1,
                         outarray[1],1);
            //Evaluate (U dv'/dx+ V dv'/dy +u' dv/dx)+v' dV/dy
            Vmath::Vvtvp(nPointsTot,grad_base_v1,1,advVel[1],1,outarray[1],1,
                         outarray[1],1);
            Vmath::Neg(nPointsTot,outarray[1],1);
        }
        break;
        case 3:  //3D
        {
            grad1 = Array<OneD, NekDouble> (nPointsTot);
            grad2 = Array<OneD, NekDouble> (nPointsTot);

            grad_base_u1 = Array<OneD, NekDouble> (nPointsTot);
            grad_base_v1 = Array<OneD, NekDouble> (nPointsTot);
            grad_base_w1 = Array<OneD, NekDouble> (nPointsTot,0.0);

            grad_base_u2 = Array<OneD, NekDouble> (nPointsTot,0.0);
            grad_base_v2 = Array<OneD, NekDouble> (nPointsTot,0.0);
            grad_base_w2 = Array<OneD, NekDouble> (nPointsTot,0.0);

            // note base flow should be moved to GetBaseFlow method
            if(m_halfMode) // can assume W = 0 and  d/dz == 0
            {
                // note base flow should be moved to GetBaseFlow method
                fields[0]->PhysDeriv(m_baseflow[0],
                                     grad_base_u0, grad_base_u1);
                fields[0]->PhysDeriv(m_baseflow[1],
                                     grad_base_v0, grad_base_v1);
            }
            else
            {
                if(m_multipleModes)
                {
                    // Differentiate base flow in physical space
                    bool oldwavespace = fields[0]->GetWaveSpace();
                    fields[0]->SetWaveSpace(false);
                    fields[0]->PhysDeriv(m_baseflow[0], grad_base_u0,
                                         grad_base_u1,  grad_base_u2);
                    fields[0]->PhysDeriv(m_baseflow[1], grad_base_v0,
                                         grad_base_v1,  grad_base_v2);
                    fields[0]->PhysDeriv(m_baseflow[2], grad_base_w0,
                                         grad_base_w1,  grad_base_w2);
                    fields[0]->SetWaveSpace(oldwavespace);


                }
                else // has to be single mode where d/dz = 0
                {
                    fields[0]->PhysDeriv(m_baseflow[0], grad_base_u0,
                                         grad_base_u1);
                    fields[0]->PhysDeriv(m_baseflow[1], grad_base_v0,
                                         grad_base_v1);
                    fields[0]->PhysDeriv(m_baseflow[2], grad_base_w0,
                                         grad_base_w1);
                }
            }

            //x-equation
            //
            // Could probably clean up independent looping if clean up
            // base flow derivative evaluation
            if(m_multipleModes)
            {
                fields[0]->PhysDeriv(inarray[0], grad0, grad1, grad2);
                // transform gradients into physical fouier space
                fields[0]->HomogeneousBwdTrans(grad0, grad0);
                fields[0]->HomogeneousBwdTrans(grad1, grad1);
                fields[0]->HomogeneousBwdTrans(grad2, grad2);
            }
            else
            {
                if(m_halfMode) //W = 0 so no need for d/dz
                {
                    fields[0]->PhysDeriv(inarray[0], grad0, grad1);
                }
                else // Single mode
                {
                    fields[0]->PhysDeriv(inarray[0], grad0, grad1, grad2);
                }
            }
            //Evaluate:  U du'/dx
            Vmath::Vmul (nPointsTot, grad0, 1,  m_baseflow[0], 1,
                         outarray[0], 1);
            //Evaluate and add: V du'/dy
            Vmath::Vvtvp(nPointsTot, grad1,  1,  m_baseflow[1], 1,
                         outarray[0], 1,  outarray[0],   1);
            //Evaluate and add: u' dU/dx
            Vmath::Vvtvp(nPointsTot,grad_base_u0,1,advVel[0],1,
                         outarray[0],1,outarray[0],1);
            //Evaluate and add: v' dU/dy
            Vmath::Vvtvp(nPointsTot,grad_base_u1,1,advVel[1],1,
                         outarray[0],1,outarray[0],1);

            if(!m_halfMode)
            {
                //Evaluate an add W du'/dz
                Vmath::Vvtvp(nPointsTot, grad2, 1, m_baseflow[2],
                             1,outarray[0], 1, outarray[0], 1);
            }

            if(m_multipleModes)
            {
                //Evaluate and add w' dU/dz
                Vmath::Vvtvp(nPointsTot,grad_base_u2,1,
                             advVel[2],1,outarray[0],1,outarray[0],1);
                fields[0]->HomogeneousFwdTrans(outarray[0],outarray[0]);
            }
            Vmath::Neg(nPointsTot,outarray[0],1);

            //y-equation------------
            if(m_multipleModes)
            {
                fields[0]->PhysDeriv(inarray[1], grad0, grad1, grad2);
                // transform gradients into physical fouier space
                fields[0]->HomogeneousBwdTrans(grad0, grad0);
                fields[0]->HomogeneousBwdTrans(grad1, grad1);
                fields[0]->HomogeneousBwdTrans(grad2, grad2);
            }
            else
            {
                if(m_halfMode) //W = 0 so no need for d/dz
                {
                    fields[0]->PhysDeriv(inarray[1], grad0, grad1);
                }
                else // Single mode
                {
                    fields[0]->PhysDeriv(inarray[1], grad0, grad1, grad2);
                }
            }

            //Evaluate U dv'/dx
            Vmath::Vmul (nPointsTot, grad0,     1,  m_baseflow[0], 1,
                         outarray[1], 1);
            //Evaluate V dv'/dy
            Vmath::Vvtvp(nPointsTot, grad1,     1,  m_baseflow[1], 1,
                         outarray[1], 1,  outarray[1],   1);
            //Evaluate u' dV/dx
            Vmath::Vvtvp(nPointsTot,grad_base_v0,1,advVel[0],1
                         ,outarray[1],1,outarray[1],1);
            //Evaluate v' dV/dy
            Vmath::Vvtvp(nPointsTot,grad_base_v1,1,advVel[1],1,
                         outarray[1],1,outarray[1],1);

            if(!m_halfMode)
            {
                //Evaluate  W du'/dz
                Vmath::Vvtvp(nPointsTot, grad2,       1,  m_baseflow[2], 1,
                             outarray[1], 1,  outarray[1],   1);
            }

            if(m_multipleModes)
            {
                //Evaluate  w' dV/dz
                Vmath::Vvtvp(nPointsTot,grad_base_v2,1,advVel[2],1,
                             outarray[1],1,outarray[1],1);
                fields[0]->HomogeneousFwdTrans(outarray[1],outarray[1]);
            }

            Vmath::Neg(nPointsTot,outarray[1],1);

            //z-equation ------------
            if(m_multipleModes)
            {
                fields[0]->PhysDeriv(inarray[2], grad0, grad1, grad2);
                // transform gradients into physical fouier space
                fields[0]->HomogeneousBwdTrans(grad0, grad0);
                fields[0]->HomogeneousBwdTrans(grad1, grad1);
                fields[0]->HomogeneousBwdTrans(grad2, grad2);
            }
            else
            {
                if(m_halfMode) //W = 0 so no need for d/dz
                {
                    fields[0]->PhysDeriv(inarray[2], grad0, grad1);
                }
                else // Single mode
                {
                    fields[0]->PhysDeriv(inarray[2], grad0, grad1, grad2);
                }
            }

            //Evaluate U dw'/dx
            Vmath::Vmul (nPointsTot, grad0,      1, m_baseflow[0], 1,
                         outarray[2],  1);
            //Evaluate V dw'/dx
            Vmath::Vvtvp(nPointsTot, grad1,      1, m_baseflow[1], 1,
                         outarray[2],  1, outarray[2],   1);

            if(!m_halfMode)// if halfmode W = 0
            {
                //Evaluate u' dW/dx
                Vmath::Vvtvp(nPointsTot,grad_base_w0,1,advVel[0],1,
                             outarray[2],1,outarray[2],1);
                //Evaluate v' dW/dy
                Vmath::Vvtvp(nPointsTot,grad_base_w1,1,advVel[1],1,
                             outarray[2],1,outarray[2],1);

                //Evaluate W dw'/dz
                Vmath::Vvtvp(nPointsTot, grad2,       1, m_baseflow[2], 1,
                             outarray[2],  1, outarray[2],   1);
            }

            if(m_multipleModes)
            {
                //Evaluate w' dW/dz
                Vmath::Vvtvp(nPointsTot,grad_base_w2,1,advVel[2],1,
                             outarray[2],1,outarray[2],1);
                fields[0]->HomogeneousFwdTrans(outarray[2],outarray[2]);
            }
            Vmath::Neg(nPointsTot,outarray[2],1);
        }
    }
}

void Nektar::LinearisedAdvection::v_InitObject ( LibUtilities::SessionReaderSharedPtr  pSession, Array< OneD, MultiRegions::ExpListSharedPtr >  pFields  )

protectedvirtual

Initialises the advection object.

This function should be overridden in derived classes to initialise the specific advection data members. However, this base class function should be called as the first statement of the overridden function to ensure the base class is correctly initialised in order.

Parameters

pSession	Session information.
pFields	Expansion lists for scalar fields.

Reimplemented from Nektar::SolverUtils::Advection.

Definition at line 70 of file LinearisedAdvection.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, DFT(), Nektar::LibUtilities::eFunctionTypeFile, eHomogeneous1D, eHomogeneous2D, eHomogeneous3D, eNotHomogeneous, ImportFldBase(), m_baseflow, m_boundaryConditions, m_expdim, m_halfMode, m_HomoDirec, m_HomogeneousType, m_LhomX, m_LhomY, m_LhomZ, m_multipleModes, m_npointsX, m_npointsY, m_npointsZ, m_period, m_session, m_singleMode, m_slices, m_spacedim, and m_useFFT.

{
    Advection::v_InitObject(pSession, pFields);

    m_session            = pSession;
    m_boundaryConditions = MemoryManager<SpatialDomains::BoundaryConditions>
        ::AllocateSharedPtr(m_session, pFields[0]->GetGraph());
    m_spacedim           = pFields[0]->GetGraph()->GetSpaceDimension();
    m_expdim             = pFields[0]->GetGraph()->GetMeshDimension();

    //Setting parameters for homogeneous problems
    m_HomoDirec          = 0;
    m_useFFT             = false;
    m_HomogeneousType    = eNotHomogeneous;
    m_singleMode         = false;
    m_halfMode           = false;
    m_multipleModes      = false;

    if(m_session->DefinesSolverInfo("HOMOGENEOUS"))
    {
        std::string HomoStr = m_session->GetSolverInfo("HOMOGENEOUS");
        m_spacedim          = 3;

        if((HomoStr == "HOMOGENEOUS1D")||(HomoStr == "Homogeneous1D")||
           (HomoStr == "1D")||(HomoStr == "Homo1D"))
        {
            m_HomogeneousType = eHomogeneous1D;
            m_LhomZ           = m_session->GetParameter("LZ");
            m_HomoDirec       = 1;

            ASSERTL0(m_session->DefinesSolverInfo("ModeType"),
                     "Need to specify ModeType as HalfMode,SingleMode or "
                     "MultipleModes");

            m_session->MatchSolverInfo("ModeType",      "SingleMode",
                                       m_singleMode,    false);
            m_session->MatchSolverInfo("ModeType",      "HalfMode",
                                       m_halfMode,      false);
            m_session->MatchSolverInfo("ModeType",      "MultipleModes",
                                       m_multipleModes, false);

            if(m_singleMode)
            {
                m_npointsZ = 2;
            }
            else if(m_halfMode)
            {
                m_npointsZ = 1;
            }
            else if(m_multipleModes)
            {
                m_npointsZ = m_session->GetParameter("HomModesZ");
            }
        }

        if((HomoStr == "HOMOGENEOUS2D")||(HomoStr == "Homogeneous2D")||
           (HomoStr == "2D")||(HomoStr == "Homo2D"))
        {
            m_HomogeneousType = eHomogeneous2D;
            m_session->LoadParameter("HomModesY", m_npointsY);
            m_session->LoadParameter("LY",        m_LhomY);
            m_session->LoadParameter("HomModesZ", m_npointsZ);
            m_session->LoadParameter("LZ",        m_LhomZ);
            m_HomoDirec       = 2;
        }

        if((HomoStr == "HOMOGENEOUS3D")||(HomoStr == "Homogeneous3D")||
           (HomoStr == "3D")||(HomoStr == "Homo3D"))
        {
            m_HomogeneousType = eHomogeneous3D;
            m_session->LoadParameter("HomModesX",m_npointsX);
            m_session->LoadParameter("LX",       m_LhomX   );
            m_session->LoadParameter("HomModesY",m_npointsY);
            m_session->LoadParameter("LY",       m_LhomY   );
            m_session->LoadParameter("HomModesZ",m_npointsZ);
            m_session->LoadParameter("LZ",       m_LhomZ   );
            m_HomoDirec       = 3;
        }

        if(m_session->DefinesSolverInfo("USEFFT"))
        {
            m_useFFT = true;
        }
    }
    else
    {
        m_npointsZ = 1; // set to default value so can use to identify 2d or 3D (homogeneous) expansions
    }

    int nvar = m_session->GetVariables().size();
    m_baseflow = Array<OneD, Array<OneD, NekDouble> >(nvar);
    for (int i = 0; i < nvar; ++i)
    {
        m_baseflow[i] = Array<OneD, NekDouble>(pFields[i]->GetTotPoints(), 0.0);
    }

    ASSERTL0(m_session->DefinesFunction("BaseFlow"),
             "Base flow must be defined for linearised forms.");
    string file = m_session->GetFunctionFilename("BaseFlow", 0);


    //Periodic base flows
    if(m_session->DefinesParameter("N_slices"))
    {
        m_session->LoadParameter("N_slices",m_slices);
        if(m_slices>1)
        {
            DFT(file,pFields,m_slices);
        }
        else
        {
            ASSERTL0(false, "Number of slices must be a positive number "
                            "greater than 1");
        }
    }
    //Steady base-flow
    else
    {
        m_slices=1;

        //BaseFlow from file
        if (m_session->GetFunctionType("BaseFlow", m_session->GetVariable(0))
            == LibUtilities::eFunctionTypeFile)
        {
            ImportFldBase(file,pFields,1);

        }
        //analytic base flow
        else
        {
            int nq = pFields[0]->GetNpoints();
            Array<OneD,NekDouble> x0(nq);
            Array<OneD,NekDouble> x1(nq);
            Array<OneD,NekDouble> x2(nq);

            // get the coordinates (assuming all fields have the same
            // discretisation)
            pFields[0]->GetCoords(x0,x1,x2);

            for(unsigned int i = 0 ; i < pFields.num_elements(); i++)
            {
                LibUtilities::EquationSharedPtr ifunc
                    = m_session->GetFunction("BaseFlow", i);

                ifunc->Evaluate(x0,x1,x2,m_baseflow[i]);
            }
        }
    }

    if(m_session->DefinesParameter("period"))
    {
        m_period=m_session->GetParameter("period");
    }
    else
    {
        m_period=(m_session->GetParameter("TimeStep")*m_slices)/(m_slices-1.);
    }

}

void Nektar::LinearisedAdvection::v_SetBaseFlow ( const Array< OneD, Array< OneD, NekDouble > > &  inarray )

protectedvirtual

Overrides the base flow used during linearised advection.

Reimplemented from Nektar::SolverUtils::Advection.

Definition at line 542 of file LinearisedAdvection.cpp.

References ASSERTL1, m_baseflow, m_session, npts, and Vmath::Vcopy().

{
    if (m_session->GetSolverInfo("EqType") == "UnsteadyNavierStokes")
    {
        // The SFD method is only applied to the velocity variables in
        // incompressible
        ASSERTL1(inarray.num_elements() == (m_baseflow.num_elements() - 1),
                 "Number of base flow variables does not match what is "
                 "expected.");
    }
    else
    {
        ASSERTL1(inarray.num_elements() == (m_baseflow.num_elements()),
             "Number of base flow variables does not match what is expected.");
    }

    int npts = inarray[0].num_elements();

    for (int i = 0; i < inarray.num_elements(); ++i)
    {
        ASSERTL1(npts == m_baseflow[i].num_elements(),
             "Size of base flow array does not match expected.");
        Vmath::Vcopy(npts, inarray[i], 1, m_baseflow[i], 1);
    }
}

Friends And Related Function Documentation

friend class MemoryManager< LinearisedAdvection >

friend

Definition at line 62 of file LinearisedAdvection.h.

Member Data Documentation

string Nektar::LinearisedAdvection::className

static

Initial value:

= SolverUtils::GetAdvectionFactory().RegisterCreatorFunction(
                "Linearised",
                LinearisedAdvection::create)

Name of class.

Definition at line 69 of file LinearisedAdvection.h.

Array<OneD, Array<OneD, NekDouble> > Nektar::LinearisedAdvection::m_baseflow

protected

Storage for base flow.

Definition at line 78 of file LinearisedAdvection.h.

Referenced by DFT(), GetFloquetBlockMatrix(), ImportFldBase(), UpdateBase(), v_Advect(), v_InitObject(), and v_SetBaseFlow().

SpatialDomains::BoundaryConditionsSharedPtr Nektar::LinearisedAdvection::m_boundaryConditions

private

Definition at line 171 of file LinearisedAdvection.h.

Referenced by v_InitObject().

int Nektar::LinearisedAdvection::m_expdim

protected

Definition at line 75 of file LinearisedAdvection.h.

Referenced by v_InitObject().

LibUtilities::NektarFFTSharedPtr Nektar::LinearisedAdvection::m_FFT

protected

auxiliary variables

Definition at line 87 of file LinearisedAdvection.h.

Referenced by DFT().

FloquetBlockMatrixMapShPtr Nektar::LinearisedAdvection::m_FloquetBlockMat

protected

Definition at line 104 of file LinearisedAdvection.h.

bool Nektar::LinearisedAdvection::m_halfMode

protected

flag to determine if use half mode or not

Definition at line 94 of file LinearisedAdvection.h.

Referenced by ImportFldBase(), v_Advect(), and v_InitObject().

int Nektar::LinearisedAdvection::m_HomoDirec

private

number of homogenous directions

Definition at line 167 of file LinearisedAdvection.h.

Referenced by v_InitObject().

enum HomogeneousType Nektar::LinearisedAdvection::m_HomogeneousType

private

Definition at line 157 of file LinearisedAdvection.h.

Referenced by v_InitObject().

Array<OneD, Array<OneD, NekDouble> > Nektar::LinearisedAdvection::m_interp

protected

interpolation vector

Definition at line 85 of file LinearisedAdvection.h.

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

NekDouble Nektar::LinearisedAdvection::m_LhomX

private

physical length in X direction (if homogeneous)

Definition at line 159 of file LinearisedAdvection.h.

Referenced by v_InitObject().

NekDouble Nektar::LinearisedAdvection::m_LhomY

private

physical length in Y direction (if homogeneous)

Definition at line 160 of file LinearisedAdvection.h.

Referenced by v_InitObject().

NekDouble Nektar::LinearisedAdvection::m_LhomZ

private

physical length in Z direction (if homogeneous)

Definition at line 161 of file LinearisedAdvection.h.

Referenced by v_InitObject().

bool Nektar::LinearisedAdvection::m_multipleModes

protected

flag to determine if use multiple mode or not

Definition at line 96 of file LinearisedAdvection.h.

Referenced by ImportFldBase(), v_Advect(), and v_InitObject().

int Nektar::LinearisedAdvection::m_npointsX

private

number of points in X direction (if homogeneous)

Definition at line 163 of file LinearisedAdvection.h.

Referenced by v_InitObject().

int Nektar::LinearisedAdvection::m_npointsY

private

number of points in Y direction (if homogeneous)

Definition at line 164 of file LinearisedAdvection.h.

Referenced by v_InitObject().

int Nektar::LinearisedAdvection::m_npointsZ

private

number of points in Z direction (if homogeneous)

Definition at line 165 of file LinearisedAdvection.h.

Referenced by ImportFldBase(), and v_InitObject().

int Nektar::LinearisedAdvection::m_NumMode

private

Mode to use in case of single mode analysis.

Definition at line 169 of file LinearisedAdvection.h.

NekDouble Nektar::LinearisedAdvection::m_period

protected

period length

Definition at line 83 of file LinearisedAdvection.h.

Referenced by UpdateBase(), v_Advect(), and v_InitObject().

LibUtilities::SessionReaderSharedPtr Nektar::LinearisedAdvection::m_session

protected

Definition at line 72 of file LinearisedAdvection.h.

Referenced by ImportFldBase(), v_Advect(), v_InitObject(), and v_SetBaseFlow().

bool Nektar::LinearisedAdvection::m_singleMode

protected

flag to determine if use single mode or not

Definition at line 92 of file LinearisedAdvection.h.

Referenced by ImportFldBase(), and v_InitObject().

int Nektar::LinearisedAdvection::m_slices

protected

number of slices

Definition at line 81 of file LinearisedAdvection.h.

Referenced by DFT(), GetFloquetBlockMatrix(), UpdateBase(), v_Advect(), and v_InitObject().

int Nektar::LinearisedAdvection::m_spacedim

protected

Definition at line 74 of file LinearisedAdvection.h.

Referenced by v_InitObject().

Array<OneD,NekDouble> Nektar::LinearisedAdvection::m_tmpIN

protected

Definition at line 88 of file LinearisedAdvection.h.

Referenced by DFT().

Array<OneD,NekDouble> Nektar::LinearisedAdvection::m_tmpOUT

protected

Definition at line 89 of file LinearisedAdvection.h.

Referenced by DFT().

bool Nektar::LinearisedAdvection::m_useFFT

private

flag to determine if use or not the FFT for transformations

Definition at line 155 of file LinearisedAdvection.h.

Referenced by v_InitObject().

bool Nektar::LinearisedAdvection::m_useFFTW

protected

Definition at line 90 of file LinearisedAdvection.h.