Nektar::MultiRegions::GJPStabilisation Class Reference

#include <GJPStabilisation.h>

Public Member Functions
	GJPStabilisation (ExpListSharedPtr field)
	~GJPStabilisation ()
void	Apply (const Array< OneD, NekDouble > &inarray, Array< OneD, NekDouble > &outarray, const Array< OneD, NekDouble > &pUnorm=NullNekDouble1DArray, const NekDouble scale=1.0) const
Array< OneD, Array< OneD, NekDouble > > &	GetTraceNormals (void)
int	GetNumTracePts (void) const
bool	IsSemiImplicit () const

Private Member Functions
void	SetUpExpansionInfoMapForGJP (SpatialDomains::MeshGraphSharedPtr graph, std::string variable)
void	MultiplyByStdDerivBaseOnTraceMat (int i, Array< OneD, NekDouble > &in, Array< OneD, NekDouble > &out) const

Private Attributes
int	m_coordDim
int	m_traceDim
bool	m_useGJPSemiImplicit
Array< OneD, Array< OneD, NekDouble > >	m_traceNormals
MultiRegions::ExpListSharedPtr	m_dgfield
	DG expansion for projection evalaution along trace. More...
MultiRegions::LocTraceToTraceMapSharedPtr	m_locTraceToTraceMap
	LocaTraceToTraceMap. More...
MultiRegions::ExpListSharedPtr	m_locElmtTrace
	Local Elemental trace expansions. More...
Array< OneD, Array< OneD, NekDouble > >	m_scalTrace
	Scale factor for phys values along trace involving the lcoal normals and tangent geometric factors n. More...
std::vector< std::pair< int, Array< OneD, DNekMatSharedPtr > > >	m_StdDBaseOnTraceMat

Detailed Description

Definition at line 48 of file GJPStabilisation.h.

Constructor & Destructor Documentation

GJPStabilisation()

Nektar::MultiRegions::GJPStabilisation::GJPStabilisation

(

ExpListSharedPtr

field

)

Definition at line 41 of file GJPStabilisation.cpp.

{
    LibUtilities::SessionReaderSharedPtr session = pField->GetSession();
 
    session->MatchSolverInfo("GJPStabilisation", "SemiImplicit",
                             m_useGJPSemiImplicit, false);
 
    // Call GetTrace on the initialising field will set up
    // DG. Store a copoy so that if we make a soft copy of
    // this class we can re-used this field for operators.
    pField->GetTrace();
    m_dgfield = pField;
 
    m_coordDim = m_dgfield->GetCoordim(0);
    m_traceDim = m_dgfield->GetShapeDimension() - 1;
 
    // set up trace normals but would be better if could use
    // equation system definition
    m_traceNormals = Array<OneD, Array<OneD, NekDouble>>(m_coordDim);
    for (int i = 0; i < m_coordDim; ++i)
    {
        m_traceNormals[i] =
            Array<OneD, NekDouble>(m_dgfield->GetTrace()->GetNpoints());
    }
    m_dgfield->GetTrace()->GetNormals(m_traceNormals);
 
    SetUpExpansionInfoMapForGJP(pField->GetGraph(), session->GetVariable(0));
 
    MultiRegions::DisContFieldSharedPtr dgfield;
 
    dgfield = MemoryManager<MultiRegions::DisContField>::AllocateSharedPtr(
        session, pField->GetGraph(), "GJP", true, false,
        Collections::eNoImpType, session->GetVariable(0));
    dgfield->GetLocTraceToTraceMap(m_locTraceToTraceMap);
 
    m_locElmtTrace = MemoryManager<MultiRegions::ExpList>::AllocateSharedPtr(
        session, *(dgfield->GetExp()), dgfield->GetGraph(), true, "GJP");
 
    m_scalTrace = Array<OneD, Array<OneD, NekDouble>>(m_traceDim + 1);
 
    const std::shared_ptr<LocalRegions::ExpansionVector> exp =
        dgfield->GetExp();
 
    Array<OneD, Array<OneD, NekDouble>> dfactors[3];
    Array<OneD, Array<OneD, NekDouble>> LocTrace(m_traceDim + 1);
    Array<OneD, NekDouble> e_tmp;
 
    for (int i = 0; i < m_traceDim + 1; ++i)
    {
        LocTrace[i] =
            Array<OneD, NekDouble>(m_locTraceToTraceMap->GetNLocTracePts());
    }
 
    int cnt         = 0;
    int offset_phys = 0;
    Array<OneD, Array<OneD, Array<OneD, NekDouble>>> dbasis;
    Array<OneD, Array<OneD, Array<OneD, unsigned int>>> traceToCoeffMap;
 
    Array<OneD, unsigned int> map, map1;
    Array<OneD, int> sign, sign1;
    NekDouble h, p;
 
    for (int e = 0; e < m_dgfield->GetExpSize(); ++e)
    {
        LocalRegions::ExpansionSharedPtr elmt = (*exp)[e];
 
        elmt->NormalTraceDerivFactors(dfactors[0], dfactors[1], dfactors[2]);
 
        for (int n = 0; n < elmt->GetNtraces(); ++n, ++cnt)
        {
            NekDouble jumpScal;
            elmt->TraceNormLen(n, h, p);
            ASSERTL0(boost::math::isnan(h) == false,
                     "h has a nan value when e = " +
                         boost::lexical_cast<std::string>(e) +
                         " n =" + boost::lexical_cast<std::string>(n));
 
            if (p == 1)
            {
                jumpScal = 0.02 * h * h;
            }
            else
            {
                jumpScal = 0.8 * pow(p + 1, -4.0) * h * h;
            }
 
            int nptrace = elmt->GetTraceNumPoints(n);
            elmt->GetTraceCoeffMap(n, map);
 
            for (int i = 0; i < m_traceDim + 1; ++i)
            {
                Vmath::Smul(nptrace, jumpScal, dfactors[i][n], 1,
                            e_tmp = LocTrace[i] + offset_phys, 1);
            }
 
            offset_phys += nptrace;
        }
    }
 
    for (int i = 0; i < m_traceDim + 1; ++i)
    {
        m_scalTrace[i] = LocTrace[i];
 
        if (m_traceDim > 0)
        {
            // multiply by Jacobian and quadrature points.
            m_locElmtTrace->MultiplyByQuadratureMetric(m_scalTrace[i],
                                                       m_scalTrace[i]);
        }
    }
 
    // Assemble list of Matrix Product
    Array<OneD, DNekMatSharedPtr> TraceMat;
 
    int nelmt = 1;
    Array<OneD, const LibUtilities::BasisSharedPtr> base_sav =
        dgfield->GetExp(0)->GetBase();
 
    dgfield->GetExp(0)->StdDerivBaseOnTraceMat(TraceMat);
 
    for (int n = 1; n < dgfield->GetExpSize(); ++n)
    {
        const Array<OneD, const LibUtilities::BasisSharedPtr> &base =
            dgfield->GetExp(n)->GetBase();
 
        int i;
        for (i = 0; i < base.size(); ++i)
        {
            if (base[i] != base_sav[i])
            {
                break;
            }
        }
 
        if (i == base.size())
        {
            nelmt++;
        }
        else
        {
            // save previous block of data.
            m_StdDBaseOnTraceMat.push_back(
                std::pair<int, Array<OneD, DNekMatSharedPtr>>(nelmt, TraceMat));
 
            // start new block
            dgfield->GetExp(n)->StdDerivBaseOnTraceMat(TraceMat);
            nelmt    = 1;
            base_sav = dgfield->GetExp(n)->GetBase();
        }
    }
    // save latest block of data.
    m_StdDBaseOnTraceMat.push_back(
        std::pair<int, Array<OneD, DNekMatSharedPtr>>(nelmt, TraceMat));
}

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::Collections::eNoImpType, m_coordDim, m_dgfield, m_locElmtTrace, m_locTraceToTraceMap, m_scalTrace, m_StdDBaseOnTraceMat, m_traceDim, m_traceNormals, m_useGJPSemiImplicit, CellMLToNektar.cellml_metadata::p, SetUpExpansionInfoMapForGJP(), sign, and Vmath::Smul().

~GJPStabilisation()

Nektar::MultiRegions::GJPStabilisation::~GJPStabilisation ( )

inline

Definition at line 53 of file GJPStabilisation.h.

{};

Member Function Documentation

Apply()

void Nektar::MultiRegions::GJPStabilisation::Apply	(	const Array< OneD, NekDouble > &	inarray,
		Array< OneD, NekDouble > &	outarray,
		const Array< OneD, NekDouble > &	pUnorm = NullNekDouble1DArray,
		const NekDouble	scale = 1.0
	)		const

Definition at line 196 of file GJPStabilisation.cpp.

{
    int ncoeffs    = m_dgfield->GetNcoeffs();
    int nphys      = m_dgfield->GetNpoints();
    int nTracePts  = m_dgfield->GetTrace()->GetTotPoints();
    int nLocETrace = m_locElmtTrace->GetTotPoints();
 
    ASSERTL1(nLocETrace == m_scalTrace[0].size(), "expect these to be similar");
    ASSERTL1(m_locElmtTrace->GetNcoeffs() <= nphys,
             "storage assumptions presume "
             "that nLocETraceCoeffs < nphys");
 
    Array<OneD, Array<OneD, NekDouble>> deriv(3, NullNekDouble1DArray);
    for (int i = 0; i < m_coordDim; ++i)
    {
        deriv[i] = Array<OneD, NekDouble>(nphys);
    }
 
    int nmax = std::max(ncoeffs, nphys);
    Array<OneD, NekDouble> FilterCoeffs(nmax, 0.0);
    Array<OneD, NekDouble> GradJumpOnTrace(nTracePts, 0.0);
    Array<OneD, NekDouble> Fwd(nTracePts), Bwd(nTracePts);
 
    Array<OneD, NekDouble> wsp(nLocETrace), tmp;
    Array<OneD, NekDouble> LocElmtTracePhys   = m_locElmtTrace->UpdatePhys();
    Array<OneD, NekDouble> LocElmtTraceCoeffs = m_locElmtTrace->UpdateCoeffs();
 
    ASSERTL1(LocElmtTracePhys.size() <= nLocETrace,
             "expect this vector to be at least of size nLocETrace");
 
    Array<OneD, NekDouble> unorm;
    if (pUnorm == NullNekDouble1DArray)
    {
        unorm = Array<OneD, NekDouble>(nTracePts, 1.0);
    }
    else
    {
        unorm = pUnorm;
    }
 
    Array<OneD, NekDouble> GradJumpOnTraceBwd;
    if (m_useGJPSemiImplicit)
    {
        GradJumpOnTraceBwd = Array<OneD, NekDouble>(nTracePts);
    }
 
    if (m_useGJPSemiImplicit)
    {
        Vmath::Zero(nTracePts, GradJumpOnTraceBwd, 1);
    }
 
    // calculate derivative
    m_dgfield->PhysDeriv(inarray, deriv[0], deriv[1], deriv[2]);
 
    // Evaluate the  normal derivative jump on the trace
    for (int n = 0; n < m_coordDim; ++n)
    {
        m_dgfield->GetFwdBwdTracePhys(deriv[n], Fwd, Bwd, true, true);
 
        if (m_useGJPSemiImplicit)
        {
            // want to put Fwd vals on bwd trace and vice versa
            Vmath::Vvtvp(nTracePts, Bwd, 1, m_traceNormals[n], 1,
                         GradJumpOnTrace, 1, GradJumpOnTrace, 1);
            Vmath::Vvtvp(nTracePts, Fwd, 1, m_traceNormals[n], 1,
                         GradJumpOnTraceBwd, 1, GradJumpOnTraceBwd, 1);
        }
        else
        {
            // Multiply by normal and add to trace evaluation
            Vmath::Vsub(nTracePts, Fwd, 1, Bwd, 1, Fwd, 1);
            Vmath::Vvtvp(nTracePts, Fwd, 1, m_traceNormals[n], 1,
                         GradJumpOnTrace, 1, GradJumpOnTrace, 1);
        }
    }
 
    if (m_useGJPSemiImplicit)
    {
        // Need to negate Bwd case when  using Fwd normal
        Vmath::Neg(nTracePts, GradJumpOnTrace, 1);
    }
 
    Vmath::Vmul(nTracePts, unorm, 1, GradJumpOnTrace, 1, GradJumpOnTrace, 1);
 
    // Interpolate GradJumpOnTrace to Local elemental traces.
    m_locTraceToTraceMap->InterpTraceToLocTrace(0, GradJumpOnTrace, wsp);
    m_locTraceToTraceMap->UnshuffleLocTraces(0, wsp, LocElmtTracePhys);
 
    if (m_useGJPSemiImplicit)
    {
        // Vmath::Neg(nTracePts,GradJumpOnTraceBwd,1);
        Vmath::Vmul(nTracePts, unorm, 1, GradJumpOnTraceBwd, 1,
                    GradJumpOnTraceBwd, 1);
        m_locTraceToTraceMap->InterpTraceToLocTrace(1, GradJumpOnTraceBwd, wsp);
        m_locTraceToTraceMap->UnshuffleLocTraces(1, wsp, LocElmtTracePhys);
    }
    else
    {
        m_locTraceToTraceMap->InterpTraceToLocTrace(1, GradJumpOnTrace, wsp);
        m_locTraceToTraceMap->UnshuffleLocTraces(1, wsp, LocElmtTracePhys);
    }
 
    // Scale jump on trace
    Vmath::Vmul(nLocETrace, m_scalTrace[0], 1, LocElmtTracePhys, 1, wsp, 1);
    MultiplyByStdDerivBaseOnTraceMat(0, wsp, FilterCoeffs);
 
    for (int i = 0; i < m_traceDim; ++i)
    {
        // Scale jump on trace
        Vmath::Vmul(nLocETrace, m_scalTrace[i + 1], 1, LocElmtTracePhys, 1, wsp,
                    1);
        MultiplyByStdDerivBaseOnTraceMat(i + 1, wsp, deriv[0]);
        Vmath::Vadd(ncoeffs, deriv[0], 1, FilterCoeffs, 1, FilterCoeffs, 1);
    }
 
    Vmath::Svtvp(ncoeffs, scale, FilterCoeffs, 1, outarray, 1, outarray, 1);
}

References ASSERTL1, m_coordDim, m_dgfield, m_locElmtTrace, m_locTraceToTraceMap, m_scalTrace, m_traceDim, m_traceNormals, m_useGJPSemiImplicit, MultiplyByStdDerivBaseOnTraceMat(), Vmath::Neg(), Nektar::NullNekDouble1DArray, Vmath::Svtvp(), Vmath::Vadd(), Vmath::Vmul(), Vmath::Vsub(), Vmath::Vvtvp(), and Vmath::Zero().

GetNumTracePts()

int Nektar::MultiRegions::GJPStabilisation::GetNumTracePts ( void  ) const

inline

Definition at line 65 of file GJPStabilisation.h.

    {
        return m_dgfield->GetTrace()->GetTotPoints();
    }

References m_dgfield.

GetTraceNormals()

Array<OneD, Array<OneD, NekDouble> >& Nektar::MultiRegions::GJPStabilisation::GetTraceNormals ( void  )

inline

Definition at line 60 of file GJPStabilisation.h.

    {
        return m_traceNormals;
    }

References m_traceNormals.

IsSemiImplicit()

bool Nektar::MultiRegions::GJPStabilisation::IsSemiImplicit ( ) const

inline

Definition at line 70 of file GJPStabilisation.h.

    {
        return m_useGJPSemiImplicit;
    }

References m_useGJPSemiImplicit.

MultiplyByStdDerivBaseOnTraceMat()

void Nektar::MultiRegions::GJPStabilisation::MultiplyByStdDerivBaseOnTraceMat ( int  i, Array< OneD, NekDouble > &  in, Array< OneD, NekDouble > &  out  ) const

private

Definition at line 376 of file GJPStabilisation.cpp.

{
    // Should probably be vectorised
 
    int cnt  = 0;
    int cnt1 = 0;
    for (auto &it : m_StdDBaseOnTraceMat)
    {
        int rows = it.second[i]->GetRows();
        int cols = it.second[i]->GetColumns();
 
        Blas::Dgemm('N', 'N', rows, it.first, cols, 1.0,
                    &(it.second[i]->GetPtr())[0], rows, &in[0] + cnt, cols, 0.0,
                    &out[0] + cnt1, rows);
 
        cnt += cols * it.first;
        cnt1 += rows * it.first;
    }
}

References Blas::Dgemm(), and m_StdDBaseOnTraceMat.

Referenced by Apply().

SetUpExpansionInfoMapForGJP()

void Nektar::MultiRegions::GJPStabilisation::SetUpExpansionInfoMapForGJP ( SpatialDomains::MeshGraphSharedPtr  graph, std::string  variable  )

private

Definition at line 317 of file GJPStabilisation.cpp.

{
 
    // check to see if already deifned and if so return
    if (graph->ExpansionInfoDefined("GJP"))
    {
        return;
    }
 
    const SpatialDomains::ExpansionInfoMap expInfo =
        graph->GetExpansionInfo(variable);
 
    SpatialDomains::ExpansionInfoMapShPtr newInfo =
        MemoryManager<SpatialDomains::ExpansionInfoMap>::AllocateSharedPtr();
 
    // loop over epxansion info
    for (auto expIt = expInfo.begin(); expIt != expInfo.end(); ++expIt)
    {
        std::vector<LibUtilities::BasisKey> BKeyVector;
 
        for (int i = 0; i < expIt->second->m_basisKeyVector.size(); ++i)
        {
            LibUtilities::BasisKey bkeyold = expIt->second->m_basisKeyVector[i];
 
            // Reset radauM alpha non-zero cases to radauM
            // Legendre at one order higher
 
            switch (bkeyold.GetPointsType())
            {
                case LibUtilities::eGaussRadauMAlpha1Beta0:
                case LibUtilities::eGaussRadauMAlpha2Beta0:
                {
                    int npts = bkeyold.GetNumPoints();
 
                    // const LibUtilities::PointsKey pkey(npts+1,
                    // LibUtilities::eGaussRadauMLegendre); trying
                    // npts to be consistent for tri faces
                    const LibUtilities::PointsKey pkey(
                        npts, LibUtilities::eGaussRadauMLegendre);
                    LibUtilities::BasisKey bkeynew(bkeyold.GetBasisType(),
                                                   bkeyold.GetNumModes(), pkey);
                    BKeyVector.push_back(bkeynew);
                }
                break;
                default:
                    BKeyVector.push_back(bkeyold);
                    break;
            }
        }
 
        (*newInfo)[expIt->first] =
            MemoryManager<SpatialDomains::ExpansionInfo>::AllocateSharedPtr(
                expIt->second->m_geomShPtr, BKeyVector);
    }
 
    graph->SetExpansionInfo("GJP", newInfo);
}

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), Nektar::LibUtilities::eGaussRadauMLegendre, Nektar::LibUtilities::BasisKey::GetBasisType(), Nektar::LibUtilities::BasisKey::GetNumModes(), Nektar::LibUtilities::BasisKey::GetNumPoints(), and Nektar::LibUtilities::BasisKey::GetPointsType().

Referenced by GJPStabilisation().

Member Data Documentation

m_coordDim

int Nektar::MultiRegions::GJPStabilisation::m_coordDim

private

Definition at line 76 of file GJPStabilisation.h.

Referenced by Apply(), and GJPStabilisation().

m_dgfield

MultiRegions::ExpListSharedPtr Nektar::MultiRegions::GJPStabilisation::m_dgfield

private

DG expansion for projection evalaution along trace.

Definition at line 84 of file GJPStabilisation.h.

Referenced by Apply(), GetNumTracePts(), and GJPStabilisation().

m_locElmtTrace

MultiRegions::ExpListSharedPtr Nektar::MultiRegions::GJPStabilisation::m_locElmtTrace

private

Local Elemental trace expansions.

Definition at line 88 of file GJPStabilisation.h.

Referenced by Apply(), and GJPStabilisation().

m_locTraceToTraceMap

MultiRegions::LocTraceToTraceMapSharedPtr Nektar::MultiRegions::GJPStabilisation::m_locTraceToTraceMap

private

LocaTraceToTraceMap.

Definition at line 86 of file GJPStabilisation.h.

Referenced by Apply(), and GJPStabilisation().

m_scalTrace

Array<OneD, Array<OneD, NekDouble> > Nektar::MultiRegions::GJPStabilisation::m_scalTrace

private

Scale factor for phys values along trace involving the lcoal normals and tangent geometric factors n.

Definition at line 92 of file GJPStabilisation.h.

Referenced by Apply(), and GJPStabilisation().

m_StdDBaseOnTraceMat

std::vector<std::pair<int, Array<OneD, DNekMatSharedPtr> > > Nektar::MultiRegions::GJPStabilisation::m_StdDBaseOnTraceMat

private

Definition at line 95 of file GJPStabilisation.h.

Referenced by GJPStabilisation(), and MultiplyByStdDerivBaseOnTraceMat().

m_traceDim

int Nektar::MultiRegions::GJPStabilisation::m_traceDim

private

Definition at line 77 of file GJPStabilisation.h.

Referenced by Apply(), and GJPStabilisation().

m_traceNormals

Array<OneD, Array<OneD, NekDouble> > Nektar::MultiRegions::GJPStabilisation::m_traceNormals

private

Definition at line 81 of file GJPStabilisation.h.

Referenced by Apply(), GetTraceNormals(), and GJPStabilisation().

m_useGJPSemiImplicit

bool Nektar::MultiRegions::GJPStabilisation::m_useGJPSemiImplicit

private

Definition at line 78 of file GJPStabilisation.h.

Referenced by Apply(), GJPStabilisation(), and IsSemiImplicit().