///////////////////////////////////////////////////////////////////////////////
//
// File: NavierStokesCFE.cpp
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: Navier Stokes equations in conservative variables
//
///////////////////////////////////////////////////////////////////////////////

#include <CompressibleFlowSolver/EquationSystems/NavierStokesCFE.h>

namespace Nektar
{

std::string NavierStokesCFE::className =
    SolverUtils::GetEquationSystemFactory().RegisterCreatorFunction(
        "NavierStokesCFE", NavierStokesCFE::create,
        "NavierStokes equations in conservative variables.");

NavierStokesCFE::NavierStokesCFE(
    const LibUtilities::SessionReaderSharedPtr &pSession,
    const SpatialDomains::MeshGraphSharedPtr &pGraph)
    : UnsteadySystem(pSession, pGraph), CompressibleFlowSystem(pSession, pGraph)
{
}

/**
 * @brief Initialization object for CompressibleFlowSystem class.
 */
void NavierStokesCFE::v_InitObject(bool DeclareFields)
{
    CompressibleFlowSystem::v_InitObject(DeclareFields);

    // rest of initialisation is in this routine so it can also be called
    // in NavierStokesImplicitCFE initialisation
    InitObject_Explicit();
}

void NavierStokesCFE::InitObject_Explicit()
{
    // Get gas constant from session file and compute Cp
    NekDouble gasConstant;
    m_session->LoadParameter("GasConstant", gasConstant, 287.058);
    m_Cp = m_gamma / (m_gamma - 1.0) * gasConstant;
    m_Cv = m_Cp / m_gamma;

    m_session->LoadParameter("Twall", m_Twall, 300.15);

    // Viscosity
    m_session->LoadSolverInfo("ViscosityType", m_ViscosityType, "Constant");
    m_session->LoadParameter("mu", m_muRef, 1.78e-05);
    if (m_ViscosityType == "Variable")
    {
        m_is_mu_variable = true;
    }

    // Thermal conductivity or Prandtl
    if (m_session->DefinesParameter("thermalConductivity"))
    {
        ASSERTL0(!m_session->DefinesParameter("Pr"),
                 "Cannot define both Pr and thermalConductivity.");

        m_session->LoadParameter("thermalConductivity",
                                 m_thermalConductivityRef);
        m_Prandtl = m_Cp * m_muRef / m_thermalConductivityRef;
    }
    else
    {
        m_session->LoadParameter("Pr", m_Prandtl, 0.72);
        m_thermalConductivityRef = m_Cp * m_muRef / m_Prandtl;
    }

    if (m_shockCaptureType == "Physical")
    {
        m_is_shockCaptPhys = true;
    }

    std::string diffName;
    m_session->LoadSolverInfo("DiffusionType", diffName, "LDGNS");

    m_diffusion =
        SolverUtils::GetDiffusionFactory().CreateInstance(diffName, diffName);
    if ("InteriorPenalty" == diffName)
    {
        m_is_diffIP = true;
        SetBoundaryConditionsBwdWeight();
    }

    if ("LDGNS" == diffName || "LDGNS3DHomogeneous1D" == diffName)
    {
        m_diffusion->SetFluxPenaltyNS(&NavierStokesCFE::v_GetFluxPenalty, this);
    }

    if (m_specHP_dealiasing)
    {
        m_diffusion->SetFluxVectorNS(
            &NavierStokesCFE::v_GetViscousFluxVectorDeAlias, this);
    }
    else
    {
        m_diffusion->SetFluxVectorNS(&NavierStokesCFE::v_GetViscousFluxVector,
                                     this);
    }

    m_diffusion->SetDiffusionFluxCons(
        &NavierStokesCFE::GetViscousFluxVectorConservVar<false>, this);

    m_diffusion->SetDiffusionFluxConsTrace(
        &NavierStokesCFE::GetViscousFluxVectorConservVar<true>, this);

    m_diffusion->SetSpecialBndTreat(&NavierStokesCFE::SpecialBndTreat, this);

    m_diffusion->SetDiffusionSymmFluxCons(
        &NavierStokesCFE::GetViscousSymmtrFluxConservVar, this);

    // Concluding initialisation of diffusion operator
    m_diffusion->InitObject(m_session, m_fields);
    m_diffusion->SetGridVelocityTrace(
        m_gridVelocityTrace); // If not ALE and movement this is just 0s
}

void NavierStokesCFE::v_DoDiffusion(
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray,
    const Array<OneD, Array<OneD, NekDouble>> &pFwd,
    const Array<OneD, Array<OneD, NekDouble>> &pBwd)
{
    size_t nvariables = inarray.size();
    size_t npointsIn  = GetNpoints();
    size_t npointsOut = m_meshDistorted
                            ? GetNcoeffs()
                            : npointsIn; // If mesh is distorted then outarray
                                         // is in coefficient space
    size_t nTracePts = GetTraceTotPoints();

    // this should be preallocated
    Array<OneD, Array<OneD, NekDouble>> outarrayDiff(nvariables);
    for (size_t i = 0; i < nvariables; ++i)
    {
        outarrayDiff[i] = Array<OneD, NekDouble>(npointsOut, 0.0);
    }

    // Set artificial viscosity based on NS viscous tensor
    if (m_is_shockCaptPhys)
    {
        if (m_varConv->GetFlagCalcDivCurl())
        {
            Array<OneD, NekDouble> div(npointsIn), curlSquare(npointsIn);
            GetDivCurlSquared(m_fields, inarray, div, curlSquare, pFwd, pBwd);

            // Set volume and trace artificial viscosity
            m_varConv->SetAv(m_fields, inarray, div, curlSquare);
        }
        else
        {
            m_varConv->SetAv(m_fields, inarray);
        }
    }

    if (m_is_diffIP)
    {
        if (m_bndEvaluateTime < 0.0)
        {
            NEKERROR(ErrorUtil::efatal, "m_bndEvaluateTime not setup");
        }

        // Diffusion term in physical rhs form
        if (m_meshDistorted)
        {
            m_diffusion->DiffuseCoeffs(nvariables, m_fields, inarray,
                                       outarrayDiff, m_bndEvaluateTime, pFwd,
                                       pBwd);
        }
        else
        {
            m_diffusion->Diffuse(nvariables, m_fields, inarray, outarrayDiff,
                                 m_bndEvaluateTime, pFwd, pBwd);
        }
        for (size_t i = 0; i < nvariables; ++i)
        {
            Vmath::Vadd(npointsOut, outarrayDiff[i], 1, outarray[i], 1,
                        outarray[i], 1);
        }
    }
    else
    {
        // Get primitive variables [u,v,w,T]
        Array<OneD, Array<OneD, NekDouble>> inarrayDiff(nvariables - 1);
        Array<OneD, Array<OneD, NekDouble>> inFwd(nvariables - 1);
        Array<OneD, Array<OneD, NekDouble>> inBwd(nvariables - 1);

        for (size_t i = 0; i < nvariables - 1; ++i)
        {
            inarrayDiff[i] = Array<OneD, NekDouble>{npointsIn};
            inFwd[i]       = Array<OneD, NekDouble>{nTracePts};
            inBwd[i]       = Array<OneD, NekDouble>{nTracePts};
        }

        // Extract temperature
        m_varConv->GetTemperature(inarray, inarrayDiff[nvariables - 2]);

        // Extract velocities
        m_varConv->GetVelocityVector(inarray, inarrayDiff);

        // Repeat calculation for trace space
        if (pFwd == NullNekDoubleArrayOfArray ||
            pBwd == NullNekDoubleArrayOfArray)
        {
            inFwd = NullNekDoubleArrayOfArray;
            inBwd = NullNekDoubleArrayOfArray;
        }
        else
        {
            m_varConv->GetTemperature(pFwd, inFwd[nvariables - 2]);
            m_varConv->GetTemperature(pBwd, inBwd[nvariables - 2]);

            m_varConv->GetVelocityVector(pFwd, inFwd);
            m_varConv->GetVelocityVector(pBwd, inBwd);
        }

        // Diffusion term in physical rhs form
        if (m_meshDistorted)
        {
            m_diffusion->DiffuseCoeffs(nvariables, m_fields, inarrayDiff,
                                       outarrayDiff, inFwd, inBwd);
        }
        else
        {
            m_diffusion->Diffuse(nvariables, m_fields, inarrayDiff,
                                 outarrayDiff, inFwd, inBwd);
        }

        for (size_t i = 0; i < nvariables; ++i)
        {
            Vmath::Vadd(npointsOut, outarrayDiff[i], 1, outarray[i], 1,
                        outarray[i], 1);
        }
    }

    // Add artificial diffusion through Laplacian operator
    if (m_artificialDiffusion)
    {
        m_artificialDiffusion->DoArtificialDiffusion(inarray, outarray);
    }
}

/**
 * @brief Return the flux vector for the LDG diffusion problem.
 * \todo Complete the viscous flux vector
 */
void NavierStokesCFE::v_GetViscousFluxVector(
    const Array<OneD, const Array<OneD, NekDouble>> &physfield,
    TensorOfArray3D<NekDouble> &derivativesO1,
    TensorOfArray3D<NekDouble> &viscousTensor)
{
    // Auxiliary variables
    size_t nScalar = physfield.size();
    size_t nPts    = physfield[0].size();
    Array<OneD, NekDouble> divVel(nPts, 0.0);

    // Stokes hypothesis
    const NekDouble lambda = -2.0 / 3.0;

    // Update viscosity and thermal conductivity
    Array<OneD, NekDouble> mu(nPts, 0.0);
    Array<OneD, NekDouble> thermalConductivity(nPts, 0.0);
    GetViscosityAndThermalCondFromTemp(physfield[nScalar - 1], mu,
                                       thermalConductivity);

    // Velocity divergence
    for (int j = 0; j < m_spacedim; ++j)
    {
        Vmath::Vadd(nPts, divVel, 1, derivativesO1[j][j], 1, divVel, 1);
    }

    // Velocity divergence scaled by lambda * mu
    Vmath::Smul(nPts, lambda, divVel, 1, divVel, 1);
    Vmath::Vmul(nPts, mu, 1, divVel, 1, divVel, 1);

    // Viscous flux vector for the rho equation = 0
    for (int i = 0; i < m_spacedim; ++i)
    {
        Vmath::Zero(nPts, viscousTensor[i][0], 1);
    }

    // Viscous stress tensor (for the momentum equations)
    for (int i = 0; i < m_spacedim; ++i)
    {
        for (int j = i; j < m_spacedim; ++j)
        {
            Vmath::Vadd(nPts, derivativesO1[i][j], 1, derivativesO1[j][i], 1,
                        viscousTensor[i][j + 1], 1);

            Vmath::Vmul(nPts, mu, 1, viscousTensor[i][j + 1], 1,
                        viscousTensor[i][j + 1], 1);

            if (i == j)
            {
                // Add divergence term to diagonal
                Vmath::Vadd(nPts, viscousTensor[i][j + 1], 1, divVel, 1,
                            viscousTensor[i][j + 1], 1);
            }
            else
            {
                // Copy to make symmetric
                Vmath::Vcopy(nPts, viscousTensor[i][j + 1], 1,
                             viscousTensor[j][i + 1], 1);
            }
        }
    }

    // Terms for the energy equation
    for (int i = 0; i < m_spacedim; ++i)
    {
        Vmath::Zero(nPts, viscousTensor[i][m_spacedim + 1], 1);
        // u_j * tau_ij
        for (int j = 0; j < m_spacedim; ++j)
        {
            Vmath::Vvtvp(nPts, physfield[j], 1, viscousTensor[i][j + 1], 1,
                         viscousTensor[i][m_spacedim + 1], 1,
                         viscousTensor[i][m_spacedim + 1], 1);
        }
        // Add k*T_i
        Vmath::Vvtvp(nPts, thermalConductivity, 1, derivativesO1[i][m_spacedim],
                     1, viscousTensor[i][m_spacedim + 1], 1,
                     viscousTensor[i][m_spacedim + 1], 1);
    }
}

/**
 * @brief Return the flux vector for the LDG diffusion problem.
 * \todo Complete the viscous flux vector
 */
void NavierStokesCFE::v_GetViscousFluxVectorDeAlias(
    const Array<OneD, const Array<OneD, NekDouble>> &physfield,
    TensorOfArray3D<NekDouble> &derivativesO1,
    TensorOfArray3D<NekDouble> &viscousTensor)
{
    // Factor to rescale 1d points in dealiasing.
    NekDouble OneDptscale = 2;
    // Get number of points to dealias a cubic non-linearity
    size_t nScalar   = physfield.size();
    size_t nPts      = m_fields[0]->Get1DScaledTotPoints(OneDptscale);
    size_t nPts_orig = physfield[0].size();

    // Auxiliary variables
    Array<OneD, NekDouble> divVel(nPts, 0.0);

    // Stokes hypothesis
    const NekDouble lambda = -2.0 / 3.0;

    // Update viscosity and thermal conductivity
    Array<OneD, NekDouble> mu(nPts, 0.0);
    Array<OneD, NekDouble> thermalConductivity(nPts, 0.0);
    GetViscosityAndThermalCondFromTemp(physfield[nScalar - 1], mu,
                                       thermalConductivity);

    // Interpolate inputs and initialise interpolated output
    Array<OneD, Array<OneD, NekDouble>> vel_interp(m_spacedim);
    TensorOfArray3D<NekDouble> deriv_interp(m_spacedim);
    TensorOfArray3D<NekDouble> out_interp(m_spacedim);
    for (int i = 0; i < m_spacedim; ++i)
    {
        // Interpolate velocity
        vel_interp[i] = Array<OneD, NekDouble>(nPts);
        m_fields[0]->PhysInterp1DScaled(OneDptscale, physfield[i],
                                        vel_interp[i]);

        // Interpolate derivatives
        deriv_interp[i] = Array<OneD, Array<OneD, NekDouble>>(m_spacedim + 1);
        for (int j = 0; j < m_spacedim + 1; ++j)
        {
            deriv_interp[i][j] = Array<OneD, NekDouble>(nPts);
            m_fields[0]->PhysInterp1DScaled(OneDptscale, derivativesO1[i][j],
                                            deriv_interp[i][j]);
        }

        // Output (start from j=1 since flux is zero for rho)
        out_interp[i] = Array<OneD, Array<OneD, NekDouble>>(m_spacedim + 2);
        for (int j = 1; j < m_spacedim + 2; ++j)
        {
            out_interp[i][j] = Array<OneD, NekDouble>(nPts);
        }
    }

    // Velocity divergence
    for (int j = 0; j < m_spacedim; ++j)
    {
        Vmath::Vadd(nPts, divVel, 1, deriv_interp[j][j], 1, divVel, 1);
    }

    // Velocity divergence scaled by lambda * mu
    Vmath::Smul(nPts, lambda, divVel, 1, divVel, 1);
    Vmath::Vmul(nPts, mu, 1, divVel, 1, divVel, 1);

    // Viscous flux vector for the rho equation = 0 (no need to dealias)
    for (int i = 0; i < m_spacedim; ++i)
    {
        Vmath::Zero(nPts_orig, viscousTensor[i][0], 1);
    }

    // Viscous stress tensor (for the momentum equations)
    for (int i = 0; i < m_spacedim; ++i)
    {
        for (int j = i; j < m_spacedim; ++j)
        {
            Vmath::Vadd(nPts, deriv_interp[i][j], 1, deriv_interp[j][i], 1,
                        out_interp[i][j + 1], 1);

            Vmath::Vmul(nPts, mu, 1, out_interp[i][j + 1], 1,
                        out_interp[i][j + 1], 1);

            if (i == j)
            {
                // Add divergence term to diagonal
                Vmath::Vadd(nPts, out_interp[i][j + 1], 1, divVel, 1,
                            out_interp[i][j + 1], 1);
            }
            else
            {
                // Make symmetric
                out_interp[j][i + 1] = out_interp[i][j + 1];
            }
        }
    }

    // Terms for the energy equation
    for (int i = 0; i < m_spacedim; ++i)
    {
        Vmath::Zero(nPts, out_interp[i][m_spacedim + 1], 1);
        // u_j * tau_ij
        for (int j = 0; j < m_spacedim; ++j)
        {
            Vmath::Vvtvp(nPts, vel_interp[j], 1, out_interp[i][j + 1], 1,
                         out_interp[i][m_spacedim + 1], 1,
                         out_interp[i][m_spacedim + 1], 1);
        }
        // Add k*T_i
        Vmath::Vvtvp(nPts, thermalConductivity, 1, deriv_interp[i][m_spacedim],
                     1, out_interp[i][m_spacedim + 1], 1,
                     out_interp[i][m_spacedim + 1], 1);
    }

    // Project to original space
    for (int i = 0; i < m_spacedim; ++i)
    {
        for (int j = 1; j < m_spacedim + 2; ++j)
        {
            m_fields[0]->PhysGalerkinProjection1DScaled(
                OneDptscale, out_interp[i][j], viscousTensor[i][j]);
        }
    }
}

/**
 * @brief For very special treatment. For general boundaries it does nothing
 * But for WallViscous and WallAdiabatic, special treatment is needed
 * because they get the same Bwd value, special treatment is needed for
 * boundary treatment of diffusion flux
 * Note: This special treatment could be removed by seperating
 * WallViscous and WallAdiabatic into two different classes.
 *
 */
void NavierStokesCFE::SpecialBndTreat(
    Array<OneD, Array<OneD, NekDouble>> &consvar)
{
    size_t nConvectiveFields = consvar.size();
    size_t ndens             = 0;
    size_t nengy             = nConvectiveFields - 1;

    Array<OneD, Array<OneD, NekDouble>> bndCons{nConvectiveFields};
    Array<OneD, NekDouble> bndTotEngy;
    Array<OneD, NekDouble> bndPressure;
    Array<OneD, NekDouble> bndRho;
    Array<OneD, NekDouble> bndIntEndy;
    size_t nLengthArray = 0;

    size_t cnt         = 0;
    size_t nBndRegions = m_fields[nengy]->GetBndCondExpansions().size();
    for (size_t j = 0; j < nBndRegions; ++j)
    {
        if (m_fields[nengy]
                ->GetBndConditions()[j]
                ->GetBoundaryConditionType() == SpatialDomains::ePeriodic)
        {
            continue;
        }

        size_t nBndEdges =
            m_fields[nengy]->GetBndCondExpansions()[j]->GetExpSize();
        for (size_t e = 0; e < nBndEdges; ++e)
        {
            size_t nBndEdgePts = m_fields[nengy]
                                     ->GetBndCondExpansions()[j]
                                     ->GetExp(e)
                                     ->GetTotPoints();

            int id2 = m_fields[0]->GetTrace()->GetPhys_Offset(
                m_fields[0]->GetTraceMap()->GetBndCondIDToGlobalTraceID(cnt++));

            // Imposing Temperature Twall at the wall
            if (boost::iequals(
                    m_fields[nengy]->GetBndConditions()[j]->GetUserDefined(),
                    "WallViscous"))
            {
                if (nBndEdgePts != nLengthArray)
                {
                    for (size_t i = 0; i < nConvectiveFields; ++i)
                    {
                        bndCons[i] = Array<OneD, NekDouble>{nBndEdgePts, 0.0};
                    }
                    bndTotEngy   = Array<OneD, NekDouble>{nBndEdgePts, 0.0};
                    bndPressure  = Array<OneD, NekDouble>{nBndEdgePts, 0.0};
                    bndRho       = Array<OneD, NekDouble>{nBndEdgePts, 0.0};
                    bndIntEndy   = Array<OneD, NekDouble>{nBndEdgePts, 0.0};
                    nLengthArray = nBndEdgePts;
                }
                else
                {
                    Vmath::Zero(nLengthArray, bndPressure, 1);
                    Vmath::Zero(nLengthArray, bndRho, 1);
                    Vmath::Zero(nLengthArray, bndIntEndy, 1);
                }

                Array<OneD, NekDouble> tmp;

                for (size_t k = 0; k < nConvectiveFields; ++k)
                {
                    Vmath::Vcopy(nBndEdgePts, tmp = consvar[k] + id2, 1,
                                 bndCons[k], 1);
                }

                m_varConv->GetPressure(bndCons, bndPressure);
                Vmath::Fill(nLengthArray, m_Twall, bndTotEngy, 1);
                m_varConv->GetRhoFromPT(bndPressure, bndTotEngy, bndRho);
                m_varConv->GetEFromRhoP(bndRho, bndPressure, bndIntEndy);
                m_varConv->GetDynamicEnergy(bndCons, bndTotEngy);

                Vmath::Vvtvp(nBndEdgePts, bndIntEndy, 1, bndCons[ndens], 1,
                             bndTotEngy, 1, bndTotEngy, 1);

                Vmath::Vcopy(nBndEdgePts, bndTotEngy, 1,
                             tmp = consvar[nengy] + id2, 1);
            }
        }
    }
}

/**
 *
 * @brief Calculate and return the Symmetric flux in IP method.
 */
void NavierStokesCFE::GetViscousSymmtrFluxConservVar(
    const size_t nDim, const Array<OneD, Array<OneD, NekDouble>> &inaverg,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    TensorOfArray3D<NekDouble> &outarray, Array<OneD, int> &nonZeroIndex,
    const Array<OneD, Array<OneD, NekDouble>> &normal)
{
    size_t nConvectiveFields = inarray.size();
    size_t nPts              = inaverg[nConvectiveFields - 1].size();
    nonZeroIndex             = Array<OneD, int>{nConvectiveFields - 1, 0};
    for (size_t i = 0; i < nConvectiveFields - 1; ++i)
    {
        nonZeroIndex[i] = i + 1;
    }

    Array<OneD, NekDouble> mu(nPts, 0.0);
    Array<OneD, NekDouble> thermalConductivity(nPts, 0.0);
    Array<OneD, NekDouble> temperature(nPts, 0.0);
    m_varConv->GetTemperature(inaverg, temperature);
    GetViscosityAndThermalCondFromTemp(temperature, mu, thermalConductivity);

    std::vector<NekDouble> inAvgTmp(nConvectiveFields);
    std::vector<NekDouble> inTmp(nConvectiveFields);
    std::vector<NekDouble> outTmp(nConvectiveFields);
    for (size_t d = 0; d < nDim; ++d)
    {
        for (size_t nderiv = 0; nderiv < nDim; ++nderiv)
        {
            for (size_t p = 0; p < nPts; ++p)
            {
                // rearrenge data
                for (size_t f = 0; f < nConvectiveFields; ++f)
                {
                    inAvgTmp[f] = inaverg[f][p];
                    inTmp[f]    = inarray[f][p];
                }

                GetViscousFluxBilinearFormKernel(nDim, d, nderiv,
                                                 inAvgTmp.data(), inTmp.data(),
                                                 mu[p], outTmp.data());

                for (size_t f = 0; f < nConvectiveFields; ++f)
                {
                    outarray[d][f][p] += normal[nderiv][p] * outTmp[f];
                }
            }
        }
    }
}

/**
 * @brief Return the penalty vector for the LDGNS diffusion problem.
 */
void NavierStokesCFE::v_GetFluxPenalty(
    const Array<OneD, const Array<OneD, NekDouble>> &uFwd,
    const Array<OneD, const Array<OneD, NekDouble>> &uBwd,
    Array<OneD, Array<OneD, NekDouble>> &penaltyCoeff)
{
    size_t nTracePts = uFwd[0].size();

    // Compute average temperature
    size_t nVariables = uFwd.size();
    Array<OneD, NekDouble> tAve{nTracePts, 0.0};
    Vmath::Svtsvtp(nTracePts, 0.5, uFwd[nVariables - 1], 1, 0.5,
                   uBwd[nVariables - 1], 1, tAve, 1);

    // Get average viscosity and thermal conductivity
    Array<OneD, NekDouble> muAve{nTracePts, 0.0};
    Array<OneD, NekDouble> tcAve{nTracePts, 0.0};

    GetViscosityAndThermalCondFromTemp(tAve, muAve, tcAve);

    // Compute penalty term
    for (size_t i = 0; i < nVariables; ++i)
    {
        // Get jump of u variables
        Vmath::Vsub(nTracePts, uFwd[i], 1, uBwd[i], 1, penaltyCoeff[i], 1);
        // Multiply by variable coefficient = {coeff} ( u^+ - u^- )
        if (i < nVariables - 1)
        {
            Vmath::Vmul(nTracePts, muAve, 1, penaltyCoeff[i], 1,
                        penaltyCoeff[i], 1);
        }
        else
        {
            Vmath::Vmul(nTracePts, tcAve, 1, penaltyCoeff[i], 1,
                        penaltyCoeff[i], 1);
        }
    }
}

/**
 * @brief Update viscosity
 * todo: add artificial viscosity here
 */
void NavierStokesCFE::GetViscosityAndThermalCondFromTemp(
    const Array<OneD, NekDouble> &temperature, Array<OneD, NekDouble> &mu,
    Array<OneD, NekDouble> &thermalCond)
{
    size_t nPts = temperature.size();

    for (size_t p = 0; p < nPts; ++p)
    {
        GetViscosityAndThermalCondFromTempKernel(temperature[p], mu[p],
                                                 thermalCond[p]);
    }

    // Add artificial viscosity if wanted
    // move this above and add in kernel
    if (m_is_shockCaptPhys)
    {
        size_t nTracePts = m_fields[0]->GetTrace()->GetTotPoints();
        if (nPts != nTracePts)
        {
            Vmath::Vadd(nPts, mu, 1, m_varConv->GetAv(), 1, mu, 1);
        }
        else
        {
            Vmath::Vadd(nPts, mu, 1, m_varConv->GetAvTrace(), 1, mu, 1);
        }

        // Update thermal conductivity
        NekDouble tRa = m_Cp / m_Prandtl;
        Vmath::Smul(nPts, tRa, mu, 1, thermalCond, 1);
    }
}

/**
 * @brief Get divergence and curl squared
 *
 * @param input
 *   fields -> expansion list pointer
 *   cnsVar -> conservative variables
 *   cnsVarFwd -> forward trace of conservative variables
 *   cnsVarBwd -> backward trace of conservative variables
 * @paran output
 *   divSquare -> divergence
 *   curlSquare -> curl squared
 *
 */
void NavierStokesCFE::GetDivCurlSquared(
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &cnsVar,
    Array<OneD, NekDouble> &div, Array<OneD, NekDouble> &curlSquare,
    const Array<OneD, Array<OneD, NekDouble>> &cnsVarFwd,
    const Array<OneD, Array<OneD, NekDouble>> &cnsVarBwd)
{
    size_t nDim    = fields[0]->GetCoordim(0);
    size_t nVar    = cnsVar.size();
    size_t nPts    = cnsVar[0].size();
    size_t nPtsTrc = cnsVarFwd[0].size();

    // These should be allocated once
    Array<OneD, Array<OneD, NekDouble>> primVar(nVar - 1), primVarFwd(nVar - 1),
        primVarBwd(nVar - 1);

    for (unsigned short d = 0; d < nVar - 2; ++d)
    {
        primVar[d]    = Array<OneD, NekDouble>(nPts, 0.0);
        primVarFwd[d] = Array<OneD, NekDouble>(nPtsTrc, 0.0);
        primVarBwd[d] = Array<OneD, NekDouble>(nPtsTrc, 0.0);
    }
    size_t ergLoc      = nVar - 2;
    primVar[ergLoc]    = Array<OneD, NekDouble>(nPts, 0.0);
    primVarFwd[ergLoc] = Array<OneD, NekDouble>(nPtsTrc, 0.0);
    primVarBwd[ergLoc] = Array<OneD, NekDouble>(nPtsTrc, 0.0);

    // Get primitive variables [u,v,w,T=0]
    // Possibly should be changed to [rho,u,v,w,T] to make IP and LDGNS more
    // consistent with each other
    for (unsigned short d = 0; d < nVar - 2; ++d)
    {
        // Volume
        for (size_t p = 0; p < nPts; ++p)
        {
            primVar[d][p] = cnsVar[d + 1][p] / cnsVar[0][p];
        }
        // Trace
        for (size_t p = 0; p < nPtsTrc; ++p)
        {
            primVarFwd[d][p] = cnsVarFwd[d + 1][p] / cnsVarFwd[0][p];
            primVarBwd[d][p] = cnsVarBwd[d + 1][p] / cnsVarBwd[0][p];
        }
    }

    // this should be allocated once
    Array<OneD, Array<OneD, Array<OneD, NekDouble>>> primVarDer(nDim);
    for (unsigned short j = 0; j < nDim; ++j)
    {
        primVarDer[j] = Array<OneD, Array<OneD, NekDouble>>(nVar - 1);
        for (unsigned short i = 0; i < nVar - 1; ++i)
        {
            primVarDer[j][i] = Array<OneD, NekDouble>(nPts, 0.0);
        }
    }

    // Get derivative tensor
    m_diffusion->DiffuseCalcDerivative(fields, primVar, primVarDer, primVarFwd,
                                       primVarBwd);

    // Get div curl squared
    GetDivCurlFromDvelT(primVarDer, div, curlSquare);
}

/**
 * @brief Get divergence and curl from velocity derivative tensor
 *
 */
void NavierStokesCFE::GetDivCurlFromDvelT(
    const TensorOfArray3D<NekDouble> &pVarDer, Array<OneD, NekDouble> &div,
    Array<OneD, NekDouble> &curlSquare)
{
    size_t nDim = pVarDer.size();
    size_t nPts = div.size();

    // div velocity
    for (size_t p = 0; p < nPts; ++p)
    {
        NekDouble divTmp = 0;
        for (unsigned short j = 0; j < nDim; ++j)
        {
            divTmp += pVarDer[j][j][p];
        }
        div[p] = divTmp;
    }

    // |curl velocity| ** 2
    if (nDim > 2)
    {
        for (size_t p = 0; p < nPts; ++p)
        {
            // curl[0] 3/2 - 2/3
            NekDouble curl032 = pVarDer[2][1][p]; // load 1x
            NekDouble curl023 = pVarDer[1][2][p]; // load 1x
            NekDouble curl0   = curl032 - curl023;
            // square curl[0]
            NekDouble curl0sqr = curl0 * curl0;

            // curl[1] 3/1 - 1/3
            NekDouble curl131 = pVarDer[2][0][p]; // load 1x
            NekDouble curl113 = pVarDer[0][2][p]; // load 1x
            NekDouble curl1   = curl131 - curl113;
            // square curl[1]
            NekDouble curl1sqr = curl1 * curl1;

            // curl[2] 1/2 - 2/1
            NekDouble curl212 = pVarDer[0][1][p]; // load 1x
            NekDouble curl221 = pVarDer[1][0][p]; // load 1x
            NekDouble curl2   = curl212 - curl221;
            // square curl[2]
            NekDouble curl2sqr = curl2 * curl2;

            // reduce
            curl0sqr += curl1sqr + curl2sqr;
            // store
            curlSquare[p] = curl0sqr; // store 1x
        }
    }
    else if (nDim > 1)
    {
        for (size_t p = 0; p < nPts; ++p)
        {
            // curl[2] 1/2
            NekDouble c212 = pVarDer[0][1][p]; // load 1x
            // curl[2] 2/1
            NekDouble c221 = pVarDer[1][0][p]; // load 1x
            // curl[2] 1/2 - 2/1
            NekDouble curl = c212 - c221;
            // square curl[2]
            curlSquare[p] = curl * curl; // store 1x
        }
    }
    else
    {
        Vmath::Fill(nPts, 0.0, curlSquare, 1);
    }
}

void NavierStokesCFE::v_ExtraFldOutput(
    std::vector<Array<OneD, NekDouble>> &fieldcoeffs,
    std::vector<std::string> &variables)
{
    bool extraFields;
    m_session->MatchSolverInfo("OutputExtraFields", "True", extraFields, true);
    if (extraFields)
    {
        const int nPhys   = m_fields[0]->GetNpoints();
        const int nCoeffs = m_fields[0]->GetNcoeffs();
        Array<OneD, Array<OneD, NekDouble>> cnsVar(m_fields.size());

        for (size_t i = 0; i < m_fields.size(); ++i)
        {
            cnsVar[i] = m_fields[i]->GetPhys();
        }

        Array<OneD, Array<OneD, NekDouble>> velocity(m_spacedim);
        Array<OneD, Array<OneD, NekDouble>> velFwd(m_spacedim);
        for (int i = 0; i < m_spacedim; ++i)
        {
            velocity[i] = Array<OneD, NekDouble>(nPhys);
            velFwd[i]   = Array<OneD, NekDouble>(nCoeffs);
        }

        Array<OneD, NekDouble> pressure(nPhys), temperature(nPhys);
        Array<OneD, NekDouble> entropy(nPhys);
        Array<OneD, NekDouble> soundspeed(nPhys), mach(nPhys);
        Array<OneD, NekDouble> sensor(nPhys), SensorKappa(nPhys);

        m_varConv->GetVelocityVector(cnsVar, velocity);
        m_varConv->GetPressure(cnsVar, pressure);
        m_varConv->GetTemperature(cnsVar, temperature);
        m_varConv->GetEntropy(cnsVar, entropy);
        m_varConv->GetSoundSpeed(cnsVar, soundspeed);
        m_varConv->GetMach(cnsVar, soundspeed, mach);

        int sensorOffset;
        m_session->LoadParameter("SensorOffset", sensorOffset, 1);
        m_varConv->GetSensor(m_fields[0], cnsVar, sensor, SensorKappa,
                             sensorOffset);

        Array<OneD, NekDouble> pFwd(nCoeffs), TFwd(nCoeffs);
        Array<OneD, NekDouble> sFwd(nCoeffs);
        Array<OneD, NekDouble> aFwd(nCoeffs), mFwd(nCoeffs);
        Array<OneD, NekDouble> sensFwd(nCoeffs);

        std::string velNames[3] = {"u", "v", "w"};
        for (int i = 0; i < m_spacedim; ++i)
        {
            m_fields[0]->FwdTransLocalElmt(velocity[i], velFwd[i]);
            variables.push_back(velNames[i]);
            fieldcoeffs.push_back(velFwd[i]);
        }

        m_fields[0]->FwdTransLocalElmt(pressure, pFwd);
        m_fields[0]->FwdTransLocalElmt(temperature, TFwd);
        m_fields[0]->FwdTransLocalElmt(entropy, sFwd);
        m_fields[0]->FwdTransLocalElmt(soundspeed, aFwd);
        m_fields[0]->FwdTransLocalElmt(mach, mFwd);
        m_fields[0]->FwdTransLocalElmt(sensor, sensFwd);

        variables.push_back("p");
        variables.push_back("T");
        variables.push_back("s");
        variables.push_back("a");
        variables.push_back("Mach");
        variables.push_back("Sensor");
        fieldcoeffs.push_back(pFwd);
        fieldcoeffs.push_back(TFwd);
        fieldcoeffs.push_back(sFwd);
        fieldcoeffs.push_back(aFwd);
        fieldcoeffs.push_back(mFwd);
        fieldcoeffs.push_back(sensFwd);

        if (m_artificialDiffusion)
        {
            // reuse pressure
            Array<OneD, NekDouble> sensorFwd(nCoeffs);
            m_artificialDiffusion->GetArtificialViscosity(cnsVar, pressure);
            m_fields[0]->FwdTransLocalElmt(pressure, sensorFwd);

            variables.push_back("ArtificialVisc");
            fieldcoeffs.push_back(sensorFwd);
        }

        if (m_is_shockCaptPhys)
        {

            Array<OneD, Array<OneD, NekDouble>> cnsVarFwd(m_fields.size()),
                cnsVarBwd(m_fields.size());

            for (size_t i = 0; i < m_fields.size(); ++i)
            {
                cnsVarFwd[i] = Array<OneD, NekDouble>(GetTraceTotPoints());
                cnsVarBwd[i] = Array<OneD, NekDouble>(GetTraceTotPoints());
                m_fields[i]->GetFwdBwdTracePhys(cnsVar[i], cnsVarFwd[i],
                                                cnsVarBwd[i]);
            }

            Array<OneD, NekDouble> div(nPhys), curlSquare(nPhys);
            GetDivCurlSquared(m_fields, cnsVar, div, curlSquare, cnsVarFwd,
                              cnsVarBwd);

            Array<OneD, NekDouble> divFwd(nCoeffs, 0.0);
            m_fields[0]->FwdTransLocalElmt(div, divFwd);
            variables.push_back("div");
            fieldcoeffs.push_back(divFwd);

            Array<OneD, NekDouble> curlFwd(nCoeffs, 0.0);
            m_fields[0]->FwdTransLocalElmt(curlSquare, curlFwd);
            variables.push_back("curl^2");
            fieldcoeffs.push_back(curlFwd);

            m_varConv->SetAv(m_fields, cnsVar, div, curlSquare);

            Array<OneD, NekDouble> muavFwd(nCoeffs);
            m_fields[0]->FwdTransLocalElmt(m_varConv->GetAv(), muavFwd);
            variables.push_back("ArtificialVisc");
            fieldcoeffs.push_back(muavFwd);
        }

        if (m_ALESolver)
        {
            ExtraFldOutputGrid(fieldcoeffs, variables);
            ExtraFldOutputGridVelocity(fieldcoeffs, variables);
        }
    }
}

bool NavierStokesCFE::v_SupportsShockCaptType(const std::string type) const
{
    if (type == "NonSmooth" || type == "Physical" || type == "Off")
    {
        return true;
    }
    else
    {
        return false;
    }
}

} // namespace Nektar
