VCSMapping.cpp

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///////////////////////////////////////////////////////////////////////////////
//
// File: VCSMapping.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: Velocity Correction Scheme w/ coordinate transformation
// for the Incompressible Navier Stokes equations
///////////////////////////////////////////////////////////////////////////////
 
#include <IncNavierStokesSolver/EquationSystems/VCSMapping.h>
#include <LibUtilities/BasicUtils/Timer.h>
#include <SolverUtils/Core/Misc.h>
 
#include <boost/algorithm/string.hpp>
 
using namespace std;
 
namespace Nektar
{
string VCSMapping::className =
    SolverUtils::GetEquationSystemFactory().RegisterCreatorFunction(
        "VCSMapping", VCSMapping::create);
 
string VCSMapping::solverTypeLookupId =
    LibUtilities::SessionReader::RegisterEnumValue("SolverType", "VCSMapping",
                                                   eVCSMapping);
 
/**
 * Constructor. Creates ...
 *
 * \param
 * \param
 */
VCSMapping::VCSMapping(const LibUtilities::SessionReaderSharedPtr &pSession,
                       const SpatialDomains::MeshGraphSharedPtr &pGraph)
    : UnsteadySystem(pSession, pGraph),
      VelocityCorrectionScheme(pSession, pGraph)
{
}
 
void VCSMapping::v_InitObject(bool DeclareField)
{
    VelocityCorrectionScheme::v_InitObject(DeclareField);
 
    m_mapping = GlobalMapping::Mapping::Load(m_session, m_fields);
    ASSERTL0(m_mapping, "Could not create mapping in VCSMapping.");
 
    std::string vExtrapolation = "Mapping";
    m_extrapolation            = GetExtrapolateFactory().CreateInstance(
        vExtrapolation, m_session, m_fields, m_pressure, m_velocity,
        m_advObject);
    m_extrapolation->SubSteppingTimeIntegration(m_intScheme);
    m_extrapolation->GenerateHOPBCMap(m_session);
 
    // Storage to extrapolate pressure forcing
    size_t physTot  = m_fields[0]->GetTotPoints();
    size_t intSteps = 1;
 
    if (m_intScheme->GetName() == "IMEX" ||
        m_intScheme->GetName() == "IMEXGear")
    {
        m_intSteps = m_intScheme->GetOrder();
    }
    else
    {
        NEKERROR(ErrorUtil::efatal,
                 "Integration method not suitable: "
                 "Options include IMEXGear or IMEXOrder{1,2,3,4}");
    }
 
    m_presForcingCorrection = Array<OneD, Array<OneD, NekDouble>>(intSteps);
    for (size_t i = 0; i < m_presForcingCorrection.size(); i++)
    {
        m_presForcingCorrection[i] = Array<OneD, NekDouble>(physTot, 0.0);
    }
    m_verbose = (m_session->DefinesCmdLineArgument("verbose")) ? true : false;
 
    // Load solve parameters related to the mapping
    // Flags determining if pressure/viscous terms should be treated implicitly
    m_session->MatchSolverInfo("MappingImplicitPressure", "True",
                               m_implicitPressure, false);
    m_session->MatchSolverInfo("MappingImplicitViscous", "True",
                               m_implicitViscous, false);
    m_session->MatchSolverInfo("MappingNeglectViscous", "True",
                               m_neglectViscous, false);
 
    if (m_neglectViscous)
    {
        m_implicitViscous = false;
    }
 
    // Tolerances and relaxation parameters for implicit terms
    m_session->LoadParameter("MappingPressureTolerance", m_pressureTolerance,
                             1e-12);
    m_session->LoadParameter("MappingViscousTolerance", m_viscousTolerance,
                             1e-12);
    m_session->LoadParameter("MappingPressureRelaxation", m_pressureRelaxation,
                             1.0);
    m_session->LoadParameter("MappingViscousRelaxation", m_viscousRelaxation,
                             1.0);
}
 
/**
 * Destructor
 */
VCSMapping::~VCSMapping(void)
{
}
 
void VCSMapping::v_DoInitialise(bool dumpInitialConditions)
{
    UnsteadySystem::v_DoInitialise(dumpInitialConditions);
 
    // Set up Field Meta Data for output files
    m_fieldMetaDataMap["Kinvis"] = boost::lexical_cast<std::string>(m_kinvis);
    m_fieldMetaDataMap["TimeStep"] =
        boost::lexical_cast<std::string>(m_timestep);
 
    // Correct Dirichlet boundary conditions to account for mapping
    m_mapping->UpdateBCs(0.0);
    //
    m_F = Array<OneD, Array<OneD, NekDouble>>(m_nConvectiveFields);
    for (int i = 0; i < m_nConvectiveFields; ++i)
    {
        m_fields[i]->ImposeDirichletConditions(m_fields[i]->UpdateCoeffs());
        m_fields[i]->BwdTrans(m_fields[i]->GetCoeffs(),
                              m_fields[i]->UpdatePhys());
        m_F[i] = Array<OneD, NekDouble>(m_fields[0]->GetTotPoints(), 0.0);
    }
 
    // Initialise m_gradP
    size_t physTot = m_fields[0]->GetTotPoints();
    m_gradP        = Array<OneD, Array<OneD, NekDouble>>(m_nConvectiveFields);
    for (int i = 0; i < m_nConvectiveFields; ++i)
    {
        m_gradP[i] = Array<OneD, NekDouble>(physTot, 0.0);
        m_pressure->PhysDeriv(MultiRegions::DirCartesianMap[i],
                              m_pressure->GetPhys(), m_gradP[i]);
        if (m_pressure->GetWaveSpace())
        {
            m_pressure->HomogeneousBwdTrans(physTot, m_gradP[i], m_gradP[i]);
        }
    }
}
 
/**
 * Explicit part of the method - Advection, Forcing + HOPBCs
 */
void VCSMapping::v_EvaluateAdvection_SetPressureBCs(
    const Array<OneD, const Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray, const NekDouble time)
{
    EvaluateAdvectionTerms(inarray, outarray, time);
 
    // Smooth advection
    if (m_SmoothAdvection)
    {
        for (int i = 0; i < m_nConvectiveFields; ++i)
        {
            m_pressure->SmoothField(outarray[i]);
        }
    }
 
    // Add forcing terms
    for (auto &x : m_forcing)
    {
        x->Apply(m_fields, inarray, outarray, time);
    }
 
    // Add mapping terms
    ApplyIncNSMappingForcing(inarray, outarray);
 
    // Calculate High-Order pressure boundary conditions
    m_extrapolation->EvaluatePressureBCs(inarray, outarray, m_kinvis);
 
    // Update mapping and deal with Dirichlet boundary conditions
    if (m_mapping->IsTimeDependent())
    {
        if (m_mapping->IsFromFunction())
        {
            // If the transformation is explicitly defined, update it here
            // Otherwise, it will be done somewhere else (ForcingMovingBody)
            m_mapping->UpdateMapping(time + m_timestep);
        }
        m_mapping->UpdateBCs(time + m_timestep);
    }
}
 
/**
 * Forcing term for Poisson solver solver
 */
void VCSMapping::v_SetUpPressureForcing(
    const Array<OneD, const Array<OneD, NekDouble>> &fields,
    Array<OneD, Array<OneD, NekDouble>> &Forcing, const NekDouble aii_Dt)
{
    if (m_mapping->HasConstantJacobian())
    {
        VelocityCorrectionScheme::v_SetUpPressureForcing(fields, Forcing,
                                                         aii_Dt);
    }
    else
    {
        size_t physTot = m_fields[0]->GetTotPoints();
        size_t nvel    = m_nConvectiveFields;
        Array<OneD, NekDouble> wk(physTot, 0.0);
 
        Array<OneD, NekDouble> Jac(physTot, 0.0);
        m_mapping->GetJacobian(Jac);
 
        // Calculate div(J*u/Dt)
        Vmath::Zero(physTot, Forcing[0], 1);
        for (size_t i = 0; i < nvel; ++i)
        {
            if (m_fields[i]->GetWaveSpace())
            {
                m_fields[i]->HomogeneousBwdTrans(physTot, fields[i], wk);
            }
            else
            {
                Vmath::Vcopy(physTot, fields[i], 1, wk, 1);
            }
            Vmath::Vmul(physTot, wk, 1, Jac, 1, wk, 1);
            if (m_fields[i]->GetWaveSpace())
            {
                m_fields[i]->HomogeneousFwdTrans(physTot, wk, wk);
            }
            m_fields[i]->PhysDeriv(MultiRegions::DirCartesianMap[i], wk, wk);
            Vmath::Vadd(physTot, wk, 1, Forcing[0], 1, Forcing[0], 1);
        }
        Vmath::Smul(physTot, 1.0 / aii_Dt, Forcing[0], 1, Forcing[0], 1);
 
        //
        // If the mapping viscous terms are being treated explicitly
        //        we need to apply a correction to the forcing
        if (!m_implicitViscous)
        {
            bool wavespace = m_fields[0]->GetWaveSpace();
            m_fields[0]->SetWaveSpace(false);
 
            //
            //  Part 1: div(J*grad(U/J . grad(J)))
            Array<OneD, Array<OneD, NekDouble>> tmp(nvel);
            Array<OneD, Array<OneD, NekDouble>> velocity(nvel);
            for (size_t i = 0; i < tmp.size(); i++)
            {
                tmp[i]      = Array<OneD, NekDouble>(physTot, 0.0);
                velocity[i] = Array<OneD, NekDouble>(physTot, 0.0);
                if (wavespace)
                {
                    m_fields[0]->HomogeneousBwdTrans(
                        physTot, m_fields[i]->GetPhys(), velocity[i]);
                }
                else
                {
                    Vmath::Vcopy(physTot, m_fields[i]->GetPhys(), 1,
                                 velocity[i], 1);
                }
            }
            // Calculate wk = U.grad(J)
            m_mapping->DotGradJacobian(velocity, wk);
            // Calculate wk = (U.grad(J))/J
            Vmath::Vdiv(physTot, wk, 1, Jac, 1, wk, 1);
            // J*grad[(U.grad(J))/J]
            for (size_t i = 0; i < nvel; ++i)
            {
                m_fields[0]->PhysDeriv(MultiRegions::DirCartesianMap[i], wk,
                                       tmp[i]);
                Vmath::Vmul(physTot, Jac, 1, tmp[i], 1, tmp[i], 1);
            }
            // div(J*grad[(U.grad(J))/J])
            Vmath::Zero(physTot, wk, 1);
            for (size_t i = 0; i < nvel; ++i)
            {
                m_fields[0]->PhysDeriv(MultiRegions::DirCartesianMap[i], tmp[i],
                                       tmp[i]);
                Vmath::Vadd(physTot, wk, 1, tmp[i], 1, wk, 1);
            }
 
            // Part 2: grad(J) . curl(curl(U))
            m_mapping->CurlCurlField(velocity, tmp, m_implicitViscous);
            // dont need velocity any more, so reuse it
            m_mapping->DotGradJacobian(tmp, velocity[0]);
 
            // Add two parts
            Vmath::Vadd(physTot, velocity[0], 1, wk, 1, wk, 1);
 
            // Multiply by kinvis and prepare to extrapolate
            size_t nlevels = m_presForcingCorrection.size();
            Vmath::Smul(physTot, m_kinvis, wk, 1,
                        m_presForcingCorrection[nlevels - 1], 1);
 
            // Extrapolate correction
            m_extrapolation->ExtrapolateArray(m_presForcingCorrection);
 
            // Put in wavespace
            if (wavespace)
            {
                m_fields[0]->HomogeneousFwdTrans(
                    physTot, m_presForcingCorrection[nlevels - 1], wk);
            }
            else
            {
                Vmath::Vcopy(physTot, m_presForcingCorrection[nlevels - 1], 1,
                             wk, 1);
            }
            // Apply correction: Forcing = Forcing - correction
            Vmath::Vsub(physTot, Forcing[0], 1, wk, 1, Forcing[0], 1);
 
            m_fields[0]->SetWaveSpace(wavespace);
        }
    }
}
 
/**
 * Forcing term for Helmholtz solver
 */
void VCSMapping::v_SetUpViscousForcing(
    const Array<OneD, const Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &Forcing, const NekDouble aii_Dt)
{
    NekDouble aii_dtinv = 1.0 / aii_Dt;
    size_t physTot      = m_fields[0]->GetTotPoints();
 
    // Grad p
    m_pressure->BwdTrans(m_pressure->GetCoeffs(), m_pressure->UpdatePhys());
 
    size_t nvel = m_velocity.size();
    if (nvel == 2)
    {
        m_pressure->PhysDeriv(m_pressure->GetPhys(), Forcing[0], Forcing[1]);
    }
    else
    {
        m_pressure->PhysDeriv(m_pressure->GetPhys(), Forcing[0], Forcing[1],
                              Forcing[2]);
    }
 
    // Copy grad p in physical space to m_gradP to reuse later
    if (m_pressure->GetWaveSpace())
    {
        for (size_t i = 0; i < nvel; i++)
        {
            m_pressure->HomogeneousBwdTrans(physTot, Forcing[i], m_gradP[i]);
        }
    }
    else
    {
        for (size_t i = 0; i < nvel; i++)
        {
            Vmath::Vcopy(physTot, Forcing[i], 1, m_gradP[i], 1);
        }
    }
 
    if ((!m_mapping->HasConstantJacobian()) || m_implicitPressure)
    {
        // If pressure terms are treated explicitly, we need to divide by J
        //    if they are implicit, we need to calculate G(p)
        if (m_implicitPressure)
        {
            m_mapping->RaiseIndex(m_gradP, Forcing);
        }
        else
        {
            Array<OneD, NekDouble> Jac(physTot, 0.0);
            m_mapping->GetJacobian(Jac);
            for (size_t i = 0; i < nvel; i++)
            {
                Vmath::Vdiv(physTot, m_gradP[i], 1, Jac, 1, Forcing[i], 1);
            }
        }
        // Transform back to wavespace
        if (m_pressure->GetWaveSpace())
        {
            for (size_t i = 0; i < nvel; i++)
            {
                m_pressure->HomogeneousFwdTrans(physTot, Forcing[i],
                                                Forcing[i]);
            }
        }
    }
 
    // Subtract inarray/(aii_dt) and divide by kinvis. Kinvis will
    // need to be updated for the convected fields.
    for (size_t i = 0; i < nvel; ++i)
    {
        Blas::Daxpy(physTot, -aii_dtinv, inarray[i], 1, Forcing[i], 1);
        Blas::Dscal(physTot, 1.0 / m_kinvis, &(Forcing[i])[0], 1);
    }
}
 
/**
 * Solve pressure system
 */
void VCSMapping::v_SolvePressure(const Array<OneD, NekDouble> &Forcing)
{
    if (!m_implicitPressure)
    {
        VelocityCorrectionScheme::v_SolvePressure(Forcing);
    }
    else
    {
        size_t physTot = m_fields[0]->GetTotPoints();
        size_t nvel    = m_nConvectiveFields;
        bool converged = false;     // flag to mark if system converged
        size_t s       = 0;         // iteration counter
        NekDouble error;            // L2 error at current iteration
        NekDouble forcing_L2 = 0.0; // L2 norm of F
 
        size_t maxIter;
        m_session->LoadParameter("MappingMaxIter", maxIter, 5000);
 
        // rhs of the equation at current iteration
        Array<OneD, NekDouble> F_corrected(physTot, 0.0);
        // Pressure field at previous iteration
        Array<OneD, NekDouble> previous_iter(physTot, 0.0);
        // Temporary variables
        Array<OneD, Array<OneD, NekDouble>> wk1(nvel);
        Array<OneD, Array<OneD, NekDouble>> wk2(nvel);
        Array<OneD, Array<OneD, NekDouble>> gradP(nvel);
        for (size_t i = 0; i < nvel; ++i)
        {
            wk1[i]   = Array<OneD, NekDouble>(physTot, 0.0);
            wk2[i]   = Array<OneD, NekDouble>(physTot, 0.0);
            gradP[i] = Array<OneD, NekDouble>(physTot, 0.0);
        }
 
        // Jacobian
        Array<OneD, NekDouble> Jac(physTot, 0.0);
        m_mapping->GetJacobian(Jac);
 
        // Factors for Laplacian system
        StdRegions::ConstFactorMap factors;
        factors[StdRegions::eFactorLambda] = 0.0;
 
        m_pressure->BwdTrans(m_pressure->GetCoeffs(), m_pressure->UpdatePhys());
        forcing_L2 = m_pressure->L2(Forcing, wk1[0]);
        while (!converged)
        {
            // Update iteration counter and set previous iteration field
            // (use previous timestep solution for first iteration)
            s++;
            ASSERTL0(s < maxIter,
                     "VCSMapping exceeded maximum number of iterations.");
 
            Vmath::Vcopy(physTot, m_pressure->GetPhys(), 1, previous_iter, 1);
 
            // Correct pressure bc to account for iteration
            m_extrapolation->CorrectPressureBCs(previous_iter);
 
            //
            // Calculate forcing term for this iteration
            //
            for (size_t i = 0; i < nvel; ++i)
            {
                m_pressure->PhysDeriv(MultiRegions::DirCartesianMap[i],
                                      previous_iter, gradP[i]);
                if (m_pressure->GetWaveSpace())
                {
                    m_pressure->HomogeneousBwdTrans(physTot, gradP[i], wk1[i]);
                }
                else
                {
                    Vmath::Vcopy(physTot, gradP[i], 1, wk1[i], 1);
                }
            }
            m_mapping->RaiseIndex(wk1, wk2); // G(p)
 
            m_mapping->Divergence(wk2, F_corrected); // div(G(p))
            if (!m_mapping->HasConstantJacobian())
            {
                Vmath::Vmul(physTot, F_corrected, 1, Jac, 1, F_corrected, 1);
            }
            // alpha*J*div(G(p))
            Vmath::Smul(physTot, m_pressureRelaxation, F_corrected, 1,
                        F_corrected, 1);
            if (m_pressure->GetWaveSpace())
            {
                m_pressure->HomogeneousFwdTrans(physTot, F_corrected,
                                                F_corrected);
            }
            // alpha*J*div(G(p)) - p_ii
            for (int i = 0; i < m_nConvectiveFields; ++i)
            {
                m_pressure->PhysDeriv(MultiRegions::DirCartesianMap[i],
                                      gradP[i], wk1[0]);
                Vmath::Vsub(physTot, F_corrected, 1, wk1[0], 1, F_corrected, 1);
            }
            // p_i,i - J*div(G(p))
            Vmath::Neg(physTot, F_corrected, 1);
            // alpha*F -  alpha*J*div(G(p)) + p_i,i
            Vmath::Smul(physTot, m_pressureRelaxation, Forcing, 1, wk1[0], 1);
            Vmath::Vadd(physTot, wk1[0], 1, F_corrected, 1, F_corrected, 1);
 
            //
            // Solve system
            //
            m_pressure->HelmSolve(F_corrected, m_pressure->UpdateCoeffs(),
                                  factors);
            m_pressure->BwdTrans(m_pressure->GetCoeffs(),
                                 m_pressure->UpdatePhys());
 
            //
            // Test convergence
            //
            error = m_pressure->L2(m_pressure->GetPhys(), previous_iter);
            if (forcing_L2 != 0)
            {
                if ((error / forcing_L2 < m_pressureTolerance))
                {
                    converged = true;
                }
            }
            else
            {
                if (error < m_pressureTolerance)
                {
                    converged = true;
                }
            }
        }
        if (m_verbose && m_session->GetComm()->GetRank() == 0)
        {
            std::cout << " Pressure system (mapping) converged in " << s
                      << " iterations with error = " << error << std::endl;
        }
    }
}
 
/**
 * Solve velocity system
 */
void VCSMapping::v_SolveViscous(
    const Array<OneD, const Array<OneD, NekDouble>> &Forcing,
    const Array<OneD, const Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray, const NekDouble aii_Dt)
{
    boost::ignore_unused(inarray);
 
    if (!m_implicitViscous)
    {
        VelocityCorrectionScheme::v_SolveViscous(Forcing, inarray, outarray,
                                                 aii_Dt);
    }
    else
    {
        size_t physTot = m_fields[0]->GetTotPoints();
        size_t nvel    = m_nConvectiveFields;
        bool converged = false;     // flag to mark if system converged
        size_t s       = 0;         // iteration counter
        NekDouble error, max_error; // L2 error at current iteration
 
        size_t maxIter;
        m_session->LoadParameter("MappingMaxIter", maxIter, 5000);
 
        // L2 norm of F
        Array<OneD, NekDouble> forcing_L2(m_nConvectiveFields, 0.0);
 
        // rhs of the equation at current iteration
        Array<OneD, Array<OneD, NekDouble>> F_corrected(nvel);
        // Solution at previous iteration
        Array<OneD, Array<OneD, NekDouble>> previous_iter(nvel);
        // Working space
        Array<OneD, Array<OneD, NekDouble>> wk(nvel);
        for (size_t i = 0; i < nvel; ++i)
        {
            F_corrected[i]   = Array<OneD, NekDouble>(physTot, 0.0);
            previous_iter[i] = Array<OneD, NekDouble>(physTot, 0.0);
            wk[i]            = Array<OneD, NekDouble>(physTot, 0.0);
        }
 
        // Factors for Helmholtz system
        StdRegions::ConstFactorMap factors;
        factors[StdRegions::eFactorLambda] =
            1.0 * m_viscousRelaxation / aii_Dt / m_kinvis;
        if (m_useSpecVanVisc)
        {
            factors[StdRegions::eFactorSVVCutoffRatio] = m_sVVCutoffRatio;
            factors[StdRegions::eFactorSVVDiffCoeff] =
                m_sVVDiffCoeff / m_kinvis;
        }
 
        // Calculate L2-norm of F and set initial solution for iteration
        for (size_t i = 0; i < nvel; ++i)
        {
            forcing_L2[i] = m_fields[0]->L2(Forcing[i], wk[0]);
            m_fields[i]->BwdTrans(m_fields[i]->GetCoeffs(), previous_iter[i]);
        }
 
        while (!converged)
        {
            converged = true;
            // Iteration counter
            s++;
            ASSERTL0(s < maxIter,
                     "VCSMapping exceeded maximum number of iterations.");
 
            max_error = 0.0;
 
            //
            // Calculate forcing term for next iteration
            //
 
            // Calculate L(U)- in this parts all components might be coupled
            if (m_fields[0]->GetWaveSpace())
            {
                for (size_t i = 0; i < nvel; ++i)
                {
                    m_fields[0]->HomogeneousBwdTrans(physTot, previous_iter[i],
                                                     wk[i]);
                }
            }
            else
            {
                for (size_t i = 0; i < nvel; ++i)
                {
                    Vmath::Vcopy(physTot, previous_iter[i], 1, wk[i], 1);
                }
            }
 
            // (L(U^i) - 1/alpha*U^i_jj)
            m_mapping->VelocityLaplacian(wk, F_corrected,
                                         1.0 / m_viscousRelaxation);
 
            if (m_fields[0]->GetWaveSpace())
            {
                for (size_t i = 0; i < nvel; ++i)
                {
                    m_fields[0]->HomogeneousFwdTrans(physTot, F_corrected[i],
                                                     F_corrected[i]);
                }
            }
            else
            {
                for (size_t i = 0; i < nvel; ++i)
                {
                    Vmath::Vcopy(physTot, F_corrected[i], 1, F_corrected[i], 1);
                }
            }
 
            // Loop velocity components
            for (size_t i = 0; i < nvel; ++i)
            {
                // (-alpha*L(U^i) + U^i_jj)
                Vmath::Smul(physTot, -1.0 * m_viscousRelaxation, F_corrected[i],
                            1, F_corrected[i], 1);
                //  F_corrected = alpha*F + (-alpha*L(U^i) + U^i_jj)
                Vmath::Smul(physTot, m_viscousRelaxation, Forcing[i], 1, wk[0],
                            1);
                Vmath::Vadd(physTot, wk[0], 1, F_corrected[i], 1,
                            F_corrected[i], 1);
 
                //
                // Solve System
                //
                m_fields[i]->HelmSolve(F_corrected[i],
                                       m_fields[i]->UpdateCoeffs(), factors);
                m_fields[i]->BwdTrans(m_fields[i]->GetCoeffs(), outarray[i]);
 
                //
                // Test convergence
                //
                error = m_fields[i]->L2(outarray[i], previous_iter[i]);
 
                if (forcing_L2[i] != 0)
                {
                    if ((error / forcing_L2[i] >= m_viscousTolerance))
                    {
                        converged = false;
                    }
                }
                else
                {
                    if (error >= m_viscousTolerance)
                    {
                        converged = false;
                    }
                }
                if (error > max_error)
                {
                    max_error = error;
                }
 
                // Copy field to previous_iter
                Vmath::Vcopy(physTot, outarray[i], 1, previous_iter[i], 1);
            }
        }
        if (m_verbose && m_session->GetComm()->GetRank() == 0)
        {
            std::cout << " Velocity system (mapping) converged in " << s
                      << " iterations with error = " << max_error << std::endl;
        }
    }
}
 
/**
 * Explicit terms of the mapping
 */
void VCSMapping::ApplyIncNSMappingForcing(
    const Array<OneD, const Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray)
{
    size_t physTot = m_fields[0]->GetTotPoints();
    Array<OneD, Array<OneD, NekDouble>> vel(m_nConvectiveFields);
    Array<OneD, Array<OneD, NekDouble>> velPhys(m_nConvectiveFields);
    Array<OneD, Array<OneD, NekDouble>> Forcing(m_nConvectiveFields);
    Array<OneD, Array<OneD, NekDouble>> tmp(m_nConvectiveFields);
    for (int i = 0; i < m_nConvectiveFields; ++i)
    {
        velPhys[i] = Array<OneD, NekDouble>(physTot, 0.0);
        Forcing[i] = Array<OneD, NekDouble>(physTot, 0.0);
        tmp[i]     = Array<OneD, NekDouble>(physTot, 0.0);
    }
 
    // Get fields and store velocity in wavespace and physical space
    if (m_fields[0]->GetWaveSpace())
    {
        for (int i = 0; i < m_nConvectiveFields; ++i)
        {
            vel[i] = inarray[i];
            m_fields[0]->HomogeneousBwdTrans(physTot, vel[i], velPhys[i]);
        }
    }
    else
    {
        for (int i = 0; i < m_nConvectiveFields; ++i)
        {
            vel[i] = inarray[i];
            Vmath::Vcopy(physTot, inarray[i], 1, velPhys[i], 1);
        }
    }
 
    // Advection contribution
    MappingAdvectionCorrection(velPhys, Forcing);
 
    // Time-derivative contribution
    if (m_mapping->IsTimeDependent())
    {
        MappingAccelerationCorrection(vel, velPhys, tmp);
        for (int i = 0; i < m_nConvectiveFields; ++i)
        {
            Vmath::Vadd(physTot, tmp[i], 1, Forcing[i], 1, Forcing[i], 1);
        }
    }
 
    // Pressure contribution
    if (!m_implicitPressure)
    {
        MappingPressureCorrection(tmp);
        for (int i = 0; i < m_nConvectiveFields; ++i)
        {
            Vmath::Vadd(physTot, tmp[i], 1, Forcing[i], 1, Forcing[i], 1);
        }
    }
    // Viscous contribution
    if ((!m_implicitViscous) && (!m_neglectViscous))
    {
        MappingViscousCorrection(velPhys, tmp);
        for (int i = 0; i < m_nConvectiveFields; ++i)
        {
            Vmath::Smul(physTot, m_kinvis, tmp[i], 1, tmp[i], 1);
            Vmath::Vadd(physTot, tmp[i], 1, Forcing[i], 1, Forcing[i], 1);
        }
    }
 
    // If necessary, transform to wavespace
    if (m_fields[0]->GetWaveSpace())
    {
        for (int i = 0; i < m_nConvectiveFields; ++i)
        {
            m_fields[0]->HomogeneousFwdTrans(physTot, Forcing[i], Forcing[i]);
        }
    }
 
    // Add to outarray
    for (int i = 0; i < m_nConvectiveFields; ++i)
    {
        Vmath::Vadd(physTot, outarray[i], 1, Forcing[i], 1, outarray[i], 1);
    }
}
 
void VCSMapping::MappingAdvectionCorrection(
    const Array<OneD, const Array<OneD, NekDouble>> &velPhys,
    Array<OneD, Array<OneD, NekDouble>> &outarray)
{
    size_t physTot = m_fields[0]->GetTotPoints();
    size_t nvel    = m_nConvectiveFields;
 
    Array<OneD, Array<OneD, NekDouble>> wk(nvel * nvel);
 
    // Apply Christoffel symbols to obtain {i,kj}vel(k)
    m_mapping->ApplyChristoffelContravar(velPhys, wk);
 
    // Calculate correction -U^j*{i,kj}vel(k)
    for (size_t i = 0; i < nvel; i++)
    {
        Vmath::Zero(physTot, outarray[i], 1);
        for (size_t j = 0; j < nvel; j++)
        {
            Vmath::Vvtvp(physTot, wk[i * nvel + j], 1, velPhys[j], 1,
                         outarray[i], 1, outarray[i], 1);
        }
        Vmath::Neg(physTot, outarray[i], 1);
    }
}
 
void VCSMapping::MappingAccelerationCorrection(
    const Array<OneD, const Array<OneD, NekDouble>> &vel,
    const Array<OneD, const Array<OneD, NekDouble>> &velPhys,
    Array<OneD, Array<OneD, NekDouble>> &outarray)
{
    size_t physTot = m_fields[0]->GetTotPoints();
    size_t nvel    = m_nConvectiveFields;
 
    Array<OneD, Array<OneD, NekDouble>> wk(nvel * nvel);
    Array<OneD, Array<OneD, NekDouble>> tmp(nvel);
    Array<OneD, Array<OneD, NekDouble>> coordVel(nvel);
    for (size_t i = 0; i < nvel; i++)
    {
        tmp[i]      = Array<OneD, NekDouble>(physTot, 0.0);
        coordVel[i] = Array<OneD, NekDouble>(physTot, 0.0);
    }
    // Get coordinates velocity in transformed system
    m_mapping->GetCoordVelocity(tmp);
    m_mapping->ContravarFromCartesian(tmp, coordVel);
 
    // Calculate first term: U^j u^i,j = U^j (du^i/dx^j + {i,kj}u^k)
    m_mapping->ApplyChristoffelContravar(velPhys, wk);
    for (size_t i = 0; i < nvel; i++)
    {
        Vmath::Zero(physTot, outarray[i], 1);
 
        m_fields[0]->PhysDeriv(velPhys[i], tmp[0], tmp[1]);
        for (size_t j = 0; j < nvel; j++)
        {
            if (j == 2)
            {
                m_fields[0]->PhysDeriv(MultiRegions::DirCartesianMap[j], vel[i],
                                       tmp[2]);
                if (m_fields[0]->GetWaveSpace())
                {
                    m_fields[0]->HomogeneousBwdTrans(physTot, tmp[2], tmp[2]);
                }
            }
 
            Vmath::Vadd(physTot, wk[i * nvel + j], 1, tmp[j], 1,
                        wk[i * nvel + j], 1);
 
            Vmath::Vvtvp(physTot, coordVel[j], 1, wk[i * nvel + j], 1,
                         outarray[i], 1, outarray[i], 1);
        }
    }
 
    // Set wavespace to false and store current value
    bool wavespace = m_fields[0]->GetWaveSpace();
    m_fields[0]->SetWaveSpace(false);
 
    // Add -u^j U^i,j
    m_mapping->ApplyChristoffelContravar(coordVel, wk);
    for (size_t i = 0; i < nvel; i++)
    {
        if (nvel == 2)
        {
            m_fields[0]->PhysDeriv(coordVel[i], tmp[0], tmp[1]);
        }
        else
        {
            m_fields[0]->PhysDeriv(coordVel[i], tmp[0], tmp[1], tmp[2]);
        }
 
        for (size_t j = 0; j < nvel; j++)
        {
            Vmath::Vadd(physTot, wk[i * nvel + j], 1, tmp[j], 1,
                        wk[i * nvel + j], 1);
            Vmath::Neg(physTot, wk[i * nvel + j], 1);
 
            Vmath::Vvtvp(physTot, velPhys[j], 1, wk[i * nvel + j], 1,
                         outarray[i], 1, outarray[i], 1);
        }
    }
 
    // Restore value of wavespace
    m_fields[0]->SetWaveSpace(wavespace);
}
 
void VCSMapping::MappingPressureCorrection(
    Array<OneD, Array<OneD, NekDouble>> &outarray)
{
    size_t physTot = m_fields[0]->GetTotPoints();
    size_t nvel    = m_nConvectiveFields;
 
    // Calculate g^(ij)p_(,j)
    m_mapping->RaiseIndex(m_gradP, outarray);
 
    // Calculate correction = (nabla p)/J - g^(ij)p_,j
    // (Jac is not required if it is constant)
    if (!m_mapping->HasConstantJacobian())
    {
        Array<OneD, NekDouble> Jac(physTot, 0.0);
        m_mapping->GetJacobian(Jac);
        for (size_t i = 0; i < nvel; ++i)
        {
            Vmath::Vdiv(physTot, m_gradP[i], 1, Jac, 1, m_gradP[i], 1);
        }
    }
    for (size_t i = 0; i < nvel; ++i)
    {
        Vmath::Vsub(physTot, m_gradP[i], 1, outarray[i], 1, outarray[i], 1);
    }
}
 
void VCSMapping::MappingViscousCorrection(
    const Array<OneD, const Array<OneD, NekDouble>> &velPhys,
    Array<OneD, Array<OneD, NekDouble>> &outarray)
{
    // L(U) - 1.0*d^2(u^i)/dx^jdx^j
    m_mapping->VelocityLaplacian(velPhys, outarray, 1.0);
}
 
} // namespace Nektar