Diffusion.cpp

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///////////////////////////////////////////////////////////////////////////////
//
// File: Diffusion.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: Abstract base class for diffusion.
//
///////////////////////////////////////////////////////////////////////////////
 
#include <SolverUtils/Diffusion/Diffusion.h>
 
namespace Nektar
{
namespace SolverUtils
{
DiffusionFactory &GetDiffusionFactory()
{
    static DiffusionFactory instance;
    return instance;
}
 
void Diffusion::InitObject(const LibUtilities::SessionReaderSharedPtr pSession,
                           Array<OneD, MultiRegions::ExpListSharedPtr> pFields)
{
    v_InitObject(pSession, pFields);
 
    // Div curl storage
    int nPts        = pFields[0]->GetTotPoints();
    m_divVel        = Array<OneD, NekDouble>(nPts, 0.0);
    m_divVelSquare  = Array<OneD, NekDouble>(nPts, 0.0);
    m_curlVelSquare = Array<OneD, NekDouble>(nPts, 0.0);
}
 
void Diffusion::Diffuse(
    const std::size_t nConvectiveFields,
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    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)
{
    v_Diffuse(nConvectiveFields, fields, inarray, outarray, pFwd, pBwd);
}
 
/**
 * @brief Similar with Diffusion::Diffuse(): calculate diffusion flux
 * The difference is in the outarray:
 *  it is the coefficients of basis for DiffuseCoeffs()
 *  it is the physics on quadrature points for Diffuse()
 */
void Diffusion::DiffuseCoeffs(
    const std::size_t nConvectiveFields,
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    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)
{
    v_DiffuseCoeffs(nConvectiveFields, fields, inarray, outarray, pFwd, pBwd);
}
 
void Diffusion::Diffuse(
    const std::size_t nConvectiveFields,
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray, NekDouble time,
    const Array<OneD, Array<OneD, NekDouble>> &pFwd,
    const Array<OneD, Array<OneD, NekDouble>> &pBwd)
{
    m_time = time;
    v_Diffuse(nConvectiveFields, fields, inarray, outarray, pFwd, pBwd);
}
 
void Diffusion::DiffuseCoeffs(
    const std::size_t nConvectiveFields,
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray, NekDouble time,
    const Array<OneD, Array<OneD, NekDouble>> &pFwd,
    const Array<OneD, Array<OneD, NekDouble>> &pBwd)
{
    m_time = time;
    v_DiffuseCoeffs(nConvectiveFields, fields, inarray, outarray, pFwd, pBwd);
}
 
void Diffusion::AddSymmFluxIntegralToOffDiag(
    const int nConvectiveFields, const int nDim, const int nPts,
    const int nTracePts,
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, const int> &nonZeroIndex,
    TensorOfArray3D<NekDouble> &Fwdflux, TensorOfArray3D<NekDouble> &Bwdflux,
    Array<OneD, Array<OneD, NekDouble>> &outarray)
{
    boost::ignore_unused(nTracePts);
 
    int nCoeffs = outarray[nConvectiveFields - 1].size();
    Array<OneD, NekDouble> tmpCoeff(nCoeffs, 0.0);
    Array<OneD, Array<OneD, NekDouble>> tmpfield(nDim);
 
    for (int i = 0; i < nDim; i++)
    {
        tmpfield[i] = Array<OneD, NekDouble>(nPts, 0.0);
    }
    int nv = 0;
 
    for (int j = 0; j < nonZeroIndex.size(); j++)
    {
        nv                                       = nonZeroIndex[j];
        MultiRegions::ExpListSharedPtr tracelist = fields[nv]->GetTrace();
        for (int nd = 0; nd < nDim; nd++)
        {
            Vmath::Zero(nPts, tmpfield[nd], 1);
 
            tracelist->MultiplyByQuadratureMetric(Fwdflux[nd][nv],
                                                  Fwdflux[nd][nv]);
            tracelist->MultiplyByQuadratureMetric(Bwdflux[nd][nv],
                                                  Bwdflux[nd][nv]);
 
            fields[nv]->AddTraceQuadPhysToOffDiag(
                Fwdflux[nd][nv], Bwdflux[nd][nv], tmpfield[nd]);
            fields[nv]->DivideByQuadratureMetric(tmpfield[nd], tmpfield[nd]);
        }
        fields[nv]->IProductWRTDerivBase(tmpfield, tmpCoeff);
        Vmath::Vadd(nCoeffs, tmpCoeff, 1, outarray[nv], 1, outarray[nv], 1);
    }
}
 
void Diffusion::v_Diffuse(
    const std::size_t nConvectiveFields,
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    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)
{
    boost::ignore_unused(nConvectiveFields, fields, inarray, outarray, pFwd,
                         pBwd);
    NEKERROR(ErrorUtil::efatal, "v_Diffuse not defined");
}
 
void Diffusion::v_DiffuseCoeffs(
    const std::size_t nConvectiveFields,
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    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)
{
    boost::ignore_unused(nConvectiveFields, fields, inarray, outarray, pFwd,
                         pBwd);
    NEKERROR(ErrorUtil::efatal, "v_DiffuseCoeffs not defined");
}
 
void Diffusion::v_DiffuseCoeffs(
    const std::size_t nConvectiveFields,
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray,
    const Array<OneD, Array<OneD, NekDouble>> &vFwd,
    const Array<OneD, Array<OneD, NekDouble>> &vBwd,
    TensorOfArray3D<NekDouble> &qfield, Array<OneD, int> &nonZeroIndex)
{
    boost::ignore_unused(nConvectiveFields, fields, inarray, outarray, vFwd,
                         vBwd, qfield, nonZeroIndex);
    NEKERROR(ErrorUtil::efatal, "v_DiffuseCoeffs not defined");
}
 
// Diffusion Calculate the physical derivatives
void Diffusion::DiffuseCalcDerivative(
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    TensorOfArray3D<NekDouble> &qfields,
    const Array<OneD, Array<OneD, NekDouble>> &pFwd,
    const Array<OneD, Array<OneD, NekDouble>> &pBwd)
{
    v_DiffuseCalcDerivative(fields, inarray, qfields, pFwd, pBwd);
}
 
const Array<OneD, const Array<OneD, NekDouble>> &Diffusion::v_GetTraceNormal()
{
    NEKERROR(ErrorUtil::efatal, "v_GetTraceNormal not defined");
    return NullNekDoubleArrayOfArray;
}
 
void Diffusion::v_ConsVarAveJump(
    const std::size_t nConvectiveFields, const size_t npnts,
    const Array<OneD, const Array<OneD, NekDouble>> &vFwd,
    const Array<OneD, const Array<OneD, NekDouble>> &vBwd,
    Array<OneD, Array<OneD, NekDouble>> &aver,
    Array<OneD, Array<OneD, NekDouble>> &jump)
{
    boost::ignore_unused(nConvectiveFields, npnts, vFwd, vBwd, aver, jump);
    NEKERROR(ErrorUtil::efatal, "v_ConsVarAveJump not defined");
}
 
void Diffusion::v_DiffuseCalcDerivative(
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    TensorOfArray3D<NekDouble> &qfields,
    const Array<OneD, Array<OneD, NekDouble>> &pFwd,
    const Array<OneD, Array<OneD, NekDouble>> &pBwd)
{
    boost::ignore_unused(fields, inarray, qfields, pFwd, pBwd);
    NEKERROR(ErrorUtil::efatal, "Not defined for function DiffuseVolumeFLux.");
}
 
void Diffusion::v_DiffuseVolumeFlux(
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    TensorOfArray3D<NekDouble> &qfields, TensorOfArray3D<NekDouble> &VolumeFlux,
    Array<OneD, int> &nonZeroIndex)
{
    boost::ignore_unused(fields, inarray, qfields, VolumeFlux, nonZeroIndex);
    NEKERROR(ErrorUtil::efatal, "Not defined for function DiffuseVolumeFLux.");
}
 
void Diffusion::v_DiffuseTraceFlux(
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    TensorOfArray3D<NekDouble> &qfields, TensorOfArray3D<NekDouble> &VolumeFlux,
    Array<OneD, Array<OneD, NekDouble>> &TraceFlux,
    const Array<OneD, Array<OneD, NekDouble>> &pFwd,
    const Array<OneD, Array<OneD, NekDouble>> &pBwd,
    Array<OneD, int> &nonZeroIndex)
{
    boost::ignore_unused(fields, inarray, qfields, VolumeFlux, TraceFlux, pFwd,
                         pBwd, nonZeroIndex);
    NEKERROR(ErrorUtil::efatal, "Not defined function DiffuseTraceFLux.");
}
 
/**
 * @brief Compute primary variables
 *
 */
void Diffusion::v_GetPrimVar(
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &primVar)
{
 
    int nDim = fields[0]->GetCoordim(0);
    int nPts = fields[0]->GetTotPoints();
    for (int i = 0; i < nDim; ++i)
    {
        primVar[i] = Array<OneD, NekDouble>(nPts, 0.0);
        Vmath::Vdiv(nPts, inarray[i + 1], 1, inarray[0], 1, primVar[i], 1);
    }
}
 
/**
 * @brief Compute and store scalars needed for shock sensor, i.e.
 * divergence and curl squared
 * @param dimensions, points, primary variables derivative
 *
 */
void Diffusion::GetDivCurl(
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const TensorOfArray3D<NekDouble> &pVarDer)
{
    int nDim = fields[0]->GetCoordim(0);
    int nPts = fields[0]->GetTotPoints();
    // Compute and store scalars needed for shock sensor
    Array<OneD, NekDouble> tmp3(nPts, 0.0);
    Array<OneD, NekDouble> tmp4(nPts, 0.0);
 
    // Zero the variables for the current iteration step
    Vmath::Zero(nPts, m_divVel, 1);
    Vmath::Zero(nPts, m_divVelSquare, 1);
    Vmath::Zero(nPts, m_curlVelSquare, 1);
 
    // div vel
    for (int j = 0; j < nDim; ++j)
    {
        Vmath::Vadd(nPts, m_divVel, 1, pVarDer[j][j], 1, m_divVel, 1);
    }
    // (div vel)**2
    Vmath::Vmul(nPts, m_divVel, 1, m_divVel, 1, m_divVelSquare, 1);
 
    // curl vel
    if (nDim > 2)
    {
        // curl[0] 3/2
        Vmath::Vadd(nPts, tmp4, 1, pVarDer[2][1], 1, tmp4, 1);
        // curl[0]-2/3
        Vmath::Vcopy(nPts, pVarDer[1][2], 1, tmp3, 1);
        Vmath::Neg(nPts, tmp3, 1);
        Vmath::Vadd(nPts, tmp4, 1, tmp3, 1, tmp4, 1);
        // square curl[0]
        Vmath::Vmul(nPts, tmp4, 1, tmp4, 1, tmp3, 1);
        Vmath::Vadd(nPts, m_curlVelSquare, 1, tmp3, 1, m_curlVelSquare, 1);
 
        tmp4 = Array<OneD, NekDouble>(nPts, 0.0);
        // curl[1] 3/1
        Vmath::Vadd(nPts, tmp4, 1, pVarDer[2][0], 1, tmp4, 1);
        // curl[1]-1/3
        Vmath::Vcopy(nPts, pVarDer[0][2], 1, tmp3, 1);
        Vmath::Neg(nPts, tmp3, 1);
        Vmath::Vadd(nPts, tmp4, 1, tmp3, 1, tmp4, 1);
        // square curl[1]
        Vmath::Vmul(nPts, tmp4, 1, tmp4, 1, tmp3, 1);
        Vmath::Vadd(nPts, m_curlVelSquare, 1, tmp3, 1, m_curlVelSquare, 1);
 
        tmp4 = Array<OneD, NekDouble>(nPts, 0.0);
        // curl[2] 1/2
        Vmath::Vadd(nPts, tmp4, 1, pVarDer[0][1], 1, tmp4, 1);
        // curl[2]-2/1
        Vmath::Vcopy(nPts, pVarDer[1][0], 1, tmp3, 1);
        Vmath::Neg(nPts, tmp3, 1);
        Vmath::Vadd(nPts, tmp4, 1, tmp3, 1, tmp4, 1);
        // square curl[2]
        Vmath::Vmul(nPts, tmp4, 1, tmp4, 1, tmp3, 1);
        Vmath::Vadd(nPts, m_curlVelSquare, 1, tmp3, 1, m_curlVelSquare, 1);
    }
    else if (nDim > 1)
    {
        // curl[2] 1/2
        Vmath::Vadd(nPts, tmp4, 1, pVarDer[0][1], 1, tmp4, 1);
        // curl[2]-2/1
        Vmath::Vcopy(nPts, pVarDer[1][0], 1, tmp3, 1);
        Vmath::Neg(nPts, tmp3, 1);
        Vmath::Vadd(nPts, tmp4, 1, tmp3, 1, tmp4, 1);
        // square curl[2]
        Vmath::Vmul(nPts, tmp4, 1, tmp4, 1, tmp3, 1);
        Vmath::Vadd(nPts, m_curlVelSquare, 1, tmp3, 1, m_curlVelSquare, 1);
    }
    else
    {
        Vmath::Fill(nPts, 0.0, m_curlVelSquare, 1);
    }
}
} // namespace SolverUtils
} // namespace Nektar