ExpList2DHomogeneous1D.cpp

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///////////////////////////////////////////////////////////////////////////////
//
// File: ExpList2DHomogeneous1D.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: An ExpList2D which is homogeneous in 1 direction and so
// uses much of the functionality from a ExpList and its daughters
//
///////////////////////////////////////////////////////////////////////////////
 
#include <MultiRegions/ExpList.h>
#include <MultiRegions/ExpList2DHomogeneous1D.h>
 
using namespace std;
 
namespace Nektar
{
namespace MultiRegions
{
// Forward declaration for typedefs
ExpList2DHomogeneous1D::ExpList2DHomogeneous1D() : ExpListHomogeneous1D(e2DH1D)
{
}
 
// Constructor for ExpList2DHomogeneous1D to act as a Explist2D field
ExpList2DHomogeneous1D::ExpList2DHomogeneous1D(
    const LibUtilities::SessionReaderSharedPtr &pSession,
    const LibUtilities::BasisKey &HomoBasis, const NekDouble lhom,
    const bool useFFT, const bool dealiasing,
    const Array<OneD, ExpListSharedPtr> &planes,
    const LibUtilities::CommSharedPtr comm)
    : ExpListHomogeneous1D(e2DH1D, pSession, HomoBasis, lhom, useFFT,
                           dealiasing)
{
    int i, n, cnt;
 
    if (comm)
    {
        m_comm = comm;
    }
 
    ASSERTL1(m_planes.size() == planes.size(),
             "Size of basis number of points and number"
             "of planes are not the same");
 
    // Set up expansion list with elements from all planes.
    m_exp = MemoryManager<LocalRegions::ExpansionVector>::AllocateSharedPtr(
        planes.size() * planes[0]->GetExpSize());
 
    for (cnt = n = 0; n < planes.size(); ++n)
    {
        m_planes[n] = planes[n];
        for (i = 0; i < planes[n]->GetExpSize(); ++i)
        {
            (*m_exp)[cnt++] = planes[n]->GetExp(i);
        }
    }
 
    SetCoeffPhys();
}
 
// Constructor for ExpList2DHomogeneous1D to act as a Explist2D field
ExpList2DHomogeneous1D::ExpList2DHomogeneous1D(
    const LibUtilities::SessionReaderSharedPtr &pSession,
    const LibUtilities::BasisKey &HomoBasis, const NekDouble lhom,
    const bool useFFT, const bool dealiasing,
    const SpatialDomains::MeshGraphSharedPtr &graph1D,
    const Collections::ImplementationType ImpType)
    : ExpListHomogeneous1D(e2DH1D, pSession, HomoBasis, lhom, useFFT,
                           dealiasing)
{
    int n, j, nel;
    ExpListSharedPtr plane_zero;
 
    // note that nzplanes can be larger than nzmodes
    m_planes[0] = plane_zero = MemoryManager<ExpList>::AllocateSharedPtr(
        m_session, graph1D, false, "DefaultVar", ImpType);
 
    m_exp = MemoryManager<LocalRegions::ExpansionVector>::AllocateSharedPtr();
 
    nel = m_planes[0]->GetExpSize();
 
    for (j = 0; j < nel; ++j)
    {
        (*m_exp).push_back(m_planes[0]->GetExp(j));
    }
 
    for (n = 1; n < m_planes.size(); ++n)
    {
        m_planes[n] =
            MemoryManager<ExpList>::AllocateSharedPtr(*plane_zero, false);
        for (j = 0; j < nel; ++j)
        {
            (*m_exp).push_back((*m_exp)[j]);
        }
    }
 
    SetCoeffPhys();
}
 
/**
 * @param   In          ExpList2DHomogeneous1D object to copy.
 */
ExpList2DHomogeneous1D::ExpList2DHomogeneous1D(const ExpList2DHomogeneous1D &In)
    : ExpListHomogeneous1D(In)
{
    ExpListSharedPtr zero_plane =
        std::dynamic_pointer_cast<ExpList>(In.m_planes[0]);
 
    for (int n = 0; n < m_planes.size(); ++n)
    {
        m_planes[n] =
            MemoryManager<ExpList>::AllocateSharedPtr(*zero_plane, false);
    }
 
    SetCoeffPhys();
}
 
/**
 * Destructor
 */
ExpList2DHomogeneous1D::~ExpList2DHomogeneous1D()
{
}
 
void ExpList2DHomogeneous1D::SetCoeffPhys(void)
{
    int i, n, cnt;
    int ncoeffs_per_plane = m_planes[0]->GetNcoeffs();
    int npoints_per_plane = m_planes[0]->GetTotPoints();
 
    int nzplanes = m_planes.size();
 
    // Set total coefficients and points
    m_ncoeffs = ncoeffs_per_plane * nzplanes;
    m_npoints = npoints_per_plane * nzplanes;
 
    m_coeffs = Array<OneD, NekDouble>(m_ncoeffs, 0.0);
    m_phys   = Array<OneD, NekDouble>(m_npoints, 0.0);
 
    int nel        = m_planes[0]->GetExpSize();
    m_coeff_offset = Array<OneD, int>(nel * nzplanes);
    m_phys_offset  = Array<OneD, int>(nel * nzplanes);
    Array<OneD, NekDouble> tmparray;
 
    for (cnt = n = 0; n < nzplanes; ++n)
    {
        m_planes[n]->SetCoeffsArray(tmparray =
                                        m_coeffs + ncoeffs_per_plane * n);
        m_planes[n]->SetPhysArray(tmparray = m_phys + npoints_per_plane * n);
 
        for (i = 0; i < nel; ++i)
        {
            m_coeff_offset[cnt] =
                m_planes[n]->GetCoeff_Offset(i) + n * ncoeffs_per_plane;
            m_phys_offset[cnt++] =
                m_planes[n]->GetPhys_Offset(i) + n * npoints_per_plane;
        }
    }
}
 
void ExpList2DHomogeneous1D::v_GetCoords(const int eid,
                                         Array<OneD, NekDouble> &xc0,
                                         Array<OneD, NekDouble> &xc1,
                                         Array<OneD, NekDouble> &xc2)
{
    int n, coordim;
    Array<OneD, NekDouble> tmp_xc, xhom;
    int nyplanes = m_planes.size();
    int npoints  = GetTotPoints(eid);
 
    switch (coordim = GetCoordim(0))
    {
        case 1:
        {
            (*m_exp)[eid]->GetCoords(xc0);
            xhom = xc1;
        }
        break;
        case 2:
            ASSERTL0(xc1.size() != 0, "output coord_1 is not defined");
            {
                (*m_exp)[eid]->GetCoords(xc0, xc1);
                xhom = xc2;
            }
            break;
        default:
            ASSERTL0(false, "Cannot have coordim being three dimensions"
                            "in a homogeneous field");
            break;
    }
 
    // Fill homogeneous-direction
    Array<OneD, const NekDouble> pts = m_homogeneousBasis->GetZ();
    Array<OneD, NekDouble> z(nyplanes);
 
    Array<OneD, NekDouble> local_pts(m_planes.size());
 
    for (n = 0; n < m_planes.size(); n++)
    {
        local_pts[n] = pts[m_transposition->GetPlaneID(n)];
    }
 
    Vmath::Smul(nyplanes, m_lhom / 2.0, local_pts, 1, z, 1);
    Vmath::Sadd(nyplanes, m_lhom / 2.0, z, 1, z, 1);
 
    for (n = 0; n < nyplanes; ++n)
    {
        Vmath::Fill(npoints, z[n], tmp_xc = xhom + npoints * n, 1);
        if (n)
        {
            Vmath::Vcopy(npoints, xc0, 1, tmp_xc = xc0 + npoints * n, 1);
            if (coordim == 2)
            {
                Vmath::Vcopy(npoints, xc1, 1, tmp_xc = xc1 + npoints * n, 1);
            }
        }
    }
}
 
/**
 * The operation calls the 2D plane coordinates through the
 * function ExpList#GetCoords and then evaluated the third
 * coordinate using the member \a m_lhom
 *
 * @param coord_0 After calculation, the \f$x_1\f$ coordinate
 *                          will be stored in this array.
 *
 * @param coord_1 After calculation, the \f$x_2\f$ coordinate
 *                          will be stored in this array.  This
 *                          coordinate might be  evaluated using the
 *                          predefined value \a m_lhom
 *
 * @param coord_2 After calculation, the \f$x_3\f$ coordinate
 *                          will be stored in this array. This
 *                          coordinate is evaluated using the
 *                          predefined value \a m_lhom
 */
void ExpList2DHomogeneous1D::v_GetCoords(Array<OneD, NekDouble> &xc0,
                                         Array<OneD, NekDouble> &xc1,
                                         Array<OneD, NekDouble> &xc2)
{
    int n, coordim;
    Array<OneD, NekDouble> tmp_xc, xhom;
    int nyplanes = m_planes.size();
    int npoints  = m_planes[0]->GetTotPoints();
 
    m_planes[0]->GetCoords(xc0, xc1);
 
    if ((coordim = GetCoordim(0)) == 1)
    {
        xhom = xc1;
    }
    else
    {
        xhom = xc2;
    }
 
    // Fill z-direction
    Array<OneD, const NekDouble> pts = m_homogeneousBasis->GetZ();
    Array<OneD, NekDouble> z(nyplanes);
    Array<OneD, NekDouble> local_pts(m_planes.size());
 
    for (n = 0; n < m_planes.size(); n++)
    {
        local_pts[n] = pts[m_transposition->GetPlaneID(n)];
    }
 
    Vmath::Smul(nyplanes, m_lhom / 2.0, local_pts, 1, z, 1);
    Vmath::Sadd(nyplanes, m_lhom / 2.0, z, 1, z, 1);
 
    for (n = 0; n < nyplanes; ++n)
    {
        Vmath::Fill(npoints, z[n], tmp_xc = xhom + npoints * n, 1);
        if (n)
        {
            Vmath::Vcopy(npoints, xc0, 1, tmp_xc = xc0 + npoints * n, 1);
            if (coordim == 2)
            {
                Vmath::Vcopy(npoints, xc1, 1, tmp_xc = xc1 + npoints * n, 1);
            }
        }
    }
}
 
/**
 * Write Tecplot Files Zone
 * @param   outfile    Output file name.
 * @param   expansion  Expansion that is considered
 */
void ExpList2DHomogeneous1D::v_WriteTecplotZone(std::ostream &outfile,
                                                int expansion)
{
    int i, j;
 
    int nquad0 = (*m_exp)[expansion]->GetNumPoints(0);
    int nquad1 = m_planes.size();
 
    Array<OneD, NekDouble> coords[3];
 
    coords[0] = Array<OneD, NekDouble>(3 * nquad0 * nquad1);
    coords[1] = coords[0] + nquad0 * nquad1;
    coords[2] = coords[1] + nquad0 * nquad1;
 
    GetCoords(expansion, coords[0], coords[1], coords[2]);
 
    outfile << "Zone, I=" << nquad0 << ", J=" << nquad1 << ", F=Block"
            << std::endl;
 
    for (j = 0; j < GetCoordim(0) + 1; ++j)
    {
        for (i = 0; i < nquad0 * nquad1; ++i)
        {
            outfile << coords[j][i] << " ";
        }
        outfile << std::endl;
    }
}
 
void ExpList2DHomogeneous1D::v_WriteVtkPieceHeader(std::ostream &outfile,
                                                   int expansion, int istrip)
{
    boost::ignore_unused(istrip);
 
    // If there is only one plane (e.g. HalfMode), we write a 2D plane.
    if (m_planes.size() == 1)
    {
        m_planes[0]->WriteVtkPieceHeader(outfile, expansion);
        return;
    }
 
    // If we are using Fourier points, output extra plane to fill domain
    int outputExtraPlane = 0;
    if (m_homogeneousBasis->GetBasisType() == LibUtilities::eFourier &&
        m_homogeneousBasis->GetPointsType() ==
            LibUtilities::eFourierEvenlySpaced)
    {
        outputExtraPlane = 1;
    }
    int i, j;
    int nquad0    = (*m_exp)[expansion]->GetNumPoints(0);
    int nquad1    = m_planes.size() + outputExtraPlane;
    int ntot      = nquad0 * nquad1;
    int ntotminus = (nquad0 - 1) * (nquad1 - 1);
 
    Array<OneD, NekDouble> coords[3];
    coords[0] = Array<OneD, NekDouble>(ntot);
    coords[1] = Array<OneD, NekDouble>(ntot);
    coords[2] = Array<OneD, NekDouble>(ntot);
    GetCoords(expansion, coords[0], coords[1], coords[2]);
 
    if (outputExtraPlane)
    {
        // Copy coords[0] and coords[1] to extra plane
        Array<OneD, NekDouble> tmp;
        Vmath::Vcopy(nquad0, coords[0], 1,
                     tmp = coords[0] + (nquad1 - 1) * nquad0, 1);
        Vmath::Vcopy(nquad0, coords[1], 1,
                     tmp = coords[1] + (nquad1 - 1) * nquad0, 1);
        // Fill coords[2] for extra plane
        NekDouble z = coords[2][nquad0 * m_planes.size() - 1] +
                      (coords[2][nquad0] - coords[2][0]);
        Vmath::Fill(nquad0, z, tmp = coords[2] + (nquad1 - 1) * nquad0, 1);
    }
 
    outfile << "    <Piece NumberOfPoints=\"" << ntot << "\" NumberOfCells=\""
            << ntotminus << "\">" << endl;
    outfile << "      <Points>" << endl;
    outfile << "        <DataArray type=\"Float64\" "
            << "NumberOfComponents=\"3\" format=\"ascii\">" << endl;
    outfile << "          ";
    for (i = 0; i < ntot; ++i)
    {
        for (j = 0; j < 3; ++j)
        {
            outfile << coords[j][i] << " ";
        }
        outfile << endl;
    }
    outfile << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "      </Points>" << endl;
    outfile << "      <Cells>" << endl;
    outfile << "        <DataArray type=\"Int32\" "
            << "Name=\"connectivity\" format=\"ascii\">" << endl;
    for (i = 0; i < nquad0 - 1; ++i)
    {
        for (j = 0; j < nquad1 - 1; ++j)
        {
            outfile << j * nquad0 + i << " " << j * nquad0 + i + 1 << " "
                    << (j + 1) * nquad0 + i + 1 << " " << (j + 1) * nquad0 + i
                    << endl;
        }
    }
    outfile << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "        <DataArray type=\"Int32\" "
            << "Name=\"offsets\" format=\"ascii\">" << endl;
    for (i = 0; i < ntotminus; ++i)
    {
        outfile << i * 4 + 4 << " ";
    }
    outfile << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "        <DataArray type=\"UInt8\" "
            << "Name=\"types\" format=\"ascii\">" << endl;
    for (i = 0; i < ntotminus; ++i)
    {
        outfile << "9 ";
    }
    outfile << endl;
    outfile << "        </DataArray>" << endl;
    outfile << "      </Cells>" << endl;
    outfile << "      <PointData>" << endl;
}
 
void ExpList2DHomogeneous1D::v_GetNormals(
    Array<OneD, Array<OneD, NekDouble>> &normals)
{
    int nPlanes   = m_planes.size();
    int nPtsPlane = m_planes[0]->GetNpoints();
    int nDim      = GetCoordim(0) + 1;
 
    ASSERTL1(normals.size() >= nDim,
             "Output vector does not have sufficient dimensions to"
             "match coordim");
    ASSERTL1(normals[0].size() >= nPtsPlane,
             "Output vector does not have sufficient dimensions to"
             "match coordim");
 
    // Calculate normals from plane 0.
    m_planes[0]->GetNormals(normals);
 
    // Copy remaining planes.
    for (int i = 0; i < nDim; ++i)
    {
        for (int n = 1; n < nPlanes; ++n)
        {
            Vmath::Vcopy(nPtsPlane, &normals[i][0], 1,
                         &normals[i][n * nPtsPlane], 1);
        }
    }
}
} // namespace MultiRegions
} // namespace Nektar