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 ExpList1D and its daughters
//
///////////////////////////////////////////////////////////////////////////////

#include <MultiRegions/ExpList2DHomogeneous1D.h>
#include <MultiRegions/ExpList1D.h>

using namespace std;

namespace Nektar
{
    namespace MultiRegions
    {
        // Forward declaration for typedefs
        ExpList2DHomogeneous1D::ExpList2DHomogeneous1D():
            ExpListHomogeneous1D()
        {
            SetExpType(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(pSession,HomoBasis,lhom,useFFT,dealiasing)
        {
            SetExpType(e2DH1D);
            int i, n, cnt, nel;

            if (comm)
            {
                m_comm = comm;
            }

            ASSERTL1(m_planes.num_elements() == planes.num_elements(),
                     "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.num_elements() * planes[0]->GetExpSize());

            for(cnt = n = 0; n < planes.num_elements(); ++n)
            {
                m_planes[n] = planes[n];
                for (i = 0; i < planes[n]->GetExpSize(); ++i)
                {
                    (*m_exp)[cnt++] = planes[n]->GetExp(i);
                }
            }

            // Setup Default optimisation information.
            nel = GetExpSize();
            m_globalOptParam = MemoryManager<NekOptimize::GlobalOptParam>
                ::AllocateSharedPtr(nel);

            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(pSession,HomoBasis,lhom,useFFT,dealiasing)
        {
            SetExpType(e2DH1D);
            int n, j, nel;
            ExpList1DSharedPtr plane_zero;

            // note that nzplanes can be larger than nzmodes
            m_planes[0] = plane_zero = MemoryManager<ExpList1D>::
                AllocateSharedPtr(m_session, graph1D, false, 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.num_elements(); ++n)
            {
                m_planes[n] = MemoryManager<ExpList1D>::
                    AllocateSharedPtr(*plane_zero, false);
                for(j = 0; j < nel; ++j)
                {
                    (*m_exp).push_back((*m_exp)[j]);
                }
            }

            // Setup Default optimisation information.
            nel = GetExpSize();
            m_globalOptParam = MemoryManager<NekOptimize::GlobalOptParam>
                ::AllocateSharedPtr(nel);

            SetCoeffPhys();
        }


        /**
         * @param   In          ExpList2DHomogeneous1D object to copy.
         */
        ExpList2DHomogeneous1D::ExpList2DHomogeneous1D(
            const ExpList2DHomogeneous1D &In):
            ExpListHomogeneous1D(In)
        {
            SetExpType(e2DH1D);
            ExpList1DSharedPtr zero_plane =
                std::dynamic_pointer_cast<ExpList1D> (In.m_planes[0]);

            for (int n = 0; n < m_planes.num_elements(); ++n)
            {
                m_planes[n] = MemoryManager<ExpList1D>::
                    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.num_elements();

            // 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::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.num_elements();
            int npoints  = GetTotPoints(eid);

            switch(coordim = GetCoordim(0))
            {
            case 1:
                {
                    (*m_exp)[eid]->GetCoords(xc0);
                    xhom = xc1;
                }
                break;
            case 2:
                ASSERTL0(xc1.num_elements() != 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.num_elements());
            
            for(n = 0; n < m_planes.num_elements(); 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.num_elements();
            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.num_elements());
            
            for(n = 0; n < m_planes.num_elements(); 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.num_elements();

            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.num_elements() == 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.num_elements() + 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.num_elements()-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.num_elements();
            int nPtsPlane = m_planes[0]->GetNpoints();
            int nDim      = GetCoordim(0) + 1;

            ASSERTL1(normals.num_elements() >= nDim,
                     "Output vector does not have sufficient dimensions to"
                     "match coordim");
            ASSERTL1(normals[0].num_elements() >= 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);
                }
            }
        }

        NekDouble ExpList2DHomogeneous1D::v_Integral(const Array<OneD,
            const NekDouble> &inarray)
        {
            NekDouble val = 0.0;
            int       i   = 0;

            for (i = 0; i < (*m_exp).size(); ++i)
            {
                val += (*m_exp)[i]->Integral(inarray + m_phys_offset[i]);
            }
            val *= m_lhom/m_homogeneousBasis->GetNumModes();
            
            m_comm->AllReduce(val, LibUtilities::ReduceSum);

            return val;
        }
    } //end of namespace
} //end of namespace