GeomFactors.cpp

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////////////////////////////////////////////////////////////////////////////////
//
//  File: GeomFactors.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).
//
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//  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
//  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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//
//  Description: Geometric factors base class.
//
////////////////////////////////////////////////////////////////////////////////
 
#include <LibUtilities/Foundations/Interp.h>
#include <SpatialDomains/GeomFactors.h>
 
namespace Nektar::SpatialDomains
{
 
/**
 * @class GeomFactors
 *
 * This class stores the various geometric factors associated with a specific
 * element, necessary for fundamental integration and differentiation operations
 * as well as edge and surface normals.
 *
 * Initially, these algorithms are provided with a mapping from the reference
 * region element to the physical element. Practically, this is represented
 * using a corresponding reference region element for each coordinate
 * component. Note that for straight-sided elements, these elements will be of
 * linear order. Curved elements are represented using higher-order coordinate
 * mappings. This geometric order is in contrast to the order of the spectral/hp
 * expansion order on the element.
 *
 * For application of the chain rule during differentiation we require the
 * partial derivatives \f[\frac{\partial \xi_i}{\partial \chi_j}\f] evaluated at
 * the physical points of the expansion basis. We also construct the inverse
 * metric tensor \f$g^{ij}\f$ which, in the case of a domain embedded in a
 * higher-dimensional space, supports the conversion of covariant quantities to
 * contravariant quantities.  When the expansion dimension is equal to the
 * coordinate dimension the Jacobian of the mapping \f$\chi_j\f$ is a square
 * matrix and consequently the required terms are the entries of the inverse of
 * the Jacobian. However, in general this is not the case, so we therefore
 * implement the construction of these terms following the derivation in
 * Cantwell, et. al. \cite CaYaKiPeSh13. Given the coordinate maps \f$\chi_i\f$,
 * this comprises of five steps
 *
 * -# Compute the terms of the Jacobian
 *    \f$\frac{\partial \chi_i}{\partial \xi_j}\f$.
 * -# Compute the metric tensor
 *    \f$g_{ij}=\mathbf{t}_{(i)}\cdot\mathbf{t}_{(j)}\f$.
 * -# Compute the square of the Jacobian determinant
 *    \f$g=|\mathbf{g}|\f$.
 * -# Compute the inverse metric tensor \f$g^{ij}\f$.
 * -# Compute the terms \f$\frac{\partial \xi_i}{\partial \chi_j}\f$.
 */
 
/**
 * @param   gtype       Specified whether the geometry is regular or
 *                      deformed.
 * @param   coordim     Specifies the dimension of the coordinate
 *                      system.
 * @param   Coords      Coordinate maps of the element.
 * @param   keyTgt      Points at which to compute stored Jacobian
 *                      and derivative factors
 */
GeomFactors::GeomFactors(const GeomType gtype, const int coordim,
                         const StdRegions::StdExpansionSharedPtr &xmap,
                         const std::vector<Array<OneD, NekDouble>> &coords,
                         const LibUtilities::PointsKeyVector &keyTgt)
    : m_type(gtype), m_expDim(xmap->GetShapeDimension()), m_coordDim(coordim),
      m_valid(true), m_keyTgt(keyTgt), m_xmap(xmap), m_coords(coords)
{
    CheckIfValid();
}
 
/**
 * @param   S           An instance of a GeomFactors class from which
 *                      to construct a new instance.
 */
GeomFactors::GeomFactors(const GeomFactors &S)
    : m_type(S.m_type), m_expDim(S.m_expDim), m_coordDim(S.m_coordDim),
      m_valid(S.m_valid), m_xmap(S.m_xmap), m_coords(S.m_coords),
      m_jac(S.m_jac), m_derivFactor(S.m_derivFactor)
{
}
 
/**
 * Member data equivalence is tested in the following order: shape type,
 * expansion dimension, coordinate dimension and coordinates.
 */
bool operator==(const GeomFactors &lhs, const GeomFactors &rhs)
{
    if (!(lhs.m_type == rhs.m_type))
    {
        return false;
    }
 
    if (!(lhs.m_expDim == rhs.m_expDim))
    {
        return false;
    }
 
    if (!(lhs.m_coordDim == rhs.m_coordDim))
    {
        return false;
    }
 
    const Array<OneD, const NekDouble> jac_lhs =
        lhs.ComputeJac(lhs.m_xmap->GetPointsKeys());
    const Array<OneD, const NekDouble> jac_rhs =
        rhs.ComputeJac(rhs.m_xmap->GetPointsKeys());
    if (!(jac_lhs == jac_rhs))
    {
        return false;
    }
 
    return true;
}
 
/**
 * Derivatives are computed at the geometry point distributions and
 * interpolated to the target point distributions.
 *
 * @param       tpoints     Target point distributions.
 * @returns                 Derivative of coordinate map evaluated at
 *                          target point distributions.
 */
DerivStorage GeomFactors::ComputeDeriv(
    const LibUtilities::PointsKeyVector &keyTgt) const
{
    if (keyTgt.size() != m_expDim)
    {
        NEKERROR(ErrorUtil::ewarning,
                 "Dimension of target point distribution does not match "
                 "expansion dimension.");
    }
 
    int i = 0, j = 0;
    int nqtot_map      = 1;
    int nqtot_tbasis   = 1;
    DerivStorage deriv = DerivStorage(m_expDim);
    DerivStorage d_map = DerivStorage(m_expDim);
    LibUtilities::PointsKeyVector map_points(m_expDim);
 
    // Allocate storage and compute number of points
    for (i = 0; i < m_expDim; ++i)
    {
        map_points[i] = m_xmap->GetBasis(i)->GetPointsKey();
        nqtot_map *= map_points[i].GetNumPoints();
        nqtot_tbasis *= keyTgt[i].GetNumPoints();
        deriv[i] = Array<OneD, Array<OneD, NekDouble>>(m_coordDim);
        d_map[i] = Array<OneD, Array<OneD, NekDouble>>(m_coordDim);
    }
 
    // Calculate local derivatives
    for (i = 0; i < m_coordDim; ++i)
    {
        Array<OneD, NekDouble> tmp(nqtot_map);
        // Transform from coefficient space to physical space
        m_xmap->BwdTrans(m_coords[i], tmp);
 
        // Allocate storage and take the derivative (calculated at the
        // points as specified in 'Coords')
        for (j = 0; j < m_expDim; ++j)
        {
            d_map[j][i] = Array<OneD, NekDouble>(nqtot_map);
            deriv[j][i] = Array<OneD, NekDouble>(nqtot_tbasis);
        }
 
        switch (m_expDim)
        {
            case 1:
                m_xmap->StdPhysDeriv(tmp, d_map[0][i]);
                break;
            case 2:
                m_xmap->StdPhysDeriv(tmp, d_map[0][i], d_map[1][i]);
                break;
            case 3:
                m_xmap->StdPhysDeriv(tmp, d_map[0][i], d_map[1][i],
                                     d_map[2][i]);
                break;
        }
    }
 
    for (i = 0; i < m_coordDim; ++i)
    {
        // Interpolate the derivatives:
        // - from the points as defined in the mapping ('Coords')
        // - to the points at which we want to know the metrics
        //   ('tbasis')
        bool same = true;
        for (j = 0; j < m_expDim; ++j)
        {
            same = same && (map_points[j] == keyTgt[j]);
        }
        if (same)
        {
            for (j = 0; j < m_expDim; ++j)
            {
                deriv[j][i] = d_map[j][i];
            }
        }
        else
        {
            for (j = 0; j < m_expDim; ++j)
            {
                Interp(map_points, d_map[j][i], keyTgt, deriv[j][i]);
            }
        }
    }
 
    return deriv;
}
 
/**
 * This routine returns an array of values specifying the Jacobian
 * of the mapping at quadrature points in the element. The array
 * is either of size 1 in the case of elements having #GeomType
 * #eRegular, or of size equal to the number of quadrature points for
 * #eDeformed elements.
 *
 * @returns             Array containing the Jacobian of the coordinate
 *                      mapping at the quadrature points of the element.
 * @see                 GeomType
 */
Array<OneD, NekDouble> GeomFactors::ComputeJac(
    const LibUtilities::PointsKeyVector &keyTgt) const
{
    if (keyTgt.size() != m_expDim)
    {
        NEKERROR(ErrorUtil::ewarning,
                 "Dimension of target point distribution does not match "
                 "expansion dimension.");
    }
 
    // A point always has a unit jacobian
    if (m_expDim == 0)
    {
        return Array<OneD, NekDouble>(1, 1.0);
    }
 
    int i = 0, j = 0, k = 0, l = 0;
    int ptsTgt = 1;
 
    if (m_type == eDeformed)
    {
        // Allocate storage and compute number of points
        for (i = 0; i < m_expDim; ++i)
        {
            ptsTgt *= keyTgt[i].GetNumPoints();
        }
    }
 
    // Get derivative at geometry points
    DerivStorage deriv = ComputeDeriv(keyTgt);
 
    Array<TwoD, NekDouble> tmp(m_expDim * m_expDim, ptsTgt, 0.0);
    Array<TwoD, NekDouble> gmat(m_expDim * m_expDim, ptsTgt, 0.0);
    Array<OneD, NekDouble> jac(ptsTgt, 0.0);
 
    // Compute g_{ij} as t_i \cdot t_j and store in tmp
    for (i = 0, l = 0; i < m_expDim; ++i)
    {
        for (j = 0; j < m_expDim; ++j, ++l)
        {
            for (k = 0; k < m_coordDim; ++k)
            {
                Vmath::Vvtvp(ptsTgt, &deriv[i][k][0], 1, &deriv[j][k][0], 1,
                             &tmp[l][0], 1, &tmp[l][0], 1);
            }
        }
    }
 
    Adjoint(tmp, gmat);
 
    // Compute g = det(g_{ij}) (= Jacobian squared) and store
    // temporarily in m_jac.
    for (i = 0; i < m_expDim; ++i)
    {
        Vmath::Vvtvp(ptsTgt, &tmp[i][0], 1, &gmat[i * m_expDim][0], 1, &jac[0],
                     1, &jac[0], 1);
    }
 
    // Compute the Jacobian = sqrt(g)
    Vmath::Vsqrt(ptsTgt, &jac[0], 1, &jac[0], 1);
 
    return jac;
}
 
/**
 * This routine returns a two-dimensional array of values specifying
 * the inverse metric terms associated with the coordinate mapping of
 * the corresponding reference region to the physical element. These
 * terms correspond to the \f$g^{ij}\f$ terms in \cite CaYaKiPeSh13 and,
 * in the case of an embedded manifold, map covariant quantities to
 * contravariant quantities. The leading index of the array is the index
 * of the term in the tensor numbered as
 * \f[\left(\begin{array}{ccc}
 *    0 & 1 & 2 \\
 *    1 & 3 & 4 \\
 *    2 & 4 & 5
 * \end{array}\right)\f].
 * The second dimension is either of size 1 in the case of elements
 * having #GeomType #eRegular, or of size equal to the number of
 * quadrature points for #eDeformed elements.
 *
 * @see [Wikipedia "Covariance and Contravariance of Vectors"]
 *      (http://en.wikipedia.org/wiki/Covariance_and_contravariance_of_vectors)
 * @returns             Two-dimensional array containing the inverse
 *                      metric tensor of the coordinate mapping.
 */
Array<TwoD, NekDouble> GeomFactors::ComputeGmat(
    const LibUtilities::PointsKeyVector &keyTgt) const
{
    if (keyTgt.size() != m_expDim)
    {
        NEKERROR(ErrorUtil::ewarning,
                 "Dimension of target point distribution does not match "
                 "expansion dimension.");
    }
 
    int i = 0, j = 0, k = 0, l = 0;
    int ptsTgt = 1;
 
    if (m_type == eDeformed)
    {
        // Allocate storage and compute number of points
        for (i = 0; i < m_expDim; ++i)
        {
            ptsTgt *= keyTgt[i].GetNumPoints();
        }
    }
 
    // Get derivative at geometry points
    DerivStorage deriv = ComputeDeriv(keyTgt);
 
    Array<TwoD, NekDouble> tmp(m_expDim * m_expDim, ptsTgt, 0.0);
    Array<TwoD, NekDouble> gmat(m_expDim * m_expDim, ptsTgt, 0.0);
    Array<OneD, NekDouble> jac(ptsTgt, 0.0);
 
    // Compute g_{ij} as t_i \cdot t_j and store in tmp
    for (i = 0, l = 0; i < m_expDim; ++i)
    {
        for (j = 0; j < m_expDim; ++j, ++l)
        {
            for (k = 0; k < m_coordDim; ++k)
            {
                Vmath::Vvtvp(ptsTgt, &deriv[i][k][0], 1, &deriv[j][k][0], 1,
                             &tmp[l][0], 1, &tmp[l][0], 1);
            }
        }
    }
 
    Adjoint(tmp, gmat);
 
    // Compute g = det(g_{ij}) (= Jacobian squared) and store
    // temporarily in m_jac.
    for (i = 0; i < m_expDim; ++i)
    {
        Vmath::Vvtvp(ptsTgt, &tmp[i][0], 1, &gmat[i * m_expDim][0], 1, &jac[0],
                     1, &jac[0], 1);
    }
 
    for (i = 0; i < m_expDim * m_expDim; ++i)
    {
        Vmath::Vdiv(ptsTgt, &gmat[i][0], 1, &jac[0], 1, &gmat[i][0], 1);
    }
 
    return gmat;
}
 
/**
 * @param   keyTgt      Target point distributions.
 * @returns             Derivative factors evaluated at the target
 *                      point distributions.
 * A 1D example: /f$ Jac =(\partial x/ \partial \xi) /f$ ;
 *               /f$ factor = 1/Jac = (\partial \xi/ \partial x) /f$
 */
Array<TwoD, NekDouble> GeomFactors::ComputeDerivFactors(
    const LibUtilities::PointsKeyVector &keyTgt) const
{
    if (keyTgt.size() != m_expDim)
    {
        NEKERROR(ErrorUtil::ewarning,
                 "Dimension of target point distribution does not match "
                 "expansion dimension.");
    }
 
    int i = 0, j = 0, k = 0, l = 0;
    int ptsTgt = 1;
 
    if (m_type == eDeformed)
    {
        // Allocate storage and compute number of points
        for (i = 0; i < m_expDim; ++i)
        {
            ptsTgt *= keyTgt[i].GetNumPoints();
        }
    }
 
    // Get derivative at geometry points
    DerivStorage deriv = ComputeDeriv(keyTgt);
 
    Array<TwoD, NekDouble> tmp(m_expDim * m_expDim, ptsTgt, 0.0);
    Array<TwoD, NekDouble> gmat(m_expDim * m_expDim, ptsTgt, 0.0);
    Array<OneD, NekDouble> jac(ptsTgt, 0.0);
    Array<TwoD, NekDouble> factors(m_expDim * m_coordDim, ptsTgt, 0.0);
 
    // Compute g_{ij} as t_i \cdot t_j and store in tmp
    for (i = 0, l = 0; i < m_expDim; ++i)
    {
        for (j = 0; j < m_expDim; ++j, ++l)
        {
            for (k = 0; k < m_coordDim; ++k)
            {
                Vmath::Vvtvp(ptsTgt, &deriv[i][k][0], 1, &deriv[j][k][0], 1,
                             &tmp[l][0], 1, &tmp[l][0], 1);
            }
        }
    }
 
    Adjoint(tmp, gmat);
 
    // Compute g = det(g_{ij}) (= Jacobian squared) and store
    // temporarily in m_jac.
    for (i = 0; i < m_expDim; ++i)
    {
        Vmath::Vvtvp(ptsTgt, &tmp[i][0], 1, &gmat[i * m_expDim][0], 1, &jac[0],
                     1, &jac[0], 1);
    }
 
    for (i = 0; i < m_expDim * m_expDim; ++i)
    {
        Vmath::Vdiv(ptsTgt, &gmat[i][0], 1, &jac[0], 1, &gmat[i][0], 1);
    }
 
    // Compute the Jacobian = sqrt(g)
    Vmath::Vsqrt(ptsTgt, &jac[0], 1, &jac[0], 1);
 
    // Compute the derivative factors
    for (k = 0, l = 0; k < m_coordDim; ++k)
    {
        for (j = 0; j < m_expDim; ++j, ++l)
        {
            for (i = 0; i < m_expDim; ++i)
            {
                Vmath::Vvtvp(ptsTgt, &deriv[i][k][0], 1,
                             &gmat[m_expDim * i + j][0], 1, &factors[l][0], 1,
                             &factors[l][0], 1);
            }
        }
    }
 
    return factors;
}
 
void GeomFactors::ComputeMovingFrames(
    const LibUtilities::PointsKeyVector &keyTgt,
    const SpatialDomains::GeomMMF MMFdir,
    const Array<OneD, const NekDouble> &factors,
    Array<OneD, Array<OneD, NekDouble>> &movingframes)
{
    if (keyTgt.size() != m_expDim)
    {
        NEKERROR(ErrorUtil::ewarning,
                 "Dimension of target point distribution does not match "
                 "expansion dimension.");
    }
 
    int i = 0, k = 0;
    int ptsTgt = 1;
    int nq     = 1;
 
    for (i = 0; i < m_expDim; ++i)
    {
        nq *= keyTgt[i].GetNumPoints();
    }
 
    if (m_type == eDeformed)
    {
        // Allocate storage and compute number of points
        for (i = 0; i < m_expDim; ++i)
        {
            ptsTgt *= keyTgt[i].GetNumPoints();
        }
    }
 
    // Get derivative at geometry points
    DerivStorage deriv = ComputeDeriv(keyTgt);
 
    // number of moving frames is requited to be 3, even for surfaces
    int MFdim = 3;
 
    Array<OneD, Array<OneD, Array<OneD, NekDouble>>> MFtmp(MFdim);
 
    // Compute g_{ij} as t_i \cdot t_j and store in tmp
    for (i = 0; i < MFdim; ++i)
    {
        MFtmp[i] = Array<OneD, Array<OneD, NekDouble>>(m_coordDim);
        for (k = 0; k < m_coordDim; ++k)
        {
            MFtmp[i][k] = Array<OneD, NekDouble>(nq);
        }
    }
 
    // Compute g_{ij} as t_i \cdot t_j and store in tmp
    for (i = 0; i < MFdim - 1; ++i)
    {
        for (k = 0; k < m_coordDim; ++k)
        {
            if (m_type == eDeformed)
            {
                Vmath::Vcopy(ptsTgt, &deriv[i][k][0], 1, &MFtmp[i][k][0], 1);
            }
            else
            {
                Vmath::Fill(nq, deriv[i][k][0], MFtmp[i][k], 1);
            }
        }
    }
 
    // Direction of MF1 is preserved: MF2 is considered in the same
    // tangent plane as MF1. MF3 is computed by cross product of MF1
    // and MF2. MF2 is consequently computed as the cross product of
    // MF3 and MF1.
    Array<OneD, Array<OneD, NekDouble>> PrincipleDir(m_coordDim);
    for (k = 0; k < m_coordDim; k++)
    {
        PrincipleDir[k] = Array<OneD, NekDouble>(nq);
    }
 
    if (!(MMFdir == eLOCAL))
    {
        ComputePrincipleDirection(keyTgt, MMFdir, factors, PrincipleDir);
    }
 
    // MF3 = MF1 \times MF2
    VectorCrossProd(MFtmp[0], MFtmp[1], MFtmp[2]);
 
    // Normalizing MF3
    VectorNormalise(MFtmp[2]);
 
    if (!(MMFdir == eLOCAL))
    {
        Array<OneD, NekDouble> temp(nq, 0.0);
 
        // Reorient MF1 along the PrincipleDir
        for (i = 0; i < m_coordDim; ++i)
        {
            Vmath::Vvtvp(nq, MFtmp[2][i], 1, PrincipleDir[i], 1, temp, 1, temp,
                         1);
        }
        Vmath::Neg(nq, temp, 1);
 
        // u2 = v2 - < u1 , v2 > ( u1 / < u1, u1 > )
        for (i = 0; i < m_coordDim; ++i)
        {
            Vmath::Vvtvp(nq, temp, 1, MFtmp[2][i], 1, PrincipleDir[i], 1,
                         MFtmp[0][i], 1);
        }
    }
 
    // Normalizing MF1
    VectorNormalise(MFtmp[0]);
 
    // MF2 = MF3 \times MF1
    VectorCrossProd(MFtmp[2], MFtmp[0], MFtmp[1]);
 
    // Normalizing MF2
    VectorNormalise(MFtmp[1]);
 
    for (i = 0; i < MFdim; ++i)
    {
        for (k = 0; k < m_coordDim; ++k)
        {
            Vmath::Vcopy(nq, &MFtmp[i][k][0], 1,
                         &movingframes[i * m_coordDim + k][0], 1);
        }
    }
}
 
/**
 * Constructs the Jacobian as per Spencer's book p158 and tests if
 * negative.
 */
void GeomFactors::CheckIfValid()
{
    // Jacobian test only makes sense when expdim = coorddim
    // If one-dimensional then element is valid.
    if (m_coordDim != m_expDim || m_expDim == 1)
    {
        m_valid = true;
        return;
    }
 
    LibUtilities::PointsKeyVector p(m_expDim);
    int nqtot = 1;
    for (int i = 0; i < m_expDim; ++i)
    {
        p[i] = m_xmap->GetBasis(i)->GetPointsKey();
        nqtot *= p[i].GetNumPoints();
    }
    int pts = (m_type == eRegular || m_type == eMovingRegular) ? 1 : nqtot;
    Array<OneD, NekDouble> jac(pts, 0.0);
 
    DerivStorage deriv = GetDeriv(p);
 
    switch (m_expDim)
    {
        case 2:
        {
            Vmath::Vvtvvtm(pts, &deriv[0][0][0], 1, &deriv[1][1][0], 1,
                           &deriv[1][0][0], 1, &deriv[0][1][0], 1, &jac[0], 1);
            break;
        }
        case 3:
        {
            Array<OneD, NekDouble> tmp(pts, 0.0);
 
            Vmath::Vvtvvtm(pts, &deriv[1][1][0], 1, &deriv[2][2][0], 1,
                           &deriv[2][1][0], 1, &deriv[1][2][0], 1, &tmp[0], 1);
            Vmath::Vvtvp(pts, &deriv[0][0][0], 1, &tmp[0], 1, &jac[0], 1,
                         &jac[0], 1);
 
            Vmath::Vvtvvtm(pts, &deriv[2][1][0], 1, &deriv[0][2][0], 1,
                           &deriv[0][1][0], 1, &deriv[2][2][0], 1, &tmp[0], 1);
            Vmath::Vvtvp(pts, &deriv[1][0][0], 1, &tmp[0], 1, &jac[0], 1,
                         &jac[0], 1);
 
            Vmath::Vvtvvtm(pts, &deriv[0][1][0], 1, &deriv[1][2][0], 1,
                           &deriv[1][1][0], 1, &deriv[0][2][0], 1, &tmp[0], 1);
            Vmath::Vvtvp(pts, &deriv[2][0][0], 1, &tmp[0], 1, &jac[0], 1,
                         &jac[0], 1);
 
            break;
        }
    }
 
    if (Vmath::Vmin(pts, &jac[0], 1) < 0)
    {
        m_valid = false;
    }
}
 
/**
 * @param   map_points  Source data point distribution.
 * @param   src         Source data to be interpolated.
 * @param   tpoints     Target data point distribution.
 * @param   tgt         Target data storage.
 */
void GeomFactors::Interp(const LibUtilities::PointsKeyVector &src_points,
                         const Array<OneD, const NekDouble> &src,
                         const LibUtilities::PointsKeyVector &tgt_points,
                         Array<OneD, NekDouble> &tgt) const
{
    if (src_points.size() != tgt_points.size())
    {
        NEKERROR(ErrorUtil::ewarning,
                 "Dimension of target point distribution does not match "
                 "expansion dimension.");
    }
 
    switch (m_expDim)
    {
        case 1:
            LibUtilities::Interp1D(src_points[0], src, tgt_points[0], tgt);
            break;
        case 2:
            LibUtilities::Interp2D(src_points[0], src_points[1], src,
                                   tgt_points[0], tgt_points[1], tgt);
            break;
        case 3:
            LibUtilities::Interp3D(src_points[0], src_points[1], src_points[2],
                                   src, tgt_points[0], tgt_points[1],
                                   tgt_points[2], tgt);
            break;
    }
}
 
/**
 * Input and output arrays are of dimension
 * (m_expDim*m_expDim) x num_points. The first index of the input and
 * output arrays are ordered row-by-row.
 * @param   src         Input data array.
 * @param   tgt         Storage for adjoint matrix data.
 */
void GeomFactors::Adjoint(const Array<TwoD, const NekDouble> &src,
                          Array<TwoD, NekDouble> &tgt) const
{
    if (src.size() != tgt.size())
    {
        NEKERROR(ErrorUtil::ewarning,
                 "Source matrix is of different size to destination"
                 "matrix for computing adjoint.");
    }
 
    int n = src[0].size();
    switch (m_expDim)
    {
        case 1:
            Vmath::Fill(n, 1.0, &tgt[0][0], 1);
            break;
        case 2:
            Vmath::Vcopy(n, &src[3][0], 1, &tgt[0][0], 1);
            Vmath::Smul(n, -1.0, &src[1][0], 1, &tgt[1][0], 1);
            Vmath::Smul(n, -1.0, &src[2][0], 1, &tgt[2][0], 1);
            Vmath::Vcopy(n, &src[0][0], 1, &tgt[3][0], 1);
            break;
        case 3:
        {
            int a, b, c, d, e, i, j;
 
            // Compute g^{ij} by computing Cofactors(g_ij)^T
            for (i = 0; i < m_expDim; ++i)
            {
                for (j = 0; j < m_expDim; ++j)
                {
                    a = ((i + 1) % m_expDim) * m_expDim + ((j + 1) % m_expDim);
                    b = ((i + 1) % m_expDim) * m_expDim + ((j + 2) % m_expDim);
                    c = ((i + 2) % m_expDim) * m_expDim + ((j + 1) % m_expDim);
                    d = ((i + 2) % m_expDim) * m_expDim + ((j + 2) % m_expDim);
                    e = j * m_expDim + i;
                    Vmath::Vvtvvtm(n, &src[a][0], 1, &src[d][0], 1, &src[b][0],
                                   1, &src[c][0], 1, &tgt[e][0], 1);
                }
            }
            break;
        }
    }
}
 
/**
 *
 */
void GeomFactors::ComputePrincipleDirection(
    const LibUtilities::PointsKeyVector &keyTgt,
    const SpatialDomains::GeomMMF MMFdir,
    const Array<OneD, const NekDouble> &factors,
    Array<OneD, Array<OneD, NekDouble>> &output)
{
    int nq = output[0].size();
 
    output = Array<OneD, Array<OneD, NekDouble>>(m_coordDim);
    for (int i = 0; i < m_coordDim; ++i)
    {
        output[i] = Array<OneD, NekDouble>(nq, 0.0);
    }
 
    // Construction of Connection
    switch (MMFdir)
    {
        // projection to x-axis
        case eTangentX:
        {
            Vmath::Fill(nq, 1.0, output[0], 1);
            break;
        }
        case eTangentY:
        {
            Vmath::Fill(nq, 1.0, output[1], 1);
            break;
        }
        case eTangentXY:
        {
            Vmath::Fill(nq, sqrt(2.0), output[0], 1);
            Vmath::Fill(nq, sqrt(2.0), output[1], 1);
            break;
        }
        case eTangentZ:
        {
            Vmath::Fill(nq, 1.0, output[2], 1);
            break;
        }
        case eTangentCircular:
        {
            // Tangent direction depends on spatial location.
            Array<OneD, Array<OneD, NekDouble>> x(m_coordDim);
            for (int k = 0; k < m_coordDim; k++)
            {
                x[k] = Array<OneD, NekDouble>(nq);
            }
 
            // m_coords are StdExpansions which store the mapping
            // between the std element and the local element. Bwd
            // transforming the std element minimum basis gives a
            // minimum physical basis for geometry. Need to then
            // interpolate this up to the quadrature basis.
            int nqtot_map = 1;
            LibUtilities::PointsKeyVector map_points(m_expDim);
            for (int i = 0; i < m_expDim; ++i)
            {
                map_points[i] = m_xmap->GetBasis(i)->GetPointsKey();
                nqtot_map *= map_points[i].GetNumPoints();
            }
            Array<OneD, NekDouble> tmp(nqtot_map);
            for (int k = 0; k < m_coordDim; k++)
            {
                m_xmap->BwdTrans(m_coords[k], tmp);
                Interp(map_points, tmp, keyTgt, x[k]);
            }
 
            // circular around the center of the domain
            NekDouble radius, xc = 0.0, yc = 0.0, xdis, ydis;
            NekDouble la, lb;
 
            if (factors.size() < 4)
            {
                NEKERROR(ErrorUtil::ewarning, "factors is too short.");
            }
 
            la = factors[0];
            lb = factors[1];
            xc = factors[2];
            yc = factors[3];
 
            for (int i = 0; i < nq; i++)
            {
                xdis   = x[0][i] - xc;
                ydis   = x[1][i] - yc;
                radius = sqrt(xdis * xdis / la / la + ydis * ydis / lb / lb);
                output[0][i] = ydis / radius;
                output[1][i] = -1.0 * xdis / radius;
            }
            break;
        }
        case eTangentIrregular:
        {
            // Tangent direction depends on spatial location.
            Array<OneD, Array<OneD, NekDouble>> x(m_coordDim);
            for (int k = 0; k < m_coordDim; k++)
            {
                x[k] = Array<OneD, NekDouble>(nq);
            }
 
            int nqtot_map = 1;
            LibUtilities::PointsKeyVector map_points(m_expDim);
            for (int i = 0; i < m_expDim; ++i)
            {
                map_points[i] = m_xmap->GetBasis(i)->GetPointsKey();
                nqtot_map *= map_points[i].GetNumPoints();
            }
            Array<OneD, NekDouble> tmp(nqtot_map);
            for (int k = 0; k < m_coordDim; k++)
            {
                m_xmap->BwdTrans(m_coords[k], tmp);
                Interp(map_points, tmp, keyTgt, x[k]);
            }
 
            // circular around the center of the domain
            NekDouble xtan, ytan, mag;
            for (int i = 0; i < nq; i++)
            {
                xtan         = -1.0 * (x[1][i] * x[1][i] * x[1][i] + x[1][i]);
                ytan         = 2.0 * x[0][i];
                mag          = sqrt(xtan * xtan + ytan * ytan);
                output[0][i] = xtan / mag;
                output[1][i] = ytan / mag;
            }
            break;
        }
        case eTangentNonconvex:
        {
            // Tangent direction depends on spatial location.
            Array<OneD, Array<OneD, NekDouble>> x(m_coordDim);
            for (int k = 0; k < m_coordDim; k++)
            {
                x[k] = Array<OneD, NekDouble>(nq);
            }
 
            int nqtot_map = 1;
            LibUtilities::PointsKeyVector map_points(m_expDim);
            for (int i = 0; i < m_expDim; ++i)
            {
                map_points[i] = m_xmap->GetBasis(i)->GetPointsKey();
                nqtot_map *= map_points[i].GetNumPoints();
            }
            Array<OneD, NekDouble> tmp(nqtot_map);
            for (int k = 0; k < m_coordDim; k++)
            {
                m_xmap->BwdTrans(m_coords[k], tmp);
                Interp(map_points, tmp, keyTgt, x[k]);
            }
 
            // circular around the center of the domain
            NekDouble xtan, ytan, mag;
            for (int i = 0; i < nq; i++)
            {
                xtan         = -2.0 * x[1][i] * x[1][i] * x[1][i] + x[1][i];
                ytan         = sqrt(3.0) * x[0][i];
                mag          = sqrt(xtan * xtan + ytan * ytan);
                output[0][i] = xtan / mag;
                output[1][i] = ytan / mag;
            }
            break;
        }
        default:
        {
            break;
        }
    }
}
 
/**
 *
 */
void GeomFactors::VectorNormalise(Array<OneD, Array<OneD, NekDouble>> &array)
{
    int ndim = array.size();
    if (ndim <= 0)
    {
        NEKERROR(ErrorUtil::efatal, "Number of components must be > 0.");
    }
    for (int i = 1; i < ndim; ++i)
    {
        if (array[i].size() != array[0].size())
        {
            NEKERROR(ErrorUtil::efatal, "Array size mismatch in coordinates.");
        }
    }
 
    int nq = array[0].size();
    Array<OneD, NekDouble> norm(nq, 0.0);
 
    // Compute the norm of each vector.
    for (int i = 0; i < ndim; ++i)
    {
        Vmath::Vvtvp(nq, array[i], 1, array[i], 1, norm, 1, norm, 1);
    }
 
    Vmath::Vsqrt(nq, norm, 1, norm, 1);
 
    // Normalise the vectors by the norm
    for (int i = 0; i < ndim; ++i)
    {
        Vmath::Vdiv(nq, array[i], 1, norm, 1, array[i], 1);
    }
}
 
/**
 * @brief Computes the vector cross-product in 3D of \a v1 and \a v2,
 * storing the result in \a v3.
 *
 * @param   v1          First input vector.
 * @param   v2          Second input vector.
 * @param   v3          Output vector computed to be orthogonal to
 *                      both \a v1 and \a v2.
 */
void GeomFactors::VectorCrossProd(
    const Array<OneD, const Array<OneD, NekDouble>> &v1,
    const Array<OneD, const Array<OneD, NekDouble>> &v2,
    Array<OneD, Array<OneD, NekDouble>> &v3)
{
    if (v1.size() != 3)
    {
        NEKERROR(ErrorUtil::efatal, "Input 1 has dimension not equal to 3.");
    }
 
    if (v2.size() != 3)
    {
        NEKERROR(ErrorUtil::efatal, "Input 2 has dimension not equal to 3.");
    }
 
    if (v3.size() != 3)
    {
        NEKERROR(ErrorUtil::efatal,
                 "Output vector has dimension not equal to 3.");
    }
 
    int nq = v1[0].size();
    Array<OneD, NekDouble> temp(nq);
 
    Vmath::Vmul(nq, v1[2], 1, v2[1], 1, temp, 1);
    Vmath::Vvtvm(nq, v1[1], 1, v2[2], 1, temp, 1, v3[0], 1);
 
    Vmath::Vmul(nq, v1[0], 1, v2[2], 1, temp, 1);
    Vmath::Vvtvm(nq, v1[2], 1, v2[0], 1, temp, 1, v3[1], 1);
 
    Vmath::Vmul(nq, v1[1], 1, v2[0], 1, temp, 1);
    Vmath::Vvtvm(nq, v1[0], 1, v2[1], 1, temp, 1, v3[2], 1);
}
 
} // namespace Nektar::SpatialDomains