sequenzo 0.1.18__cp39-cp39-macosx_10_9_universal2.whl → 0.1.19__cp39-cp39-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h

@@ -1,187 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr>
-
-/* NOTE The functions of this file have been adapted from the GMM++ library */
-
-//========================================================================
-//
-// Copyright (C) 2002-2007 Yves Renard
-//
-// This file is a part of GETFEM++
-//
-// Getfem++ is free software; you can redistribute it and/or modify
-// it under the terms of the GNU Lesser General Public License as
-// published by the Free Software Foundation; version 2.1 of the License.
-//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-// GNU Lesser General Public License for more details.
-// You should have received a copy of the GNU Lesser General Public
-// License along with this program; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301,
-// USA.
-//
-//========================================================================
-
-#include "../../../../Eigen/src/Core/util/NonMPL2.h"
-
-#ifndef EIGEN_CONSTRAINEDCG_H
-#define EIGEN_CONSTRAINEDCG_H
-
-#include "../../../../Eigen/Core"
-
-namespace Eigen { 
-
-namespace internal {
-
-/** \ingroup IterativeLinearSolvers_Module
-  * Compute the pseudo inverse of the non-square matrix C such that
-  * \f$ CINV = (C * C^T)^{-1} * C \f$ based on a conjugate gradient method.
-  *
-  * This function is internally used by constrained_cg.
-  */
-template <typename CMatrix, typename CINVMatrix>
-void pseudo_inverse(const CMatrix &C, CINVMatrix &CINV)
-{
-  // optimisable : copie de la ligne, precalcul de C * trans(C).
-  typedef typename CMatrix::Scalar Scalar;
-  typedef typename CMatrix::Index Index;
-  // FIXME use sparse vectors ?
-  typedef Matrix<Scalar,Dynamic,1> TmpVec;
-
-  Index rows = C.rows(), cols = C.cols();
-
-  TmpVec d(rows), e(rows), l(cols), p(rows), q(rows), r(rows);
-  Scalar rho, rho_1, alpha;
-  d.setZero();
-
-  typedef Triplet<double> T;
-  std::vector<T> tripletList;
-    
-  for (Index i = 0; i < rows; ++i)
-  {
-    d[i] = 1.0;
-    rho = 1.0;
-    e.setZero();
-    r = d;
-    p = d;
-
-    while (rho >= 1e-38)
-    { /* conjugate gradient to compute e             */
-      /* which is the i-th row of inv(C * trans(C))  */
-      l = C.transpose() * p;
-      q = C * l;
-      alpha = rho / p.dot(q);
-      e +=  alpha * p;
-      r += -alpha * q;
-      rho_1 = rho;
-      rho = r.dot(r);
-      p = (rho/rho_1) * p + r;
-    }
-
-    l = C.transpose() * e; // l is the i-th row of CINV
-    // FIXME add a generic "prune/filter" expression for both dense and sparse object to sparse
-    for (Index j=0; j<l.size(); ++j)
-      if (l[j]<1e-15)
-	tripletList.push_back(T(i,j,l(j)));
-
-	
-    d[i] = 0.0;
-  }
-  CINV.setFromTriplets(tripletList.begin(), tripletList.end());
-}
-
-
-
-/** \ingroup IterativeLinearSolvers_Module
-  * Constrained conjugate gradient
-  *
-  * Computes the minimum of \f$ 1/2((Ax).x) - bx \f$ under the constraint \f$ Cx \le f \f$
-  */
-template<typename TMatrix, typename CMatrix,
-         typename VectorX, typename VectorB, typename VectorF>
-void constrained_cg(const TMatrix& A, const CMatrix& C, VectorX& x,
-                       const VectorB& b, const VectorF& f, IterationController &iter)
-{
-  using std::sqrt;
-  typedef typename TMatrix::Scalar Scalar;
-  typedef typename TMatrix::Index Index;
-  typedef Matrix<Scalar,Dynamic,1>  TmpVec;
-
-  Scalar rho = 1.0, rho_1, lambda, gamma;
-  Index xSize = x.size();
-  TmpVec  p(xSize), q(xSize), q2(xSize),
-          r(xSize), old_z(xSize), z(xSize),
-          memox(xSize);
-  std::vector<bool> satured(C.rows());
-  p.setZero();
-  iter.setRhsNorm(sqrt(b.dot(b))); // gael vect_sp(PS, b, b)
-  if (iter.rhsNorm() == 0.0) iter.setRhsNorm(1.0);
-
-  SparseMatrix<Scalar,RowMajor> CINV(C.rows(), C.cols());
-  pseudo_inverse(C, CINV);
-
-  while(true)
-  {
-    // computation of residual
-    old_z = z;
-    memox = x;
-    r = b;
-    r += A * -x;
-    z = r;
-    bool transition = false;
-    for (Index i = 0; i < C.rows(); ++i)
-    {
-      Scalar al = C.row(i).dot(x) - f.coeff(i);
-      if (al >= -1.0E-15)
-      {
-        if (!satured[i])
-        {
-          satured[i] = true;
-          transition = true;
-        }
-        Scalar bb = CINV.row(i).dot(z);
-        if (bb > 0.0)
-          // FIXME: we should allow that: z += -bb * C.row(i);
-          for (typename CMatrix::InnerIterator it(C,i); it; ++it)
-            z.coeffRef(it.index()) -= bb*it.value();
-      }
-      else
-        satured[i] = false;
-    }
-
-    // descent direction
-    rho_1 = rho;
-    rho = r.dot(z);
-
-    if (iter.finished(rho)) break;
-    if (transition || iter.first()) gamma = 0.0;
-    else gamma = (std::max)(0.0, (rho - old_z.dot(z)) / rho_1);
-    p = z + gamma*p;
-
-    ++iter;
-    // one dimensionnal optimization
-    q = A * p;
-    lambda = rho / q.dot(p);
-    for (Index i = 0; i < C.rows(); ++i)
-    {
-      if (!satured[i])
-      {
-        Scalar bb = C.row(i).dot(p) - f[i];
-        if (bb > 0.0)
-          lambda = (std::min)(lambda, (f.coeff(i)-C.row(i).dot(x)) / bb);
-      }
-    }
-    x += lambda * p;
-    memox -= x;
-  }
-}
-
-} // end namespace internal
-
-} // end namespace Eigen
-
-#endif // EIGEN_CONSTRAINEDCG_H

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/DGMRES.h

@@ -1,511 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_DGMRES_H
-#define EIGEN_DGMRES_H
-
-#include "../../../../Eigen/Eigenvalues"
-
-namespace Eigen { 
-  
-template< typename _MatrixType,
-          typename _Preconditioner = DiagonalPreconditioner<typename _MatrixType::Scalar> >
-class DGMRES;
-
-namespace internal {
-
-template< typename _MatrixType, typename _Preconditioner>
-struct traits<DGMRES<_MatrixType,_Preconditioner> >
-{
-  typedef _MatrixType MatrixType;
-  typedef _Preconditioner Preconditioner;
-};
-
-/** \brief Computes a permutation vector to have a sorted sequence
-  * \param vec The vector to reorder.
-  * \param perm gives the sorted sequence on output. Must be initialized with 0..n-1
-  * \param ncut Put  the ncut smallest elements at the end of the vector
-  * WARNING This is an expensive sort, so should be used only 
-  * for small size vectors
-  * TODO Use modified QuickSplit or std::nth_element to get the smallest values 
-  */
-template <typename VectorType, typename IndexType>
-void sortWithPermutation (VectorType& vec, IndexType& perm, typename IndexType::Scalar& ncut)
-{
-  eigen_assert(vec.size() == perm.size());
-  bool flag; 
-  for (Index k  = 0; k < ncut; k++)
-  {
-    flag = false;
-    for (Index j = 0; j < vec.size()-1; j++)
-    {
-      if ( vec(perm(j)) < vec(perm(j+1)) )
-      {
-        std::swap(perm(j),perm(j+1)); 
-        flag = true;
-      }
-      if (!flag) break; // The vector is in sorted order
-    }
-  }
-}
-
-}
-/**
- * \ingroup IterativeLinearSolvers_Module
- * \brief A Restarted GMRES with deflation.
- * This class implements a modification of the GMRES solver for
- * sparse linear systems. The basis is built with modified 
- * Gram-Schmidt. At each restart, a few approximated eigenvectors
- * corresponding to the smallest eigenvalues are used to build a
- * preconditioner for the next cycle. This preconditioner 
- * for deflation can be combined with any other preconditioner, 
- * the IncompleteLUT for instance. The preconditioner is applied 
- * at right of the matrix and the combination is multiplicative.
- * 
- * \tparam _MatrixType the type of the sparse matrix A, can be a dense or a sparse matrix.
- * \tparam _Preconditioner the type of the preconditioner. Default is DiagonalPreconditioner
- * Typical usage :
- * \code
- * SparseMatrix<double> A;
- * VectorXd x, b; 
- * //Fill A and b ...
- * DGMRES<SparseMatrix<double> > solver;
- * solver.set_restart(30); // Set restarting value
- * solver.setEigenv(1); // Set the number of eigenvalues to deflate
- * solver.compute(A);
- * x = solver.solve(b);
- * \endcode
- * 
- * DGMRES can also be used in a matrix-free context, see the following \link MatrixfreeSolverExample example \endlink.
- *
- * References :
- * [1] D. NUENTSA WAKAM and F. PACULL, Memory Efficient Hybrid
- *  Algebraic Solvers for Linear Systems Arising from Compressible
- *  Flows, Computers and Fluids, In Press,
- *  https://doi.org/10.1016/j.compfluid.2012.03.023   
- * [2] K. Burrage and J. Erhel, On the performance of various 
- * adaptive preconditioned GMRES strategies, 5(1998), 101-121.
- * [3] J. Erhel, K. Burrage and B. Pohl, Restarted GMRES 
- *  preconditioned by deflation,J. Computational and Applied
- *  Mathematics, 69(1996), 303-318. 
-
- * 
- */
-template< typename _MatrixType, typename _Preconditioner>
-class DGMRES : public IterativeSolverBase<DGMRES<_MatrixType,_Preconditioner> >
-{
-    typedef IterativeSolverBase<DGMRES> Base;
-    using Base::matrix;
-    using Base::m_error;
-    using Base::m_iterations;
-    using Base::m_info;
-    using Base::m_isInitialized;
-    using Base::m_tolerance; 
-  public:
-    using Base::_solve_impl;
-    using Base::_solve_with_guess_impl;
-    typedef _MatrixType MatrixType;
-    typedef typename MatrixType::Scalar Scalar;
-    typedef typename MatrixType::StorageIndex StorageIndex;
-    typedef typename MatrixType::RealScalar RealScalar;
-    typedef _Preconditioner Preconditioner;
-    typedef Matrix<Scalar,Dynamic,Dynamic> DenseMatrix; 
-    typedef Matrix<RealScalar,Dynamic,Dynamic> DenseRealMatrix; 
-    typedef Matrix<Scalar,Dynamic,1> DenseVector;
-    typedef Matrix<RealScalar,Dynamic,1> DenseRealVector; 
-    typedef Matrix<std::complex<RealScalar>, Dynamic, 1> ComplexVector;
- 
-    
-  /** Default constructor. */
-  DGMRES() : Base(),m_restart(30),m_neig(0),m_r(0),m_maxNeig(5),m_isDeflAllocated(false),m_isDeflInitialized(false) {}
-
-  /** Initialize the solver with matrix \a A for further \c Ax=b solving.
-    * 
-    * This constructor is a shortcut for the default constructor followed
-    * by a call to compute().
-    * 
-    * \warning this class stores a reference to the matrix A as well as some
-    * precomputed values that depend on it. Therefore, if \a A is changed
-    * this class becomes invalid. Call compute() to update it with the new
-    * matrix A, or modify a copy of A.
-    */
-  template<typename MatrixDerived>
-  explicit DGMRES(const EigenBase<MatrixDerived>& A) : Base(A.derived()), m_restart(30),m_neig(0),m_r(0),m_maxNeig(5),m_isDeflAllocated(false),m_isDeflInitialized(false) {}
-
-  ~DGMRES() {}
-  
-  /** \internal */
-  template<typename Rhs,typename Dest>
-  void _solve_vector_with_guess_impl(const Rhs& b, Dest& x) const
-  {
-    EIGEN_STATIC_ASSERT(Rhs::ColsAtCompileTime==1 || Dest::ColsAtCompileTime==1, YOU_TRIED_CALLING_A_VECTOR_METHOD_ON_A_MATRIX);
-    
-    m_iterations = Base::maxIterations();
-    m_error = Base::m_tolerance;
-    
-    dgmres(matrix(), b, x, Base::m_preconditioner);
-  }
-
-  /** 
-   * Get the restart value
-    */
-  Index restart() { return m_restart; }
-  
-  /** 
-   * Set the restart value (default is 30)  
-   */
-  void set_restart(const Index restart) { m_restart=restart; }
-  
-  /** 
-   * Set the number of eigenvalues to deflate at each restart 
-   */
-  void setEigenv(const Index neig) 
-  {
-    m_neig = neig;
-    if (neig+1 > m_maxNeig) m_maxNeig = neig+1; // To allow for complex conjugates
-  }
-  
-  /** 
-   * Get the size of the deflation subspace size
-   */ 
-  Index deflSize() {return m_r; }
-  
-  /**
-   * Set the maximum size of the deflation subspace
-   */
-  void setMaxEigenv(const Index maxNeig) { m_maxNeig = maxNeig; }
-  
-  protected:
-    // DGMRES algorithm 
-    template<typename Rhs, typename Dest>
-    void dgmres(const MatrixType& mat,const Rhs& rhs, Dest& x, const Preconditioner& precond) const;
-    // Perform one cycle of GMRES
-    template<typename Dest>
-    Index dgmresCycle(const MatrixType& mat, const Preconditioner& precond, Dest& x, DenseVector& r0, RealScalar& beta, const RealScalar& normRhs, Index& nbIts) const; 
-    // Compute data to use for deflation 
-    Index dgmresComputeDeflationData(const MatrixType& mat, const Preconditioner& precond, const Index& it, StorageIndex& neig) const;
-    // Apply deflation to a vector
-    template<typename RhsType, typename DestType>
-    Index dgmresApplyDeflation(const RhsType& In, DestType& Out) const; 
-    ComplexVector schurValues(const ComplexSchur<DenseMatrix>& schurofH) const;
-    ComplexVector schurValues(const RealSchur<DenseMatrix>& schurofH) const;
-    // Init data for deflation
-    void dgmresInitDeflation(Index& rows) const; 
-    mutable DenseMatrix m_V; // Krylov basis vectors
-    mutable DenseMatrix m_H; // Hessenberg matrix 
-    mutable DenseMatrix m_Hes; // Initial hessenberg matrix without Givens rotations applied
-    mutable Index m_restart; // Maximum size of the Krylov subspace
-    mutable DenseMatrix m_U; // Vectors that form the basis of the invariant subspace 
-    mutable DenseMatrix m_MU; // matrix operator applied to m_U (for next cycles)
-    mutable DenseMatrix m_T; /* T=U^T*M^{-1}*A*U */
-    mutable PartialPivLU<DenseMatrix> m_luT; // LU factorization of m_T
-    mutable StorageIndex m_neig; //Number of eigenvalues to extract at each restart
-    mutable Index m_r; // Current number of deflated eigenvalues, size of m_U
-    mutable Index m_maxNeig; // Maximum number of eigenvalues to deflate
-    mutable RealScalar m_lambdaN; //Modulus of the largest eigenvalue of A
-    mutable bool m_isDeflAllocated;
-    mutable bool m_isDeflInitialized;
-    
-    //Adaptive strategy 
-    mutable RealScalar m_smv; // Smaller multiple of the remaining number of steps allowed
-    mutable bool m_force; // Force the use of deflation at each restart
-    
-}; 
-/** 
- * \brief Perform several cycles of restarted GMRES with modified Gram Schmidt, 
- * 
- * A right preconditioner is used combined with deflation.
- * 
- */
-template< typename _MatrixType, typename _Preconditioner>
-template<typename Rhs, typename Dest>
-void DGMRES<_MatrixType, _Preconditioner>::dgmres(const MatrixType& mat,const Rhs& rhs, Dest& x,
-              const Preconditioner& precond) const
-{
-  const RealScalar considerAsZero = (std::numeric_limits<RealScalar>::min)();
-
-  RealScalar normRhs = rhs.norm();
-  if(normRhs <= considerAsZero) 
-  {
-    x.setZero();
-    m_error = 0;
-    return;
-  }
-
-  //Initialization
-  m_isDeflInitialized = false;
-  Index n = mat.rows(); 
-  DenseVector r0(n); 
-  Index nbIts = 0; 
-  m_H.resize(m_restart+1, m_restart);
-  m_Hes.resize(m_restart, m_restart);
-  m_V.resize(n,m_restart+1);
-  //Initial residual vector and initial norm
-  if(x.squaredNorm()==0) 
-    x = precond.solve(rhs);
-  r0 = rhs - mat * x; 
-  RealScalar beta = r0.norm(); 
-  
-  m_error = beta/normRhs; 
-  if(m_error < m_tolerance)
-    m_info = Success; 
-  else
-    m_info = NoConvergence;
-  
-  // Iterative process
-  while (nbIts < m_iterations && m_info == NoConvergence)
-  {
-    dgmresCycle(mat, precond, x, r0, beta, normRhs, nbIts); 
-    
-    // Compute the new residual vector for the restart 
-    if (nbIts < m_iterations && m_info == NoConvergence) {
-      r0 = rhs - mat * x;
-      beta = r0.norm();
-    }
-  }
-} 
-
-/**
- * \brief Perform one restart cycle of DGMRES
- * \param mat The coefficient matrix
- * \param precond The preconditioner
- * \param x the new approximated solution
- * \param r0 The initial residual vector
- * \param beta The norm of the residual computed so far
- * \param normRhs The norm of the right hand side vector
- * \param nbIts The number of iterations
- */
-template< typename _MatrixType, typename _Preconditioner>
-template<typename Dest>
-Index DGMRES<_MatrixType, _Preconditioner>::dgmresCycle(const MatrixType& mat, const Preconditioner& precond, Dest& x, DenseVector& r0, RealScalar& beta, const RealScalar& normRhs, Index& nbIts) const
-{
-  //Initialization 
-  DenseVector g(m_restart+1); // Right hand side of the least square problem
-  g.setZero();  
-  g(0) = Scalar(beta); 
-  m_V.col(0) = r0/beta; 
-  m_info = NoConvergence; 
-  std::vector<JacobiRotation<Scalar> >gr(m_restart); // Givens rotations
-  Index it = 0; // Number of inner iterations 
-  Index n = mat.rows();
-  DenseVector tv1(n), tv2(n);  //Temporary vectors
-  while (m_info == NoConvergence && it < m_restart && nbIts < m_iterations)
-  {    
-    // Apply preconditioner(s) at right
-    if (m_isDeflInitialized )
-    {
-      dgmresApplyDeflation(m_V.col(it), tv1); // Deflation
-      tv2 = precond.solve(tv1); 
-    }
-    else
-    {
-      tv2 = precond.solve(m_V.col(it)); // User's selected preconditioner
-    }
-    tv1 = mat * tv2; 
-   
-    // Orthogonalize it with the previous basis in the basis using modified Gram-Schmidt
-    Scalar coef; 
-    for (Index i = 0; i <= it; ++i)
-    { 
-      coef = tv1.dot(m_V.col(i));
-      tv1 = tv1 - coef * m_V.col(i); 
-      m_H(i,it) = coef; 
-      m_Hes(i,it) = coef; 
-    }
-    // Normalize the vector 
-    coef = tv1.norm(); 
-    m_V.col(it+1) = tv1/coef;
-    m_H(it+1, it) = coef;
-//     m_Hes(it+1,it) = coef; 
-    
-    // FIXME Check for happy breakdown 
-    
-    // Update Hessenberg matrix with Givens rotations
-    for (Index i = 1; i <= it; ++i) 
-    {
-      m_H.col(it).applyOnTheLeft(i-1,i,gr[i-1].adjoint());
-    }
-    // Compute the new plane rotation 
-    gr[it].makeGivens(m_H(it, it), m_H(it+1,it)); 
-    // Apply the new rotation
-    m_H.col(it).applyOnTheLeft(it,it+1,gr[it].adjoint());
-    g.applyOnTheLeft(it,it+1, gr[it].adjoint()); 
-    
-    beta = std::abs(g(it+1));
-    m_error = beta/normRhs; 
-    // std::cerr << nbIts << " Relative Residual Norm " << m_error << std::endl;
-    it++; nbIts++; 
-    
-    if (m_error < m_tolerance)
-    {
-      // The method has converged
-      m_info = Success;
-      break;
-    }
-  }
-  
-  // Compute the new coefficients by solving the least square problem
-//   it++;
-  //FIXME  Check first if the matrix is singular ... zero diagonal
-  DenseVector nrs(m_restart); 
-  nrs = m_H.topLeftCorner(it,it).template triangularView<Upper>().solve(g.head(it)); 
-  
-  // Form the new solution
-  if (m_isDeflInitialized)
-  {
-    tv1 = m_V.leftCols(it) * nrs; 
-    dgmresApplyDeflation(tv1, tv2); 
-    x = x + precond.solve(tv2);
-  }
-  else
-    x = x + precond.solve(m_V.leftCols(it) * nrs); 
-  
-  // Go for a new cycle and compute data for deflation
-  if(nbIts < m_iterations && m_info == NoConvergence && m_neig > 0 && (m_r+m_neig) < m_maxNeig)
-    dgmresComputeDeflationData(mat, precond, it, m_neig); 
-  return 0; 
-  
-}
-
-
-template< typename _MatrixType, typename _Preconditioner>
-void DGMRES<_MatrixType, _Preconditioner>::dgmresInitDeflation(Index& rows) const
-{
-  m_U.resize(rows, m_maxNeig);
-  m_MU.resize(rows, m_maxNeig); 
-  m_T.resize(m_maxNeig, m_maxNeig);
-  m_lambdaN = 0.0; 
-  m_isDeflAllocated = true; 
-}
-
-template< typename _MatrixType, typename _Preconditioner>
-inline typename DGMRES<_MatrixType, _Preconditioner>::ComplexVector DGMRES<_MatrixType, _Preconditioner>::schurValues(const ComplexSchur<DenseMatrix>& schurofH) const
-{
-  return schurofH.matrixT().diagonal();
-}
-
-template< typename _MatrixType, typename _Preconditioner>
-inline typename DGMRES<_MatrixType, _Preconditioner>::ComplexVector DGMRES<_MatrixType, _Preconditioner>::schurValues(const RealSchur<DenseMatrix>& schurofH) const
-{
-  const DenseMatrix& T = schurofH.matrixT();
-  Index it = T.rows();
-  ComplexVector eig(it);
-  Index j = 0;
-  while (j < it-1)
-  {
-    if (T(j+1,j) ==Scalar(0))
-    {
-      eig(j) = std::complex<RealScalar>(T(j,j),RealScalar(0)); 
-      j++; 
-    }
-    else
-    {
-      eig(j) = std::complex<RealScalar>(T(j,j),T(j+1,j)); 
-      eig(j+1) = std::complex<RealScalar>(T(j,j+1),T(j+1,j+1));
-      j++;
-    }
-  }
-  if (j < it-1) eig(j) = std::complex<RealScalar>(T(j,j),RealScalar(0));
-  return eig;
-}
-
-template< typename _MatrixType, typename _Preconditioner>
-Index DGMRES<_MatrixType, _Preconditioner>::dgmresComputeDeflationData(const MatrixType& mat, const Preconditioner& precond, const Index& it, StorageIndex& neig) const
-{
-  // First, find the Schur form of the Hessenberg matrix H
-  typename internal::conditional<NumTraits<Scalar>::IsComplex, ComplexSchur<DenseMatrix>, RealSchur<DenseMatrix> >::type schurofH; 
-  bool computeU = true;
-  DenseMatrix matrixQ(it,it); 
-  matrixQ.setIdentity();
-  schurofH.computeFromHessenberg(m_Hes.topLeftCorner(it,it), matrixQ, computeU); 
-  
-  ComplexVector eig(it);
-  Matrix<StorageIndex,Dynamic,1>perm(it);
-  eig = this->schurValues(schurofH);
-  
-  // Reorder the absolute values of Schur values
-  DenseRealVector modulEig(it); 
-  for (Index j=0; j<it; ++j) modulEig(j) = std::abs(eig(j)); 
-  perm.setLinSpaced(it,0,internal::convert_index<StorageIndex>(it-1));
-  internal::sortWithPermutation(modulEig, perm, neig);
-  
-  if (!m_lambdaN)
-  {
-    m_lambdaN = (std::max)(modulEig.maxCoeff(), m_lambdaN);
-  }
-  //Count the real number of extracted eigenvalues (with complex conjugates)
-  Index nbrEig = 0; 
-  while (nbrEig < neig)
-  {
-    if(eig(perm(it-nbrEig-1)).imag() == RealScalar(0)) nbrEig++; 
-    else nbrEig += 2; 
-  }
-  // Extract the  Schur vectors corresponding to the smallest Ritz values
-  DenseMatrix Sr(it, nbrEig); 
-  Sr.setZero();
-  for (Index j = 0; j < nbrEig; j++)
-  {
-    Sr.col(j) = schurofH.matrixU().col(perm(it-j-1));
-  }
-  
-  // Form the Schur vectors of the initial matrix using the Krylov basis
-  DenseMatrix X; 
-  X = m_V.leftCols(it) * Sr;
-  if (m_r)
-  {
-   // Orthogonalize X against m_U using modified Gram-Schmidt
-   for (Index j = 0; j < nbrEig; j++)
-     for (Index k =0; k < m_r; k++)
-      X.col(j) = X.col(j) - (m_U.col(k).dot(X.col(j)))*m_U.col(k); 
-  }
-  
-  // Compute m_MX = A * M^-1 * X
-  Index m = m_V.rows();
-  if (!m_isDeflAllocated) 
-    dgmresInitDeflation(m); 
-  DenseMatrix MX(m, nbrEig);
-  DenseVector tv1(m);
-  for (Index j = 0; j < nbrEig; j++)
-  {
-    tv1 = mat * X.col(j);
-    MX.col(j) = precond.solve(tv1);
-  }
-  
-  //Update m_T = [U'MU U'MX; X'MU X'MX]
-  m_T.block(m_r, m_r, nbrEig, nbrEig) = X.transpose() * MX; 
-  if(m_r)
-  {
-    m_T.block(0, m_r, m_r, nbrEig) = m_U.leftCols(m_r).transpose() * MX; 
-    m_T.block(m_r, 0, nbrEig, m_r) = X.transpose() * m_MU.leftCols(m_r);
-  }
-  
-  // Save X into m_U and m_MX in m_MU
-  for (Index j = 0; j < nbrEig; j++) m_U.col(m_r+j) = X.col(j);
-  for (Index j = 0; j < nbrEig; j++) m_MU.col(m_r+j) = MX.col(j);
-  // Increase the size of the invariant subspace
-  m_r += nbrEig; 
-  
-  // Factorize m_T into m_luT
-  m_luT.compute(m_T.topLeftCorner(m_r, m_r));
-  
-  //FIXME CHeck if the factorization was correctly done (nonsingular matrix)
-  m_isDeflInitialized = true;
-  return 0; 
-}
-template<typename _MatrixType, typename _Preconditioner>
-template<typename RhsType, typename DestType>
-Index DGMRES<_MatrixType, _Preconditioner>::dgmresApplyDeflation(const RhsType &x, DestType &y) const
-{
-  DenseVector x1 = m_U.leftCols(m_r).transpose() * x; 
-  y = x + m_U.leftCols(m_r) * ( m_lambdaN * m_luT.solve(x1) - x1);
-  return 0; 
-}
-
-} // end namespace Eigen
-#endif