sequenzo 0.1.18__cp310-cp310-macosx_10_9_universal2.whl → 0.1.19__cp310-cp310-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h

@@ -1,923 +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>
-// Copyright (C) 2012-2014 Gael Guennebaud <gael.guennebaud@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_SPARSE_LU_H
-#define EIGEN_SPARSE_LU_H
-
-namespace Eigen {
-
-template <typename _MatrixType, typename _OrderingType = COLAMDOrdering<typename _MatrixType::StorageIndex> > class SparseLU;
-template <typename MappedSparseMatrixType> struct SparseLUMatrixLReturnType;
-template <typename MatrixLType, typename MatrixUType> struct SparseLUMatrixUReturnType;
-
-template <bool Conjugate,class SparseLUType>
-class SparseLUTransposeView : public SparseSolverBase<SparseLUTransposeView<Conjugate,SparseLUType> >
-{
-protected:
-  typedef SparseSolverBase<SparseLUTransposeView<Conjugate,SparseLUType> > APIBase;
-  using APIBase::m_isInitialized;
-public:
-  typedef typename SparseLUType::Scalar Scalar;
-  typedef typename SparseLUType::StorageIndex StorageIndex;
-  typedef typename SparseLUType::MatrixType MatrixType;
-  typedef typename SparseLUType::OrderingType OrderingType;
-
-  enum {
-    ColsAtCompileTime = MatrixType::ColsAtCompileTime,
-    MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
-  };
-
-  SparseLUTransposeView() : m_sparseLU(NULL) {}
-  SparseLUTransposeView(const SparseLUTransposeView& view) {
-    this->m_sparseLU = view.m_sparseLU;
-  }
-  void setIsInitialized(const bool isInitialized) {this->m_isInitialized = isInitialized;}
-  void setSparseLU(SparseLUType* sparseLU) {m_sparseLU = sparseLU;}
-  using APIBase::_solve_impl;
-  template<typename Rhs, typename Dest>
-  bool _solve_impl(const MatrixBase<Rhs> &B, MatrixBase<Dest> &X_base) const
-  {
-    Dest& X(X_base.derived());
-    eigen_assert(m_sparseLU->info() == Success && "The matrix should be factorized first");
-    EIGEN_STATIC_ASSERT((Dest::Flags&RowMajorBit)==0,
-                        THIS_METHOD_IS_ONLY_FOR_COLUMN_MAJOR_MATRICES);
-
-
-    // this ugly const_cast_derived() helps to detect aliasing when applying the permutations
-    for(Index j = 0; j < B.cols(); ++j){
-      X.col(j) = m_sparseLU->colsPermutation() * B.const_cast_derived().col(j);
-    }
-    //Forward substitution with transposed or adjoint of U
-    m_sparseLU->matrixU().template solveTransposedInPlace<Conjugate>(X);
-
-    //Backward substitution with transposed or adjoint of L
-    m_sparseLU->matrixL().template solveTransposedInPlace<Conjugate>(X);
-
-    // Permute back the solution
-    for (Index j = 0; j < B.cols(); ++j)
-      X.col(j) = m_sparseLU->rowsPermutation().transpose() * X.col(j);
-    return true;
-  }
-  inline Index rows() const { return m_sparseLU->rows(); }
-  inline Index cols() const { return m_sparseLU->cols(); }
-
-private:
-  SparseLUType *m_sparseLU;
-  SparseLUTransposeView& operator=(const SparseLUTransposeView&);
-};
-
-
-/** \ingroup SparseLU_Module
-  * \class SparseLU
-  * 
-  * \brief Sparse supernodal LU factorization for general matrices
-  * 
-  * This class implements the supernodal LU factorization for general matrices.
-  * It uses the main techniques from the sequential SuperLU package 
-  * (http://crd-legacy.lbl.gov/~xiaoye/SuperLU/). It handles transparently real 
-  * and complex arithmetic with single and double precision, depending on the 
-  * scalar type of your input matrix. 
-  * The code has been optimized to provide BLAS-3 operations during supernode-panel updates. 
-  * It benefits directly from the built-in high-performant Eigen BLAS routines. 
-  * Moreover, when the size of a supernode is very small, the BLAS calls are avoided to 
-  * enable a better optimization from the compiler. For best performance, 
-  * you should compile it with NDEBUG flag to avoid the numerous bounds checking on vectors. 
-  * 
-  * An important parameter of this class is the ordering method. It is used to reorder the columns 
-  * (and eventually the rows) of the matrix to reduce the number of new elements that are created during 
-  * numerical factorization. The cheapest method available is COLAMD. 
-  * See  \link OrderingMethods_Module the OrderingMethods module \endlink for the list of 
-  * built-in and external ordering methods. 
-  *
-  * Simple example with key steps 
-  * \code
-  * VectorXd x(n), b(n);
-  * SparseMatrix<double> A;
-  * SparseLU<SparseMatrix<double>, COLAMDOrdering<int> >   solver;
-  * // fill A and b;
-  * // Compute the ordering permutation vector from the structural pattern of A
-  * solver.analyzePattern(A); 
-  * // Compute the numerical factorization 
-  * solver.factorize(A); 
-  * //Use the factors to solve the linear system 
-  * x = solver.solve(b); 
-  * \endcode
-  * 
-  * \warning The input matrix A should be in a \b compressed and \b column-major form.
-  * Otherwise an expensive copy will be made. You can call the inexpensive makeCompressed() to get a compressed matrix.
-  * 
-  * \note Unlike the initial SuperLU implementation, there is no step to equilibrate the matrix. 
-  * For badly scaled matrices, this step can be useful to reduce the pivoting during factorization. 
-  * If this is the case for your matrices, you can try the basic scaling method at
-  *  "unsupported/Eigen/src/IterativeSolvers/Scaling.h"
-  * 
-  * \tparam _MatrixType The type of the sparse matrix. It must be a column-major SparseMatrix<>
-  * \tparam _OrderingType The ordering method to use, either AMD, COLAMD or METIS. Default is COLMAD
-  *
-  * \implsparsesolverconcept
-  * 
-  * \sa \ref TutorialSparseSolverConcept
-  * \sa \ref OrderingMethods_Module
-  */
-template <typename _MatrixType, typename _OrderingType>
-class SparseLU : public SparseSolverBase<SparseLU<_MatrixType,_OrderingType> >, public internal::SparseLUImpl<typename _MatrixType::Scalar, typename _MatrixType::StorageIndex>
-{
-  protected:
-    typedef SparseSolverBase<SparseLU<_MatrixType,_OrderingType> > APIBase;
-    using APIBase::m_isInitialized;
-  public:
-    using APIBase::_solve_impl;
-    
-    typedef _MatrixType MatrixType; 
-    typedef _OrderingType OrderingType;
-    typedef typename MatrixType::Scalar Scalar; 
-    typedef typename MatrixType::RealScalar RealScalar; 
-    typedef typename MatrixType::StorageIndex StorageIndex;
-    typedef SparseMatrix<Scalar,ColMajor,StorageIndex> NCMatrix;
-    typedef internal::MappedSuperNodalMatrix<Scalar, StorageIndex> SCMatrix;
-    typedef Matrix<Scalar,Dynamic,1> ScalarVector;
-    typedef Matrix<StorageIndex,Dynamic,1> IndexVector;
-    typedef PermutationMatrix<Dynamic, Dynamic, StorageIndex> PermutationType;
-    typedef internal::SparseLUImpl<Scalar, StorageIndex> Base;
-
-    enum {
-      ColsAtCompileTime = MatrixType::ColsAtCompileTime,
-      MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
-    };
-    
-  public:
-
-    SparseLU():m_lastError(""),m_Ustore(0,0,0,0,0,0),m_symmetricmode(false),m_diagpivotthresh(1.0),m_detPermR(1)
-    {
-      initperfvalues(); 
-    }
-    explicit SparseLU(const MatrixType& matrix)
-      : m_lastError(""),m_Ustore(0,0,0,0,0,0),m_symmetricmode(false),m_diagpivotthresh(1.0),m_detPermR(1)
-    {
-      initperfvalues(); 
-      compute(matrix);
-    }
-    
-    ~SparseLU()
-    {
-      // Free all explicit dynamic pointers 
-    }
-    
-    void analyzePattern (const MatrixType& matrix);
-    void factorize (const MatrixType& matrix);
-    void simplicialfactorize(const MatrixType& matrix);
-    
-    /**
-      * Compute the symbolic and numeric factorization of the input sparse matrix.
-      * The input matrix should be in column-major storage. 
-      */
-    void compute (const MatrixType& matrix)
-    {
-      // Analyze 
-      analyzePattern(matrix); 
-      //Factorize
-      factorize(matrix);
-    } 
-
-    /** \returns an expression of the transposed of the factored matrix.
-      *
-      * A typical usage is to solve for the transposed problem A^T x = b:
-      * \code
-      * solver.compute(A);
-      * x = solver.transpose().solve(b);
-      * \endcode
-      *
-      * \sa adjoint(), solve()
-      */
-    const SparseLUTransposeView<false,SparseLU<_MatrixType,_OrderingType> > transpose()
-    {
-      SparseLUTransposeView<false,  SparseLU<_MatrixType,_OrderingType> > transposeView;
-      transposeView.setSparseLU(this);
-      transposeView.setIsInitialized(this->m_isInitialized);
-      return transposeView;
-    }
-
-
-    /** \returns an expression of the adjoint of the factored matrix
-      *
-      * A typical usage is to solve for the adjoint problem A' x = b:
-      * \code
-      * solver.compute(A);
-      * x = solver.adjoint().solve(b);
-      * \endcode
-      *
-      * For real scalar types, this function is equivalent to transpose().
-      *
-      * \sa transpose(), solve()
-      */
-    const SparseLUTransposeView<true, SparseLU<_MatrixType,_OrderingType> > adjoint()
-    {
-      SparseLUTransposeView<true,  SparseLU<_MatrixType,_OrderingType> > adjointView;
-      adjointView.setSparseLU(this);
-      adjointView.setIsInitialized(this->m_isInitialized);
-      return adjointView;
-    }
-    
-    inline Index rows() const { return m_mat.rows(); }
-    inline Index cols() const { return m_mat.cols(); }
-    /** Indicate that the pattern of the input matrix is symmetric */
-    void isSymmetric(bool sym)
-    {
-      m_symmetricmode = sym;
-    }
-    
-    /** \returns an expression of the matrix L, internally stored as supernodes
-      * The only operation available with this expression is the triangular solve
-      * \code
-      * y = b; matrixL().solveInPlace(y);
-      * \endcode
-      */
-    SparseLUMatrixLReturnType<SCMatrix> matrixL() const
-    {
-      return SparseLUMatrixLReturnType<SCMatrix>(m_Lstore);
-    }
-    /** \returns an expression of the matrix U,
-      * The only operation available with this expression is the triangular solve
-      * \code
-      * y = b; matrixU().solveInPlace(y);
-      * \endcode
-      */
-    SparseLUMatrixUReturnType<SCMatrix,MappedSparseMatrix<Scalar,ColMajor,StorageIndex> > matrixU() const
-    {
-      return SparseLUMatrixUReturnType<SCMatrix, MappedSparseMatrix<Scalar,ColMajor,StorageIndex> >(m_Lstore, m_Ustore);
-    }
-
-    /**
-      * \returns a reference to the row matrix permutation \f$ P_r \f$ such that \f$P_r A P_c^T = L U\f$
-      * \sa colsPermutation()
-      */
-    inline const PermutationType& rowsPermutation() const
-    {
-      return m_perm_r;
-    }
-    /**
-      * \returns a reference to the column matrix permutation\f$ P_c^T \f$ such that \f$P_r A P_c^T = L U\f$
-      * \sa rowsPermutation()
-      */
-    inline const PermutationType& colsPermutation() const
-    {
-      return m_perm_c;
-    }
-    /** Set the threshold used for a diagonal entry to be an acceptable pivot. */
-    void setPivotThreshold(const RealScalar& thresh)
-    {
-      m_diagpivotthresh = thresh; 
-    }
-
-#ifdef EIGEN_PARSED_BY_DOXYGEN
-    /** \returns the solution X of \f$ A X = B \f$ using the current decomposition of A.
-      *
-      * \warning the destination matrix X in X = this->solve(B) must be colmun-major.
-      *
-      * \sa compute()
-      */
-    template<typename Rhs>
-    inline const Solve<SparseLU, Rhs> solve(const MatrixBase<Rhs>& B) const;
-#endif // EIGEN_PARSED_BY_DOXYGEN
-    
-    /** \brief Reports whether previous computation was successful.
-      *
-      * \returns \c Success if computation was successful,
-      *          \c NumericalIssue if the LU factorization reports a problem, zero diagonal for instance
-      *          \c InvalidInput if the input matrix is invalid
-      *
-      * \sa iparm()          
-      */
-    ComputationInfo info() const
-    {
-      eigen_assert(m_isInitialized && "Decomposition is not initialized.");
-      return m_info;
-    }
-    
-    /**
-      * \returns A string describing the type of error
-      */
-    std::string lastErrorMessage() const
-    {
-      return m_lastError; 
-    }
-
-    template<typename Rhs, typename Dest>
-    bool _solve_impl(const MatrixBase<Rhs> &B, MatrixBase<Dest> &X_base) const
-    {
-      Dest& X(X_base.derived());
-      eigen_assert(m_factorizationIsOk && "The matrix should be factorized first");
-      EIGEN_STATIC_ASSERT((Dest::Flags&RowMajorBit)==0,
-                        THIS_METHOD_IS_ONLY_FOR_COLUMN_MAJOR_MATRICES);
-      
-      // Permute the right hand side to form X = Pr*B
-      // on return, X is overwritten by the computed solution
-      X.resize(B.rows(),B.cols());
-
-      // this ugly const_cast_derived() helps to detect aliasing when applying the permutations
-      for(Index j = 0; j < B.cols(); ++j)
-        X.col(j) = rowsPermutation() * B.const_cast_derived().col(j);
-      
-      //Forward substitution with L
-      this->matrixL().solveInPlace(X);
-      this->matrixU().solveInPlace(X);
-      
-      // Permute back the solution 
-      for (Index j = 0; j < B.cols(); ++j)
-        X.col(j) = colsPermutation().inverse() * X.col(j);
-      
-      return true; 
-    }
-    
-    /**
-      * \returns the absolute value of the determinant of the matrix of which
-      * *this is the QR decomposition.
-      *
-      * \warning a determinant can be very big or small, so for matrices
-      * of large enough dimension, there is a risk of overflow/underflow.
-      * One way to work around that is to use logAbsDeterminant() instead.
-      *
-      * \sa logAbsDeterminant(), signDeterminant()
-      */
-    Scalar absDeterminant()
-    {
-      using std::abs;
-      eigen_assert(m_factorizationIsOk && "The matrix should be factorized first.");
-      // Initialize with the determinant of the row matrix
-      Scalar det = Scalar(1.);
-      // Note that the diagonal blocks of U are stored in supernodes,
-      // which are available in the  L part :)
-      for (Index j = 0; j < this->cols(); ++j)
-      {
-        for (typename SCMatrix::InnerIterator it(m_Lstore, j); it; ++it)
-        {
-          if(it.index() == j)
-          {
-            det *= abs(it.value());
-            break;
-          }
-        }
-      }
-      return det;
-    }
-
-    /** \returns the natural log of the absolute value of the determinant of the matrix
-      * of which **this is the QR decomposition
-      *
-      * \note This method is useful to work around the risk of overflow/underflow that's
-      * inherent to the determinant computation.
-      *
-      * \sa absDeterminant(), signDeterminant()
-      */
-    Scalar logAbsDeterminant() const
-    {
-      using std::log;
-      using std::abs;
-
-      eigen_assert(m_factorizationIsOk && "The matrix should be factorized first.");
-      Scalar det = Scalar(0.);
-      for (Index j = 0; j < this->cols(); ++j)
-      {
-        for (typename SCMatrix::InnerIterator it(m_Lstore, j); it; ++it)
-        {
-          if(it.row() < j) continue;
-          if(it.row() == j)
-          {
-            det += log(abs(it.value()));
-            break;
-          }
-        }
-      }
-      return det;
-    }
-
-    /** \returns A number representing the sign of the determinant
-      *
-      * \sa absDeterminant(), logAbsDeterminant()
-      */
-    Scalar signDeterminant()
-    {
-      eigen_assert(m_factorizationIsOk && "The matrix should be factorized first.");
-      // Initialize with the determinant of the row matrix
-      Index det = 1;
-      // Note that the diagonal blocks of U are stored in supernodes,
-      // which are available in the  L part :)
-      for (Index j = 0; j < this->cols(); ++j)
-      {
-        for (typename SCMatrix::InnerIterator it(m_Lstore, j); it; ++it)
-        {
-          if(it.index() == j)
-          {
-            if(it.value()<0)
-              det = -det;
-            else if(it.value()==0)
-              return 0;
-            break;
-          }
-        }
-      }
-      return det * m_detPermR * m_detPermC;
-    }
-    
-    /** \returns The determinant of the matrix.
-      *
-      * \sa absDeterminant(), logAbsDeterminant()
-      */
-    Scalar determinant()
-    {
-      eigen_assert(m_factorizationIsOk && "The matrix should be factorized first.");
-      // Initialize with the determinant of the row matrix
-      Scalar det = Scalar(1.);
-      // Note that the diagonal blocks of U are stored in supernodes,
-      // which are available in the  L part :)
-      for (Index j = 0; j < this->cols(); ++j)
-      {
-        for (typename SCMatrix::InnerIterator it(m_Lstore, j); it; ++it)
-        {
-          if(it.index() == j)
-          {
-            det *= it.value();
-            break;
-          }
-        }
-      }
-      return (m_detPermR * m_detPermC) > 0 ? det : -det;
-    }
-
-    Index nnzL() const { return m_nnzL; };
-    Index nnzU() const { return m_nnzU; };
-
-  protected:
-    // Functions 
-    void initperfvalues()
-    {
-      m_perfv.panel_size = 16;
-      m_perfv.relax = 1; 
-      m_perfv.maxsuper = 128; 
-      m_perfv.rowblk = 16; 
-      m_perfv.colblk = 8; 
-      m_perfv.fillfactor = 20;  
-    }
-      
-    // Variables 
-    mutable ComputationInfo m_info;
-    bool m_factorizationIsOk;
-    bool m_analysisIsOk;
-    std::string m_lastError;
-    NCMatrix m_mat; // The input (permuted ) matrix 
-    SCMatrix m_Lstore; // The lower triangular matrix (supernodal)
-    MappedSparseMatrix<Scalar,ColMajor,StorageIndex> m_Ustore; // The upper triangular matrix
-    PermutationType m_perm_c; // Column permutation 
-    PermutationType m_perm_r ; // Row permutation
-    IndexVector m_etree; // Column elimination tree 
-    
-    typename Base::GlobalLU_t m_glu; 
-                               
-    // SparseLU options 
-    bool m_symmetricmode;
-    // values for performance 
-    internal::perfvalues m_perfv;
-    RealScalar m_diagpivotthresh; // Specifies the threshold used for a diagonal entry to be an acceptable pivot
-    Index m_nnzL, m_nnzU; // Nonzeros in L and U factors
-    Index m_detPermR, m_detPermC; // Determinants of the permutation matrices
-  private:
-    // Disable copy constructor 
-    SparseLU (const SparseLU& );
-}; // End class SparseLU
-
-
-
-// Functions needed by the anaysis phase
-/** 
-  * Compute the column permutation to minimize the fill-in
-  * 
-  *  - Apply this permutation to the input matrix - 
-  * 
-  *  - Compute the column elimination tree on the permuted matrix 
-  * 
-  *  - Postorder the elimination tree and the column permutation
-  * 
-  */
-template <typename MatrixType, typename OrderingType>
-void SparseLU<MatrixType, OrderingType>::analyzePattern(const MatrixType& mat)
-{
-  
-  //TODO  It is possible as in SuperLU to compute row and columns scaling vectors to equilibrate the matrix mat.
-  
-  // Firstly, copy the whole input matrix. 
-  m_mat = mat;
-  
-  // Compute fill-in ordering
-  OrderingType ord; 
-  ord(m_mat,m_perm_c);
-  
-  // Apply the permutation to the column of the input  matrix
-  if (m_perm_c.size())
-  {
-    m_mat.uncompress(); //NOTE: The effect of this command is only to create the InnerNonzeros pointers. FIXME : This vector is filled but not subsequently used.  
-    // Then, permute only the column pointers
-    ei_declare_aligned_stack_constructed_variable(StorageIndex,outerIndexPtr,mat.cols()+1,mat.isCompressed()?const_cast<StorageIndex*>(mat.outerIndexPtr()):0);
-    
-    // If the input matrix 'mat' is uncompressed, then the outer-indices do not match the ones of m_mat, and a copy is thus needed.
-    if(!mat.isCompressed()) 
-      IndexVector::Map(outerIndexPtr, mat.cols()+1) = IndexVector::Map(m_mat.outerIndexPtr(),mat.cols()+1);
-    
-    // Apply the permutation and compute the nnz per column.
-    for (Index i = 0; i < mat.cols(); i++)
-    {
-      m_mat.outerIndexPtr()[m_perm_c.indices()(i)] = outerIndexPtr[i];
-      m_mat.innerNonZeroPtr()[m_perm_c.indices()(i)] = outerIndexPtr[i+1] - outerIndexPtr[i];
-    }
-  }
-  
-  // Compute the column elimination tree of the permuted matrix 
-  IndexVector firstRowElt;
-  internal::coletree(m_mat, m_etree,firstRowElt); 
-     
-  // In symmetric mode, do not do postorder here
-  if (!m_symmetricmode) {
-    IndexVector post, iwork; 
-    // Post order etree
-    internal::treePostorder(StorageIndex(m_mat.cols()), m_etree, post); 
-      
-   
-    // Renumber etree in postorder 
-    Index m = m_mat.cols(); 
-    iwork.resize(m+1);
-    for (Index i = 0; i < m; ++i) iwork(post(i)) = post(m_etree(i));
-    m_etree = iwork;
-    
-    // Postmultiply A*Pc by post, i.e reorder the matrix according to the postorder of the etree
-    PermutationType post_perm(m); 
-    for (Index i = 0; i < m; i++) 
-      post_perm.indices()(i) = post(i); 
-        
-    // Combine the two permutations : postorder the permutation for future use
-    if(m_perm_c.size()) {
-      m_perm_c = post_perm * m_perm_c;
-    }
-    
-  } // end postordering 
-  
-  m_analysisIsOk = true; 
-}
-
-// Functions needed by the numerical factorization phase
-
-
-/** 
-  *  - Numerical factorization 
-  *  - Interleaved with the symbolic factorization 
-  * On exit,  info is 
-  * 
-  *    = 0: successful factorization
-  * 
-  *    > 0: if info = i, and i is
-  * 
-  *       <= A->ncol: U(i,i) is exactly zero. The factorization has
-  *          been completed, but the factor U is exactly singular,
-  *          and division by zero will occur if it is used to solve a
-  *          system of equations.
-  * 
-  *       > A->ncol: number of bytes allocated when memory allocation
-  *         failure occurred, plus A->ncol. If lwork = -1, it is
-  *         the estimated amount of space needed, plus A->ncol.  
-  */
-template <typename MatrixType, typename OrderingType>
-void SparseLU<MatrixType, OrderingType>::factorize(const MatrixType& matrix)
-{
-  using internal::emptyIdxLU;
-  eigen_assert(m_analysisIsOk && "analyzePattern() should be called first"); 
-  eigen_assert((matrix.rows() == matrix.cols()) && "Only for squared matrices");
-  
-  m_isInitialized = true;
-  
-  // Apply the column permutation computed in analyzepattern()
-  //   m_mat = matrix * m_perm_c.inverse(); 
-  m_mat = matrix;
-  if (m_perm_c.size()) 
-  {
-    m_mat.uncompress(); //NOTE: The effect of this command is only to create the InnerNonzeros pointers.
-    //Then, permute only the column pointers
-    const StorageIndex * outerIndexPtr;
-    if (matrix.isCompressed()) outerIndexPtr = matrix.outerIndexPtr();
-    else
-    {
-      StorageIndex* outerIndexPtr_t = new StorageIndex[matrix.cols()+1];
-      for(Index i = 0; i <= matrix.cols(); i++) outerIndexPtr_t[i] = m_mat.outerIndexPtr()[i];
-      outerIndexPtr = outerIndexPtr_t;
-    }
-    for (Index i = 0; i < matrix.cols(); i++)
-    {
-      m_mat.outerIndexPtr()[m_perm_c.indices()(i)] = outerIndexPtr[i];
-      m_mat.innerNonZeroPtr()[m_perm_c.indices()(i)] = outerIndexPtr[i+1] - outerIndexPtr[i];
-    }
-    if(!matrix.isCompressed()) delete[] outerIndexPtr;
-  } 
-  else 
-  { //FIXME This should not be needed if the empty permutation is handled transparently
-    m_perm_c.resize(matrix.cols());
-    for(StorageIndex i = 0; i < matrix.cols(); ++i) m_perm_c.indices()(i) = i;
-  }
-  
-  Index m = m_mat.rows();
-  Index n = m_mat.cols();
-  Index nnz = m_mat.nonZeros();
-  Index maxpanel = m_perfv.panel_size * m;
-  // Allocate working storage common to the factor routines
-  Index lwork = 0;
-  Index info = Base::memInit(m, n, nnz, lwork, m_perfv.fillfactor, m_perfv.panel_size, m_glu); 
-  if (info) 
-  {
-    m_lastError = "UNABLE TO ALLOCATE WORKING MEMORY\n\n" ;
-    m_factorizationIsOk = false;
-    return ; 
-  }
-  
-  // Set up pointers for integer working arrays 
-  IndexVector segrep(m); segrep.setZero();
-  IndexVector parent(m); parent.setZero();
-  IndexVector xplore(m); xplore.setZero();
-  IndexVector repfnz(maxpanel);
-  IndexVector panel_lsub(maxpanel);
-  IndexVector xprune(n); xprune.setZero();
-  IndexVector marker(m*internal::LUNoMarker); marker.setZero();
-  
-  repfnz.setConstant(-1); 
-  panel_lsub.setConstant(-1);
-  
-  // Set up pointers for scalar working arrays 
-  ScalarVector dense; 
-  dense.setZero(maxpanel);
-  ScalarVector tempv; 
-  tempv.setZero(internal::LUnumTempV(m, m_perfv.panel_size, m_perfv.maxsuper, /*m_perfv.rowblk*/m) );
-  
-  // Compute the inverse of perm_c
-  PermutationType iperm_c(m_perm_c.inverse()); 
-  
-  // Identify initial relaxed snodes
-  IndexVector relax_end(n);
-  if ( m_symmetricmode == true ) 
-    Base::heap_relax_snode(n, m_etree, m_perfv.relax, marker, relax_end);
-  else
-    Base::relax_snode(n, m_etree, m_perfv.relax, marker, relax_end);
-  
-  
-  m_perm_r.resize(m); 
-  m_perm_r.indices().setConstant(-1);
-  marker.setConstant(-1);
-  m_detPermR = 1; // Record the determinant of the row permutation
-  
-  m_glu.supno(0) = emptyIdxLU; m_glu.xsup.setConstant(0);
-  m_glu.xsup(0) = m_glu.xlsub(0) = m_glu.xusub(0) = m_glu.xlusup(0) = Index(0);
-  
-  // Work on one 'panel' at a time. A panel is one of the following :
-  //  (a) a relaxed supernode at the bottom of the etree, or
-  //  (b) panel_size contiguous columns, <panel_size> defined by the user
-  Index jcol; 
-  Index pivrow; // Pivotal row number in the original row matrix
-  Index nseg1; // Number of segments in U-column above panel row jcol
-  Index nseg; // Number of segments in each U-column 
-  Index irep; 
-  Index i, k, jj; 
-  for (jcol = 0; jcol < n; )
-  {
-    // Adjust panel size so that a panel won't overlap with the next relaxed snode. 
-    Index panel_size = m_perfv.panel_size; // upper bound on panel width
-    for (k = jcol + 1; k < (std::min)(jcol+panel_size, n); k++)
-    {
-      if (relax_end(k) != emptyIdxLU) 
-      {
-        panel_size = k - jcol; 
-        break; 
-      }
-    }
-    if (k == n) 
-      panel_size = n - jcol; 
-      
-    // Symbolic outer factorization on a panel of columns 
-    Base::panel_dfs(m, panel_size, jcol, m_mat, m_perm_r.indices(), nseg1, dense, panel_lsub, segrep, repfnz, xprune, marker, parent, xplore, m_glu); 
-    
-    // Numeric sup-panel updates in topological order 
-    Base::panel_bmod(m, panel_size, jcol, nseg1, dense, tempv, segrep, repfnz, m_glu); 
-    
-    // Sparse LU within the panel, and below the panel diagonal 
-    for ( jj = jcol; jj< jcol + panel_size; jj++) 
-    {
-      k = (jj - jcol) * m; // Column index for w-wide arrays 
-      
-      nseg = nseg1; // begin after all the panel segments
-      //Depth-first-search for the current column
-      VectorBlock<IndexVector> panel_lsubk(panel_lsub, k, m);
-      VectorBlock<IndexVector> repfnz_k(repfnz, k, m); 
-      info = Base::column_dfs(m, jj, m_perm_r.indices(), m_perfv.maxsuper, nseg, panel_lsubk, segrep, repfnz_k, xprune, marker, parent, xplore, m_glu); 
-      if ( info ) 
-      {
-        m_lastError =  "UNABLE TO EXPAND MEMORY IN COLUMN_DFS() ";
-        m_info = NumericalIssue; 
-        m_factorizationIsOk = false; 
-        return; 
-      }
-      // Numeric updates to this column 
-      VectorBlock<ScalarVector> dense_k(dense, k, m); 
-      VectorBlock<IndexVector> segrep_k(segrep, nseg1, m-nseg1); 
-      info = Base::column_bmod(jj, (nseg - nseg1), dense_k, tempv, segrep_k, repfnz_k, jcol, m_glu); 
-      if ( info ) 
-      {
-        m_lastError = "UNABLE TO EXPAND MEMORY IN COLUMN_BMOD() ";
-        m_info = NumericalIssue; 
-        m_factorizationIsOk = false; 
-        return; 
-      }
-      
-      // Copy the U-segments to ucol(*)
-      info = Base::copy_to_ucol(jj, nseg, segrep, repfnz_k ,m_perm_r.indices(), dense_k, m_glu); 
-      if ( info ) 
-      {
-        m_lastError = "UNABLE TO EXPAND MEMORY IN COPY_TO_UCOL() ";
-        m_info = NumericalIssue; 
-        m_factorizationIsOk = false; 
-        return; 
-      }
-      
-      // Form the L-segment 
-      info = Base::pivotL(jj, m_diagpivotthresh, m_perm_r.indices(), iperm_c.indices(), pivrow, m_glu);
-      if ( info ) 
-      {
-        m_lastError = "THE MATRIX IS STRUCTURALLY SINGULAR ... ZERO COLUMN AT ";
-        std::ostringstream returnInfo;
-        returnInfo << info; 
-        m_lastError += returnInfo.str();
-        m_info = NumericalIssue; 
-        m_factorizationIsOk = false; 
-        return; 
-      }
-      
-      // Update the determinant of the row permutation matrix
-      // FIXME: the following test is not correct, we should probably take iperm_c into account and pivrow is not directly the row pivot.
-      if (pivrow != jj) m_detPermR = -m_detPermR;
-
-      // Prune columns (0:jj-1) using column jj
-      Base::pruneL(jj, m_perm_r.indices(), pivrow, nseg, segrep, repfnz_k, xprune, m_glu); 
-      
-      // Reset repfnz for this column 
-      for (i = 0; i < nseg; i++)
-      {
-        irep = segrep(i); 
-        repfnz_k(irep) = emptyIdxLU; 
-      }
-    } // end SparseLU within the panel  
-    jcol += panel_size;  // Move to the next panel
-  } // end for -- end elimination 
-  
-  m_detPermR = m_perm_r.determinant();
-  m_detPermC = m_perm_c.determinant();
-  
-  // Count the number of nonzeros in factors 
-  Base::countnz(n, m_nnzL, m_nnzU, m_glu); 
-  // Apply permutation  to the L subscripts 
-  Base::fixupL(n, m_perm_r.indices(), m_glu);
-  
-  // Create supernode matrix L 
-  m_Lstore.setInfos(m, n, m_glu.lusup, m_glu.xlusup, m_glu.lsub, m_glu.xlsub, m_glu.supno, m_glu.xsup); 
-  // Create the column major upper sparse matrix  U; 
-  new (&m_Ustore) MappedSparseMatrix<Scalar, ColMajor, StorageIndex> ( m, n, m_nnzU, m_glu.xusub.data(), m_glu.usub.data(), m_glu.ucol.data() );
-  
-  m_info = Success;
-  m_factorizationIsOk = true;
-}
-
-template<typename MappedSupernodalType>
-struct SparseLUMatrixLReturnType : internal::no_assignment_operator
-{
-  typedef typename MappedSupernodalType::Scalar Scalar;
-  explicit SparseLUMatrixLReturnType(const MappedSupernodalType& mapL) : m_mapL(mapL)
-  { }
-  Index rows() const { return m_mapL.rows(); }
-  Index cols() const { return m_mapL.cols(); }
-  template<typename Dest>
-  void solveInPlace( MatrixBase<Dest> &X) const
-  {
-    m_mapL.solveInPlace(X);
-  }
-  template<bool Conjugate, typename Dest>
-  void solveTransposedInPlace( MatrixBase<Dest> &X) const
-  {
-    m_mapL.template solveTransposedInPlace<Conjugate>(X);
-  }
-
-  const MappedSupernodalType& m_mapL;
-};
-
-template<typename MatrixLType, typename MatrixUType>
-struct SparseLUMatrixUReturnType : internal::no_assignment_operator
-{
-  typedef typename MatrixLType::Scalar Scalar;
-  SparseLUMatrixUReturnType(const MatrixLType& mapL, const MatrixUType& mapU)
-  : m_mapL(mapL),m_mapU(mapU)
-  { }
-  Index rows() const { return m_mapL.rows(); }
-  Index cols() const { return m_mapL.cols(); }
-
-  template<typename Dest>   void solveInPlace(MatrixBase<Dest> &X) const
-  {
-    Index nrhs = X.cols();
-    Index n    = X.rows();
-    // Backward solve with U
-    for (Index k = m_mapL.nsuper(); k >= 0; k--)
-    {
-      Index fsupc = m_mapL.supToCol()[k];
-      Index lda = m_mapL.colIndexPtr()[fsupc+1] - m_mapL.colIndexPtr()[fsupc]; // leading dimension
-      Index nsupc = m_mapL.supToCol()[k+1] - fsupc;
-      Index luptr = m_mapL.colIndexPtr()[fsupc];
-
-      if (nsupc == 1)
-      {
-        for (Index j = 0; j < nrhs; j++)
-        {
-          X(fsupc, j) /= m_mapL.valuePtr()[luptr];
-        }
-      }
-      else
-      {
-        // FIXME: the following lines should use Block expressions and not Map!
-        Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > A( &(m_mapL.valuePtr()[luptr]), nsupc, nsupc, OuterStride<>(lda) );
-        Map< Matrix<Scalar,Dynamic,Dest::ColsAtCompileTime, ColMajor>, 0, OuterStride<> > U (&(X.coeffRef(fsupc,0)), nsupc, nrhs, OuterStride<>(n) );
-        U = A.template triangularView<Upper>().solve(U);
-      }
-
-      for (Index j = 0; j < nrhs; ++j)
-      {
-        for (Index jcol = fsupc; jcol < fsupc + nsupc; jcol++)
-        {
-          typename MatrixUType::InnerIterator it(m_mapU, jcol);
-          for ( ; it; ++it)
-          {
-            Index irow = it.index();
-            X(irow, j) -= X(jcol, j) * it.value();
-          }
-        }
-      }
-    } // End For U-solve
-  }
-
-  template<bool Conjugate, typename Dest>   void solveTransposedInPlace(MatrixBase<Dest> &X) const
-  {
-    using numext::conj;
-    Index nrhs = X.cols();
-    Index n    = X.rows();
-    // Forward solve with U
-    for (Index k = 0; k <=  m_mapL.nsuper(); k++)
-    {
-      Index fsupc = m_mapL.supToCol()[k];
-      Index lda = m_mapL.colIndexPtr()[fsupc+1] - m_mapL.colIndexPtr()[fsupc]; // leading dimension
-      Index nsupc = m_mapL.supToCol()[k+1] - fsupc;
-      Index luptr = m_mapL.colIndexPtr()[fsupc];
-
-      for (Index j = 0; j < nrhs; ++j)
-      {
-        for (Index jcol = fsupc; jcol < fsupc + nsupc; jcol++)
-        {
-          typename MatrixUType::InnerIterator it(m_mapU, jcol);
-          for ( ; it; ++it)
-          {
-            Index irow = it.index();
-            X(jcol, j) -= X(irow, j) * (Conjugate? conj(it.value()): it.value());
-          }
-        }
-      }
-      if (nsupc == 1)
-      {
-        for (Index j = 0; j < nrhs; j++)
-        {
-          X(fsupc, j) /= (Conjugate? conj(m_mapL.valuePtr()[luptr]) : m_mapL.valuePtr()[luptr]);
-        }
-      }
-      else
-      {
-        Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > A( &(m_mapL.valuePtr()[luptr]), nsupc, nsupc, OuterStride<>(lda) );
-        Map< Matrix<Scalar,Dynamic,Dest::ColsAtCompileTime, ColMajor>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) );
-        if(Conjugate)
-          U = A.adjoint().template triangularView<Lower>().solve(U);
-        else
-          U = A.transpose().template triangularView<Lower>().solve(U);
-      }
-    }// End For U-solve
-  }
-
-
-  const MatrixLType& m_mapL;
-  const MatrixUType& m_mapU;
-};
-
-} // End namespace Eigen 
-
-#endif