This file is indexed.

/usr/include/dolfin/la/CholmodCholeskySolver.h is in libdolfin1.0-dev 1.0.0-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
// Copyright (C) 2008 Dag Lindbo and Garth N. Wells
//
// This file is part of DOLFIN.
//
// DOLFIN 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, either version 3 of the License, or
// (at your option) any later version.
//
// DOLFIN 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 DOLFIN. If not, see <http://www.gnu.org/licenses/>.
//
// Modified by Anders Logg 2011
//
// First added:  2008-08-15
// Last changed: 2011-11-11

#ifndef __CHOLMOD_CHOLESKY_SOLVER_H
#define __CHOLMOD_CHOLESKY_SOLVER_H

#include <boost/shared_ptr.hpp>
#include "GenericLinearSolver.h"

#ifdef HAS_CHOLMOD
extern "C"
{
  #include <cholmod.h>
}
#endif

namespace dolfin
{

  /// Forward declarations
  class GenericVector;
  class GenericMatrix;

  /// This class implements the direct solution (Cholesky
  /// factorization) of linear systems of the form Ax = b. Sparse
  /// matrices are solved using CHOLMOD
  /// http://www.cise.ufl.edu/research/sparse/cholmod/ if installed.

  class CholmodCholeskySolver : public GenericLinearSolver
  {

  public:

    /// Constructor
    CholmodCholeskySolver();

    /// Constructor
    CholmodCholeskySolver(boost::shared_ptr<const GenericMatrix> A);

    /// Destructor
    ~CholmodCholeskySolver();

    /// Solve the operator (matrix)
    void set_operator(const boost::shared_ptr<const GenericMatrix> A)
    {
      dolfin_error("CholmodCholeskySolver.h",
                   "set operator for CHOLMOD Cholesky solver",
                   "Not implemented");
    }

    /// Solve linear system Ax = b for a sparse matrix using CHOLMOD
    virtual uint solve(const GenericMatrix& A, GenericVector& x, const GenericVector& b);

    /// Cholesky-factor sparse matrix A if CHOLMOD is installed
    virtual uint factorize(const GenericMatrix& A);

    /// Solve factorized system (CHOLMOD).
    virtual uint factorized_solve(GenericVector& x, const GenericVector& b);

    /// Default parameter values
    static Parameters default_parameters();

  private:

    // Operator (the matrix)
    boost::shared_ptr<const GenericMatrix> _A;

#ifdef HAS_CHOLMOD
    // Data for Cholesky factorization of sparse ublas matrix (cholmod only)
    class Cholmod
    {
    public:

      Cholmod();
      ~Cholmod();

      /// Clear data
      void clear();

      /// Initialise with matrix
      void init(long int* Ap, long int* Ai, double* Ax, uint M, uint nz);

      /// Factorize
      void factorize();

      /// Factorized solve
      void factorized_solve(double*x, const double* b);

      uint N;
      bool factorized;

    private:

      /// Compute residual: b-Ax
      cholmod_dense* residual(cholmod_dense* x, cholmod_dense* b);

      /// Compute residual norm
      double residual_norm(cholmod_dense* r, cholmod_dense* x,
			                     cholmod_dense* b);

      /// Perform one refinement
      void refine_once(cholmod_dense* x, cholmod_dense* r);

      /// Check status flag returned by an CHOLMOD function
      void check_status(std::string function);

      // CHOLMOD data
      cholmod_sparse* A_chol;
      cholmod_factor* L_chol;
      cholmod_common c;
    };

    Cholmod cholmod;
#endif
  };

}

#endif