This file is indexed.

/usr/include/CGAL/OpenNL/preconditioner.h is in libcgal-dev 4.11-2build1.

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
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
// Copyright (c) 2005-2008  Inria Loria (France).
/*
 * author:  Bruno Levy, INRIA, project ALICE
 * website: http://www.loria.fr/~levy/software
 * 
 * This library 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.
 * 
 * This library 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 library; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 *
 * Scientific work that use this software can reference the website and
 * the following publication:
 *
 * @INPROCEEDINGS {levy:NMDGP:05,
 *    AUTHOR = Bruno Levy,
 *    TITLE  = Numerical Methods for Digital Geometry Processing,
 *    BOOKTITLE =Israel Korea Bi-National Conference,
 *    YEAR=November 2005,
 *    URL=http://www.loria.fr/~levy/php/article.php?pub=../publications/papers/2005/Numerics
 * }
 *
 *  Laurent Saboret 2006: Changes for CGAL:
 *      - copied Jacobi preconditioner from Graphite 1.9 code
 *      - Added OpenNL namespace
 */

#ifndef __OPENNL_PRECONDITIONER__
#define __OPENNL_PRECONDITIONER__

#include <CGAL/OpenNL/blas.h>
#include <CGAL/OpenNL/sparse_matrix.h>
#include <CGAL/OpenNL/full_vector.h>

#include <CGAL/assertions.h>
#include <CGAL/tss.h>

namespace OpenNL {


/**
 * Base class for some preconditioners.
 */

template <class T> 
class Preconditioner {
public:
    typedef T CoeffType ;

public:
    /**
     * The matrix A should be square.
     */
    Preconditioner(
        const SparseMatrix<T>& A, CoeffType omega = 1.0
    ) ;
    
    const SparseMatrix<T>& A() const { return A_ ; }
    CoeffType omega() const { return omega_ ; }

    /**
     * To use this function, the matrix A should be symmetric.
     */
    void mult_upper_inverse(const FullVector<T>& x, FullVector<T>& y) const ;

    /**
     * To use this function, the matrix A should be symmetric.
     */
    void mult_lower_inverse(const FullVector<T>& x, FullVector<T>& y) const ;

    void mult_diagonal(FullVector<T>& xy) const ;
    void mult_diagonal_inverse(FullVector<T>& xy) const ;
    
private:
    const SparseMatrix<T>& A_ ;
    CoeffType omega_ ;
} ;

template <class T> 
Preconditioner<T>::Preconditioner(
    const SparseMatrix<T>& A, CoeffType omega
) : A_(A), omega_(omega) {
    //CGAL_assertion(A.is_square()) ;
}

template <class T> 
void Preconditioner<T>::mult_lower_inverse(
    const FullVector<T>& x, FullVector<T>& y
) const {
    //CGAL_assertion(A_.has_symmetric_storage()) ;
    //CGAL_assertion(A_.rows_are_stored()) ;
    int n = A_.dimension() ;
    for(int i=0; i<n; i++) {
        double S = 0 ;
        const typename SparseMatrix<T>::Row& Ri = A_.row(i) ;
        for(int ij=0; ij < Ri.size(); ij++) {
            const typename SparseMatrix<T>::Coeff& c = Ri[ij] ;
            if (c.index < i) // traverse only lower half matrix
                S += c.a * y[c.index] ;
        }
        y[i] = (x[i] - S) * omega_ / A_.get_coef(i,i) ;
    }
}
template <class T> 
void Preconditioner<T>::mult_upper_inverse(
    const FullVector<T>& x, FullVector<T>& y
) const {
    //CGAL_assertion(A_.has_symmetric_storage()) ;
    //CGAL_assertion(A_.columns_are_stored()) ;
    int n = A_.dimension() ;
    for(int i=n-1; i>=0; i--) {
        double S = 0 ;
        const typename SparseMatrix<T>::Row& Ci = A_.row(i) ; // column i == row i
        for(int ij=0; ij < Ci.size(); ij++) {
            const typename SparseMatrix<T>::Coeff& c = Ci[ij] ;
            if(c.index > i) // traverse only upper half matrix
                S += c.a * y[c.index] ;
        }
        y[i] = (x[i] - S) * omega_ / A_.get_coef(i,i) ;
    }
}

template <class T> 
void Preconditioner<T>::mult_diagonal(FullVector<T>& xy) const {
    int n = A_.dimension() ;
    for(int i=0; i<n; i++) {
        xy[i] *= ( A_.get_coef(i,i) / omega_ ) ;
    }
}

template <class T> 
void Preconditioner<T>::mult_diagonal_inverse(FullVector<T>& xy) const {
    int n = A_.dimension() ;
    for(int i=0; i<n; i++) {
        xy[i] *= ( omega_ / A_.get_coef(i,i) ) ;
    }
}
    
/**
 * Jacobi preconditioner
 */

template <class T> 
class Jacobi_Preconditioner : public Preconditioner<T> {
public:
    typedef T CoeffType ;

public:
    Jacobi_Preconditioner(
        const SparseMatrix<T>& A, CoeffType omega = 1.0
    ) ;
} ;

template <class T> 
Jacobi_Preconditioner<T>::Jacobi_Preconditioner(
    const SparseMatrix<T>& A, CoeffType omega
) : Preconditioner<T>(A, omega) {
}

template <class T> 
void mult(const Jacobi_Preconditioner<T>& M, const FullVector<T>& x, FullVector<T>& y) {
    BLAS< FullVector<T> >::copy(x, y) ;
    M.mult_diagonal_inverse(y) ;
}


/**
 * The SSOR preconditioner, sharing storage with the matrix.
 */
 
template <class T> 
class SSOR_Preconditioner : public Preconditioner<T> {
public:
    typedef T CoeffType ;

public:
    /**
     * The matrix A should be symmetric.
     */
    SSOR_Preconditioner(
        const SparseMatrix<T>& A, CoeffType omega = 1.0
    ) ;
} ;

template <class T> 
SSOR_Preconditioner<T>::SSOR_Preconditioner(
    const SparseMatrix<T>& A, CoeffType omega
) : Preconditioner<T>(A, omega) {
}

/** y <- M*x */
template <class T> 
void mult(const SSOR_Preconditioner<T>& M, const FullVector<T>& x, FullVector<T>& y) {

    CGAL_STATIC_THREAD_LOCAL_VARIABLE(FullVector<T>, work,0) ;

    const SparseMatrix<T>& A = M.A() ;
    int n = A.dimension() ;

    if(work.dimension() != n) {
        work = FullVector<T>(n) ;
    }

    M.mult_lower_inverse(x, work) ;
    M.mult_diagonal(work) ;
    M.mult_upper_inverse(work, y) ;

    BLAS< FullVector<T> >::scal(2 - M.omega(), y) ;
}


} // namespace OpenNL

#endif // __OPENNL_PRECONDITIONER__