This file is indexed.

/usr/include/trilinos/LOCA_Epetra_LowRankUpdateRowMatrix.H is in libtrilinos-nox-dev 12.10.1-3.

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
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
// $Id$
// $Source$

//@HEADER
// ************************************************************************
//
//            LOCA: Library of Continuation Algorithms Package
//                 Copyright (2005) Sandia Corporation
//
// Under terms of Contract DE-AC04-94AL85000, there is a non-exclusive
// license for use of this work by or on behalf of the U.S. Government.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Roger Pawlowski (rppawlo@sandia.gov) or
// Eric Phipps (etphipp@sandia.gov), Sandia National Laboratories.
// ************************************************************************
//  CVS Information
//  $Source$
//  $Author$
//  $Date$
//  $Revision$
// ************************************************************************
//@HEADER

#ifndef LOCA_EPETRA_LOWRANKUPDATEROWMATRIX_H
#define LOCA_EPETRA_LOWRANKUPDATEROWMATRIX_H

#include "Teuchos_RCP.hpp"

#include "LOCA_Epetra_LowRankUpdateOp.H" // base class
#include "Epetra_RowMatrix.h"        // base class

namespace LOCA {

  namespace Epetra {

    /*!
     * \brief An Epetra row matrix for implementing the operator
     * \f$P = J + U V^T\f$.
     */
    /*!
     * This class implements the Epetra_RowMatrix interface for
     * \f$P = J + U V^T\f$ where \f$J\f$ is an Epetra_RowMatrix and
     * \f$U\f$ and \f$V\f$ are Epetra_MultiVectors.  It is derived
     * from LOCA::Epetra::LowRankUpdateOp to implement the Epetra_Operator
     * interface.  The interface here implements the Epetra_RowMatrix
     * interface when the matrix \f$J\f$ is itself a row matrix.  This
     * allows preconditioners to be computed and scaling in linear systems
     * to be performed when using this operator.  The implementation
     * here merely adds the corresponding entries for \f$U V^T\f$ to the
     * rows of \f$J\f$.  Note however this is only an approximation to the
     * true matrix \f$J + U V^T\f$.
     *
     * This class assumes \f$U\f$ and \f$V\f$ have the same distribution
     * as the rows of \f$J\f$.
     */
    class LowRankUpdateRowMatrix :
      public LOCA::Epetra::LowRankUpdateOp,
      public virtual Epetra_RowMatrix {

    public:

      //! Constructor
      /*!
       * \param global_data [in] The global data object
       * \param jacRowMatrix [in] Jacobian operator J as a row matrix
       * \param U_multiVec [in] Multivector representing U
       * \param V_multiVec [in] Multivector representing V
       * \param setup_for_solve [in] Setup data structures for ApplyInverse()
       * \param include_UV_terms [in] Include \f$U V^T\f$ terms in RowMatrix
       *        routines ExtractRowCopy(), ExtactDiagonalCopy(), InvRowSums(),
       *        InvColSums(), NormInf() and NormOne().
       */
      LowRankUpdateRowMatrix(
        const Teuchos::RCP<LOCA::GlobalData>& global_data,
    const Teuchos::RCP<Epetra_RowMatrix>& jacRowMatrix,
    const Teuchos::RCP<Epetra_MultiVector>& U_multiVec,
    const Teuchos::RCP<Epetra_MultiVector>& V_multiVec,
    bool setup_for_solve,
    bool include_UV_terms);

      //! Destructor
      virtual ~LowRankUpdateRowMatrix();

      //! Returns a reference to the Epetra_BlockMap for this object.
      virtual const Epetra_BlockMap & Map() const;

      //@{ \name Matrix data extraction routines

      //! Returns the number of nonzero entries in MyRow.
      virtual int NumMyRowEntries(int MyRow, int & NumEntries) const;


      //! Returns the maximum of NumMyRowEntries() over all rows.
      virtual int MaxNumEntries() const;

      //! Returns a copy of the specified local row in user-provided arrays.
      virtual int ExtractMyRowCopy(int MyRow, int Length, int & NumEntries,
                   double *Values, int * Indices) const;

      //! Returns a copy of the main diagonal in a user-provided vector.
      virtual int ExtractDiagonalCopy(Epetra_Vector & Diagonal) const;

      //@}

      //@{ \name Mathematical functions.

      /*!
       * \brief Returns the result of a Epetra_RowMatrix multiplied by a
       * Epetra_MultiVector X in Y.
       */
      virtual int Multiply(bool TransA, const Epetra_MultiVector& X,
               Epetra_MultiVector& Y) const;

      /*!
       * \brief Returns result of a local-only solve using a triangular
       * Epetra_RowMatrix with Epetra_MultiVectors X and Y.
       */
      virtual int Solve(bool Upper, bool Trans, bool UnitDiagonal,
            const Epetra_MultiVector& X,
            Epetra_MultiVector& Y) const;

      /*!
       * \brief Computes the sum of absolute values of the rows of the
       * Epetra_RowMatrix, results returned in x.
       */
      virtual int InvRowSums(Epetra_Vector& x) const;

      //! Scales the Epetra_RowMatrix on the left with a Epetra_Vector x.
      virtual int LeftScale(const Epetra_Vector& x);

      /*!
       * \brief Computes the sum of absolute values of the columns of the
       * Epetra_RowMatrix, results returned in x.
       */
      virtual int InvColSums(Epetra_Vector& x) const;

      //! Scales the Epetra_RowMatrix on the right with a Epetra_Vector x.
      virtual int RightScale(const Epetra_Vector& x);

      //@}

      //@{ \name Attribute access functions

      /*!
       * \brief If FillComplete() has been called, this query returns true,
       * otherwise it returns false.
       */
      virtual bool Filled() const;

      //! Returns the infinity norm of the global matrix.
      virtual double NormInf() const;

      //! Returns the one norm of the global matrix.
      virtual double NormOne() const;

      //! Returns the number of nonzero entries in the global matrix.
#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
      virtual int NumGlobalNonzeros() const;
#endif
      virtual long long NumGlobalNonzeros64() const;

      //! Returns the number of global matrix rows.
#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
      virtual int NumGlobalRows() const;
#endif
      virtual long long NumGlobalRows64() const;

      //! Returns the number of global matrix columns.
#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
      virtual int NumGlobalCols() const;
#endif
      virtual long long NumGlobalCols64() const;

      /*!
       * \brief Returns the number of global nonzero diagonal entries,
       * based on global row/column index comparisons.
       */
#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
      virtual int NumGlobalDiagonals() const;
#endif
      virtual long long NumGlobalDiagonals64() const;

      /*!
       * \brief Returns the number of nonzero entries in the calling
       * processor's portion of the matrix.
       */
      virtual int NumMyNonzeros() const;

      //! Returns the number of matrix rows owned by the calling processor.
      virtual int NumMyRows() const;

      //! Returns the number of matrix columns owned by the calling processor.
      virtual int NumMyCols() const;

      /*!
       * \brief Returns the number of local nonzero diagonal entries, based
       * on global row/column index comparisons.
       */
      virtual int NumMyDiagonals() const;

      /*!
       * \brief If matrix is lower triangular in local index space,
       * this query returns true, otherwise it returns false.
       */
      virtual bool LowerTriangular() const;

      /*!
       * \brief If matrix is upper triangular in local index space, this
       * query returns true, otherwise it returns false.
       */
      virtual bool UpperTriangular() const;

      /*!
       * \brief Returns the Epetra_Map object associated with the rows of
       * this matrix.
       */
      virtual const Epetra_Map & RowMatrixRowMap() const;

      /*!
       * \brief Returns the Epetra_Map object associated with the columns of
       * this matrix.
       */
      virtual const Epetra_Map & RowMatrixColMap() const;

      /*!
       * \brief Returns the Epetra_Import object that contains the import
       * operations for distributed operations.
       */
      virtual const Epetra_Import * RowMatrixImporter() const;

      //@}

    protected:

      //! Compute \c MyRow, \c MyCol entry of \f$U V^T\f$.
      double computeUV(int MyRow, int MyCol) const;

    private:

      //! Private to prohibit copying
      LowRankUpdateRowMatrix(const LowRankUpdateRowMatrix&);

      //! Private to prohibit copying
      LowRankUpdateRowMatrix& operator=(const LowRankUpdateRowMatrix&);

    protected:

      //! Stores row matrix representing J
      Teuchos::RCP<Epetra_RowMatrix> J_rowMatrix;

      //! Stores pointer to non-const U
      Teuchos::RCP<Epetra_MultiVector> nonconst_U;

      //! Stores pointer to non-const V
      Teuchos::RCP<Epetra_MultiVector> nonconst_V;

      //! Flag indicating whether to include U*V^T terms
      bool includeUV;

      //! Number of columns in U and V
      int m;

      //! Map for U
      const Epetra_BlockMap& U_map;

      //! Map for V
      const Epetra_BlockMap& V_map;

      //! Row map for J
      const Epetra_BlockMap& row_map;

    };
  } // namespace Epetra
} // namespace LOCA

#endif