This file is indexed.

/usr/include/trilinos/Epetra_SerialSymDenseMatrix.h is in libtrilinos-epetra-dev 12.4.2-2.

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
/*
//@HEADER
// ************************************************************************
//
//               Epetra: Linear Algebra Services Package
//                 Copyright 2011 Sandia Corporation
//
// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
// the U.S. Government retains certain rights in this software.
//
// 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 Michael A. Heroux (maherou@sandia.gov)
//
// ************************************************************************
//@HEADER
*/

#ifndef EPETRA_SERIALSYMDENSEMATRIX_H
#define EPETRA_SERIALSYMDENSEMATRIX_H
#include "Epetra_SerialDenseMatrix.h"


//! Epetra_SerialSymDenseMatrix: A class for constructing and using symmetric positive definite dense matrices.

/*! The Epetra_SerialSymDenseMatrix class enables the construction and use of
    real-valued, symmetric positive definite,
    double-precision dense matrices.  It is built on the Epetra_SerialDenseMatrix class which
    in turn is built on the
    BLAS via the Epetra_BLAS class.

The Epetra_SerialSymDenseMatrix class is intended to provide full-featured support for solving
linear and eigen system
problems for symmetric positive definite matrices.  It is written on top of BLAS and LAPACK
and thus has excellent
performance and numerical capabilities.  Using this class, one can either perform simple
factorizations and solves or
apply all the tricks available in LAPACK to get the best possible solution for very
ill-conditioned problems.

<b>Epetra_SerialSymDenseMatrix vs. Epetra_LAPACK</b>

The Epetra_LAPACK class provides access to most of the same functionality as
Epetra_SerialSymDenseMatrix.
The primary difference is that Epetra_LAPACK is a "thin" layer on top of
LAPACK and Epetra_SerialSymDenseMatrix
attempts to provide easy access to the more sophisticated aspects of
solving dense linear and eigensystems.
<ul>
<li> When you should use Epetra_LAPACK:  If you are simply looking for a
     convenient wrapper around the Fortran LAPACK
     routines and you have a well-conditioned problem, you should probably use Epetra_LAPACK directly.
<li> When you should use Epetra_SerialSymDenseMatrix: If you want to (or potentially want to)
     solve ill-conditioned
     problems or want to work with a more object-oriented interface, you should
     probably use Epetra_SerialSymDenseMatrix.

</ul>

<b>Constructing Epetra_SerialSymDenseMatrix Objects</b>

There are three Epetra_DenseMatrix constructors.  The first constructs a zero-sized object
which should be made
to appropriate length using the Shape() or Reshape() functions and then filled with
the [] or () operators.
The second is a constructor that accepts user
data as a 2D array, the third is a copy constructor. The second constructor has
two data access modes (specified by the Epetra_DataAccess argument):
<ol>
  <li> Copy mode - Allocates memory and makes a copy of the user-provided data. In this case, the
       user data is not needed after construction.
  <li> View mode - Creates a "view" of the user data. In this case, the
       user data is required to remain intact for the life of the object.
</ol>

\warning View mode is \e extremely dangerous from a data hiding perspective.
Therefore, we strongly encourage users to develop code using Copy mode first and
only use the View mode in a secondary optimization phase.

<b>Extracting Data from Epetra_SerialSymDenseMatrix Objects</b>

Once a Epetra_SerialSymDenseMatrix is constructed, it is possible to view the data via access functions.

\warning Use of these access functions cam be \e extremely dangerous from a data hiding perspective.


<b>Vector and Utility Functions</b>

Once a Epetra_SerialSymDenseMatrix is constructed, several mathematical functions can be applied to
the object.  Specifically:
<ul>
  <li> Multiplication.
  <li> Norms.
</ul>

<b>Counting floating point operations </b>
The Epetra_SerialSymDenseMatrix class has Epetra_CompObject as a base class.  Thus, floating
point operations
are counted and accumulated in the Epetra_Flop object (if any) that was set using the SetFlopCounter()
method in the Epetra_CompObject base class.

*/

//=========================================================================
class EPETRA_LIB_DLL_EXPORT Epetra_SerialSymDenseMatrix : public Epetra_SerialDenseMatrix {

 public:
   //! @name Constructor/Destructor Methods
  //@{
  //! Default constructor; defines a zero size object.
  /*!
    Epetra_SerialSymDenseMatrix objects defined by the default constructor
    should be sized with the Shape()
    or Reshape() functions.
    Values should be defined by using the [] or ()operators.

    Note: By default the active part of the matrix is assumed to be in the lower triangle.
    To set the upper part as active, call SetUpper().
    See Detailed Description section for further discussion.
   */
  Epetra_SerialSymDenseMatrix(void);
  //! Set object values from two-dimensional array.
  /*!
    \param In
           Epetra_DataAccess - Enumerated type set to Copy or View.
    \param In
           A - Pointer to an array of double precision numbers.  The first vector starts at A.
	   The second vector starts at A+LDA, the third at A+2*LDA, and so on.
    \param In
           LDA - The "Leading Dimension", or stride between vectors in memory.
    \param In
           NumRowsCols - Number of rows and columns in object.

	   Note: By default the active part of the matrix is assumed to be in the lower triangle.
	   To set the upper part as active, call SetUpper().
	   See Detailed Description section for further discussion.
  */
  Epetra_SerialSymDenseMatrix(Epetra_DataAccess CV, double *A, int LDA, int NumRowsCols);

  //! Epetra_SerialSymDenseMatrix copy constructor.

  Epetra_SerialSymDenseMatrix(const Epetra_SerialSymDenseMatrix& Source);


  //! Epetra_SerialSymDenseMatrix destructor.
  virtual ~Epetra_SerialSymDenseMatrix ();
  //@}

  //! @name Set Methods
  //@{

  //let the compiler know we intend to overload the base-class Shape function,
  //rather than hide it.
  using Epetra_SerialDenseMatrix::Shape;

  //! Set dimensions of a Epetra_SerialSymDenseMatrix object; init values to zero.
  /*!
    \param In
           NumRowsCols - Number of rows and columns in object.

	   Allows user to define the dimensions of a Epetra_DenseMatrix at any point. This function can
	   be called at any point after construction.  Any values that were previously in this object are
	   destroyed and the resized matrix starts off with all zero values.

    \return Integer error code, set to 0 if successful.
  */
  int Shape(int NumRowsCols) {return(Epetra_SerialDenseMatrix::Shape(NumRowsCols,NumRowsCols));};

  //let the compiler know we intend to overload the base-class Reshape function,
  //rather than hide it.

  using Epetra_SerialDenseMatrix::Reshape;

  //! Reshape a Epetra_SerialSymDenseMatrix object.
  /*!
    \param In
           NumRowsCols - Number of rows and columns in object.

	   Allows user to define the dimensions of a Epetra_SerialSymDenseMatrix at any point. This function can
	   be called at any point after construction.  Any values that were previously in this object are
	   copied into the new shape.  If the new shape is smaller than the original, the upper left portion
	   of the original matrix (the principal submatrix) is copied to the new matrix.

    \return Integer error code, set to 0 if successful.
  */
  int Reshape(int NumRowsCols) {return(Epetra_SerialDenseMatrix::Reshape(NumRowsCols,NumRowsCols));};


  //! Specify that the lower triangle of the \e this matrix should be used.
  void SetLower() {Upper_ = false; UPLO_ = 'L';};

  //! Specify that the upper triangle of the \e this matrix should be used.
  void SetUpper() {Upper_ = true; UPLO_ = 'U';};
  //@}

  //! @name Query methods
  //@{

  //! Returns true if upper triangle of \e this matrix has and will be used.
  bool Upper() const {return(Upper_);};

  //! Returns character value of UPLO used by LAPACK routines.
  char UPLO() const {return(UPLO_);};
  //@}

  //! @name Mathematical Methods
  //@{

  //! Inplace scalar-matrix product A = \e a A.
  /*! Scale a matrix, entry-by-entry using the value ScalarA.  This method is sensitive to
      the UPLO() parameter.


  \param ScalarA (In) Scalar to multiply with A.

   \return Integer error code, set to 0 if successful.
	
  */
  int  Scale ( double ScalarA );


  //! Computes the 1-Norm of the \e this matrix.
  /*!
    \return Integer error code, set to 0 if successful.
  */
  double NormOne() const;

  //! Computes the Infinity-Norm of the \e this matrix.
  double NormInf() const;

  //@}

  void CopyUPLOMat(bool Upper, double * A, int LDA, int NumRows);

  //! @name Deprecated methods (will be removed in later versions of this class)
  //@{

  //! Computes the 1-Norm of the \e this matrix (identical to NormOne() method).
  /*!
    \return Integer error code, set to 0 if successful.
  */
  double OneNorm() const {return(Epetra_SerialSymDenseMatrix::NormOne());};

  //! Computes the Infinity-Norm of the \e this matrix (identical to NormInf() method).
  double InfNorm() const {return(Epetra_SerialSymDenseMatrix::NormInf());};
  //@}

 private:

  bool Upper_;

  char UPLO_;


};

#endif /* EPETRA_SERIALSYMDENSEMATRIX_H */