This file is indexed.

/usr/include/trilinos/Epetra_FEVector.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
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
/*
//@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_FEVECTOR_H
#define EPETRA_FEVECTOR_H

#include <Epetra_ConfigDefs.h>
#include <Epetra_CombineMode.h>
#include <Epetra_Map.h>
#include <Epetra_MultiVector.h>

#include <vector>

class Epetra_IntSerialDenseVector;

#ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
class Epetra_LongLongSerialDenseVector;
#endif

class Epetra_SerialDenseVector;


/** Epetra Finite-Element Vector. This class inherits Epetra_MultiVector
  and thus provides all Epetra_MultiVector functionality.

  The added functionality provided by Epetra_FEVector is the ability to
  perform finite-element style vector assembly. It accepts sub-vector
  contributions, such as those that would come from element-load vectors, etc.
  These sub-vectors need not be owned by the local processor. In other
  words, the user can assemble overlapping data (e.g., corresponding to shared
  finite-element nodes). When the user is finished assembling their vector
  data, they then call the method Epetra_FEVector::GlobalAssemble() which
  gathers the overlapping data (all non-local data that was input on each
  processor) into the data-distribution specified by the map with which the
  Epetra_FEVector was constructed.
*/

class EPETRA_LIB_DLL_EXPORT Epetra_FEVector : public Epetra_MultiVector {
 public:
   /** Constructor that requires a map specifying a non-overlapping
      data layout.
      @param Map Map describing a non-overlapping distribution for the
        underlying Epetra_MultiVector into which this Epetra_FEVector will
        funnel data.

      @param numVectors Optional argument, default value is 1. (See the
        documentation for Epetra_MultiVector for the meaning of this
        argument.

      @param ignoreNonLocalEntries Optional argument, default value is
        false.  Under certain special circumstances it is desirable to
        have non-local contributions ignored rather than saving them
        for the GlobalAssemble step.
   */
   Epetra_FEVector(const Epetra_BlockMap& Map,
                   int numVectors=1,
       bool ignoreNonLocalEntries=false);

  //! Set multi-vector values from two-dimensional array.
  /*!
    \param In
    Epetra_DataAccess - Enumerated type set to Copy or View.
    \param In
    Map - A Epetra_LocalMap, Epetra_Map or Epetra_BlockMap.
    \param In
    A - Pointer to an array of double precision numbers.  The first vector starts at A.
    The second vector starts at A+MyLDA, the third at A+2*MyLDA, and so on.
    \param In
    MyLDA - The "Leading Dimension", or stride between vectors in memory.
    \warning This value refers to the stride on the calling processor.  Thus it is a
    local quantity, not a global quantity.
    \param In
    NumVectors - Number of vectors in multi-vector.

    \return Integer error code, set to 0 if successful.

    See Detailed Description section for further discussion.
  */
  Epetra_FEVector(Epetra_DataAccess CV, const Epetra_BlockMap& Map,
         double *A, int MyLDA, int NumVectors,
        bool ignoreNonLocalEntries=false);

  //! Set multi-vector values from array of pointers.
  /*!
    \param In
    Epetra_DataAccess - Enumerated type set to Copy or View.
    \param In
    Map - A Epetra_LocalMap, Epetra_Map or Epetra_BlockMap.
    \param In
    ArrayOfPointers - An array of pointers such that ArrayOfPointers[i] points to the memory
    location containing ith vector to be copied.
    \param In
    NumVectors - Number of vectors in multi-vector.

    \return Integer error code, set to 0 if successful.

    See Detailed Description section for further discussion.
  */
  Epetra_FEVector(Epetra_DataAccess CV, const Epetra_BlockMap& Map,
         double **ArrayOfPointers, int NumVectors,
            bool ignoreNonLocalEntries=false);

  /** Copy constructor. */
  Epetra_FEVector(const Epetra_FEVector& source);

   /** Destructor */
   virtual ~Epetra_FEVector();

   /** Accumulate values into the vector, adding them to any values that
       already exist for the specified indices.
   */
#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
   int SumIntoGlobalValues(int numIDs,
                           const int* GIDs, const double* values,
                           int vectorIndex=0);
#endif
#ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
   int SumIntoGlobalValues(int numIDs,
                           const long long* GIDs, const double* values,
                           int vectorIndex=0);
#endif

   /** Accumulate values into the vector, adding them to any values that
       already exist for the specified GIDs.

       @param GIDs List of global ids. Must be the same length as the
       accompanying list of values.

       @param values List of coefficient values. Must be the same length as
       the accompanying list of GIDs.
   */
   int SumIntoGlobalValues(const Epetra_IntSerialDenseVector& GIDs,
         const Epetra_SerialDenseVector& values,
                           int vectorIndex=0);
#ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
   int SumIntoGlobalValues(const Epetra_LongLongSerialDenseVector& GIDs,
         const Epetra_SerialDenseVector& values,
                           int vectorIndex=0);
#endif

   /** Copy values into the vector overwriting any values that already exist
        for the specified indices.
    */
#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
   int ReplaceGlobalValues(int numIDs, const int* GIDs, const double* values,
                           int vectorIndex=0);
#endif
#ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
   int ReplaceGlobalValues(int numIDs, const long long* GIDs, const double* values,
                           int vectorIndex=0);
#endif

   /** Copy values into the vector, replacing any values that
       already exist for the specified GIDs.

       @param GIDs List of global ids. Must be the same length as the
       accompanying list of values.

       @param values List of coefficient values. Must be the same length as
       the accompanying list of GIDs.
   */
   int ReplaceGlobalValues(const Epetra_IntSerialDenseVector& GIDs,
         const Epetra_SerialDenseVector& values,
                           int vectorIndex=0);
#ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
   int ReplaceGlobalValues(const Epetra_LongLongSerialDenseVector& GIDs,
         const Epetra_SerialDenseVector& values,
                           int vectorIndex=0);
#endif
#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
   int SumIntoGlobalValues(int numIDs,
                           const int* GIDs,
         const int* numValuesPerID,
         const double* values,
                           int vectorIndex=0);
#endif
#ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
   int SumIntoGlobalValues(int numIDs,
                           const long long* GIDs,
         const int* numValuesPerID,
         const double* values,
                           int vectorIndex=0);
#endif

#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
   int ReplaceGlobalValues(int numIDs, const int* GIDs,
         const int* numValuesPerID,
         const double* values,
                           int vectorIndex=0);
#endif
#ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
   int ReplaceGlobalValues(int numIDs, const long long* GIDs,
         const int* numValuesPerID,
         const double* values,
                           int vectorIndex=0);
#endif

   /** Gather any overlapping/shared data into the non-overlapping partitioning
      defined by the Map that was passed to this vector at construction time.
      Data imported from other processors is stored on the owning processor
      with a "sumInto" or accumulate operation.
      This is a collective method -- every processor must enter it before any
      will complete it.

      Optimization for power-users:
      The optional parameter 'reuse_map_and_exporter' defaults to false.
      By default, a map that describes the non-local data is re-created at
      each call to GlobalAssemble, along with an exporter used to do the
      communication.
      This is expensive. If you know that the layout of your nonlocal data has
      not changed since your previous call to GlobalAssemble, you can set this
      flag to true and it will reuse the previously created map and exporter
      rather than creating new ones.
   */
   int GlobalAssemble(Epetra_CombineMode mode = Add,
                      bool reuse_map_and_exporter = false);

   /** Set whether or not non-local data values should be ignored.
    */
   void setIgnoreNonLocalEntries(bool flag) {
     ignoreNonLocalEntries_ = flag;
   }

   Epetra_FEVector& operator=(const Epetra_FEVector& source);

 protected:
  template<typename int_type>
  int inputValues(int numIDs,
                  const int_type* GIDs, const double* values,
                  bool suminto,
                  int vectorIndex);

  template<typename int_type>
  int inputValues(int numIDs,
                  const int_type* GIDs, const int* numValuesPerID,
      const double* values,
                  bool suminto,
                  int vectorIndex);

  template<typename int_type>
  int inputNonlocalValue(int_type GID, double value, bool suminto,
                         int vectorIndex);

  template<typename int_type>
  int inputNonlocalValues(int_type GID, int numValues, const double* values,
        bool suminto, int vectorIndex);

  //! Allocate the Map, Export object, and MultiVector for nonlocal data.
  template<typename int_type>
  void createNonlocalMapAndExporter();

  //! Deallocate the Map, Export object, and MultiVector for nonlocal data.
  void destroyNonlocalMapAndExporter();

  //! Make all the nonlocal multivector entries zero.
  template<typename int_type>
  void zeroNonlocalData();

  /// \brief Deallocate storage for nonlocal data.
  ///
  /// This does not include whatever \c destroyNonlocalMapAndExporter()
  /// deallocates.
  void destroyNonlocalData();

  long long myFirstID_;
  int myNumIDs_;

#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
  std::vector<int> nonlocalIDs_int_;
#endif
#ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
  std::vector<long long> nonlocalIDs_LL_;
#endif

  template<typename int_type> std::vector<int_type>& nonlocalIDs();

  std::vector<int> nonlocalElementSize_;

  /// \brief Array of arrays (one per column) of nonlocal coefficients.
  ///
  /// Entry j in this array is an array of nonlocal coefficients for
  /// column j of the multivector.  \c nonlocalCoefs_[j] in turn
  /// contains the data for all the nonlocal block entries.  Entries
  /// within a block are stored in column-major order (Fortran style),
  /// in contiguous chunks of \c Map().MaxElementSize() entries.
  ///
  /// In summary: for k = 0 to numNonlocalIDs_ - 1,
  /// nonlocalCoefs_[j][j*M + i] contains the entries of nonlocal
  /// block entry k, for i = 0 to nonlocalElementSize_[k] - 1.
  std::vector<std::vector<double> > nonlocalCoefs_;

  //! Map describing distribution of nonlocal data.
  Epetra_BlockMap* nonlocalMap_;

  //! Export object that sums nonlocal data into a nonoverlapping distribution.
  Epetra_Export* exporter_;

  //! Multivector that holds nonlocal data; source for the Export operation.
  Epetra_MultiVector* nonlocalVector_;

  bool ignoreNonLocalEntries_;

private:
  template<typename int_type>
  int GlobalAssemble(Epetra_CombineMode mode, bool reuse_map_and_exporter);
};

#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
template<> inline std::vector<int>& Epetra_FEVector::nonlocalIDs<int>()
{
   return nonlocalIDs_int_;
}
#endif

#ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
template<> inline std::vector<long long>& Epetra_FEVector::nonlocalIDs<long long>()
{
  return nonlocalIDs_LL_;
}
#endif

#endif