This file is indexed.

/usr/include/trilinos/ml_MatrixFreePreconditioner.h is in libtrilinos-ml-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
/* ******************************************************************** */
/* See the file COPYRIGHT for a complete copyright notice, contact      */
/* person and disclaimer.                                               */
/* ******************************************************************** */
#ifndef ML_MATRIX_FREE_PRECONDITIONER
#define ML_MATRIX_FREE_PRECONDITIONER

/*!
 * \file ml_MatrixFreePreconditioner.h
 *
 * \class MatrixFreePreconditioner
 *
 * \brief ML preconditioner for Matrix-Free operators
 *
 * \author Marzio Sala, ETHZ/D-INFK
 *
 * \date Last update to Doxygen: 01-Apr-06
 *
 */

#include "ml_include.h"
#if defined(HAVE_ML_EPETRA) && defined(HAVE_ML_TEUCHOS) && defined(HAVE_ML_EPETRAEXT) && defined(HAVE_ML_IFPACK)
#include <string>
#include "ml_epetra.h"
#include "Epetra_Time.h"
#include "Epetra_Operator.h"
#include "Epetra_Comm.h"
#include "Epetra_CrsMatrix.h"
#include "Teuchos_ParameterList.hpp"
#include "Teuchos_RefCountPtr.hpp"
#include <vector>
#include <map>
#include "ml_MultiLevelPreconditioner.h"

class Epetra_Map;
class Epetra_BlockMap;
class Epetra_CrsGraph;
class Epetra_Vector;
class Epetra_MultiVector;
class Epetra_RowMatrix;
class Epetra_FECrsMatrix;
class Ifpack_Chebyshev;

namespace ML_Epetra {

class MultiLevelPreconditioner;

/*!
\brief MatrixFreePreconditioner: a class to define preconditioners for Epetra_Operator's

This file requires ML to be configured with the following options:
- \c --enable-epetra
- \c --enable-epetraext
- \c --enable-teuchos

The following options are suggested:
- \c --enable-amesos
- \c --enable-ifpack

This class does not support Maxwell problems. It has been tested on symmetric problems; however it can in principle be used with non-symmetric problems as well.

\author Marzio Sala, ETHZ/D-INFK
*/
class MatrixFreePreconditioner : public Epetra_Operator
{
  public:
    //@{ \name Constructors and destructors.

    //! Constructor
    MatrixFreePreconditioner(const Epetra_Operator& Operator,
                             const Epetra_CrsGraph& Graph,
                             Epetra_MultiVector& NullSpace,
                             const Epetra_Vector& PointDiagonal,
                             Teuchos::ParameterList& List);

    //! destructor
    virtual ~MatrixFreePreconditioner();

    // @}
    // @{ \name Query methods.

    //! Sets the use of the transpose of the operator (NOT SUPPORTED).
    int SetUseTranspose(bool UseTranspose);

    //! Applies the operator to a std::vector (NOT SUPPORTED).
    int Apply(const Epetra_MultiVector& X, Epetra_MultiVector& Y) const;

    //! Applies the preconditioner to std::vector \c X, returns the result in \c Y.
    int ApplyInverse(const Epetra_MultiVector& X, Epetra_MultiVector& Y) const;

    //! Returns the infinite norm of the operator (NOT SUPPORTED).
    double NormInf() const
    {
      return(-1.0);
    }

    //! Returns the label of \c this operator.
    const char * Label() const
    {
      return(Label_.c_str());
    }

    //! Returns \c true if the tranpose of the operator is considerd (NOT SUPPORTED).
    bool UseTranspose() const
    {
      return(false);
    }

    //! Returns \c false.
    bool HasNormInf() const
    {
      return(false);
    }

    //! Returns a reference to the communicator object.
    const Epetra_Comm& Comm() const
    {
      return(Comm_);
    }

    //! Returns the domain map of the operator.
    const Epetra_Map & OperatorDomainMap() const
    {
      return(Operator_.OperatorDomainMap());
    }

    //! Returns the range map of the operator.
    const Epetra_Map & OperatorRangeMap() const
    {
      return(Operator_.OperatorRangeMap());
    }

    //! Returns the coarser-level operator as an Epetra_RowMatrix.
    const Epetra_RowMatrix& C() const
    {
      if (!IsComputed())
        throw(-1); // prec not computed yet

      return(*C_);
    }

    const MultiLevelPreconditioner& MLP() const
    {
      if (!IsComputed())
        throw(-1); // prec not computed yet

      return(*MLP_);
    }

    //! Returns the restriction operator as an Epetra_CrsMatrix.
    const Epetra_CrsMatrix& R() const
    {
      return(*R_);
    }

    //! Returns the ML communicator of \c this object.
    ML_Comm* Comm_ML()
    {
      return(Comm_ML_);
    }

    //! Returns the PID of the calling processor.
    inline int MyPID() const
    {
      return(Comm().MyPID());
    }

    //! Returns the number of processors in the communicator.
    inline int NumProc() const
    {
      return(Comm().NumProc());
    }

    //! Returns \c true if the preconditioner has been successfully computed.
    bool IsComputed() const
    {
      return(IsComputed_);
    }

    //! Returns the total CPU time spent in \c this class.
    double TotalCPUTime() const;

    bool CheckSPD(const Epetra_Operator& Op,
                  const bool UseApply = true,
                  const int NumChecks = 1,
                  const int NumVectors = 1) const;

    // @}
    // @{ \name Construction methods.

    //! Performs coarsening for a given operator \c A.
    int Coarsen(ML_Operator* A, ML_Aggregate** aggr, ML_Operator** P,
                ML_Operator** R, ML_Operator** C, int NumPDEEqns = 1,
                int NullSpaceDim = 1, double* NullSpace = NULL);

    //! Probes for the block diagonal of the given operator.
    int GetBlockDiagonal(const Epetra_CrsGraph& Graph, std::string DiagonalColoringType);

  private:

    //! Computes the preconditioner.
    int Compute(const Epetra_CrsGraph& Graph, Epetra_MultiVector& NullSpace);

    // @}
    // @{ \name Basic smoothers

    //! Applies the pre-smoother (using zero starting solution).
    int ApplyPreSmoother(Epetra_MultiVector& X) const;

    //! Applies the post-smoother (using non-zero starting solution).
    int ApplyPostSmoother(Epetra_MultiVector& X, const Epetra_MultiVector& Y,
                          Epetra_MultiVector& tmp) const;

    //! Applies one sweep of Jacobi to std::vector \c X.
    int ApplyJacobi(Epetra_MultiVector& X, const double omega) const;

    //! Applies one sweep of Jacobi to std::vector \c X, using \c X as starting solution.
    int ApplyJacobi(Epetra_MultiVector& X, const Epetra_MultiVector& B,
                    const double omega, Epetra_MultiVector& tmp) const;

    //! Applies one sweep of block Jacobi to std::vector \c X.
    int ApplyBlockJacobi(Epetra_MultiVector& X, const double omega) const;

    //! Applies one sweep of block Jacobi to std::vector \c X, using \c X as starting solution.
    int ApplyBlockJacobi(Epetra_MultiVector& X, const Epetra_MultiVector& B,
                    const double omega, Epetra_MultiVector& tmp) const;

    int ApplyInvBlockDiag(const double alpha, Epetra_MultiVector& X,
                          const double gamma, const Epetra_MultiVector& B) const;

    // @}
    // @{ \name Timing

    inline void ResetStartTime() const
    {
      Time_->ResetStartTime();
    }

    inline void AddAndResetStartTime(const std::string& Label, const int print = false) const
    {
      TimeTable[Label] += Time_->ElapsedTime();
      Time_->ResetStartTime();
      if (print)
      {
        if (MyPID() == 0 && ML_Get_PrintLevel() > 5)
          std::cout << "Time for " << Label << " = " << TimeTable[Label] << " (s)" << std::endl;
      }
    }

    void PrintTimings() const
    {
      if (MyPID() == 0)
      {
        double Total = 0.0;
        std::cout << "Cumulative timing so far:" << std::endl;
        std::cout << "- for coarsening = " << TimeTable["coarsening"] << std::endl;
        std::cout << "- total time     = " << Total << std::endl;
      }
    }

    // @}
    // @{ \name Private data

    //! Toggles output level.
    bool verbose_;
    //! Communicator for ML.
    ML_Comm* Comm_ML_;
    //! Communicator object for Epetra.
    const Epetra_Comm& Comm_;

    //! Label of this object
    std::string Label_;
    //! Set to \c true if the preconditioner has been successfully computed.
    bool IsComputed_;
    //! Type of preconditioner (additive or hybrid)
    int PrecType_;
    //! Type of smoother (Jacobi, block Jacobi, or Chebyshev)
    int SmootherType_;
    //! Damping parameter for Jacobi.
    double omega_;
    //! List containing all the parameters
    Teuchos::ParameterList List_;

    //! Fine-level operator
    const Epetra_Operator& Operator_;
    //! Inverse of the point diagonal of the operator.
    Teuchos::RefCountPtr<Epetra_Vector> InvPointDiagonal_;
    //! Inverse of the diagonal of \c Operator_ as provided by the user.
    std::vector<double> InvBlockDiag_;

    //! Presmoother
    Teuchos::RefCountPtr<Ifpack_Chebyshev> PreSmoother_;
    //! Presmoother
    Teuchos::RefCountPtr<Ifpack_Chebyshev> PostSmoother_;
    //! Restriction from fine to coarse.
    Teuchos::RefCountPtr<Epetra_CrsMatrix> R_;
    //! Coarser-level operator as an Epetra_RowMatrix (wrapper for C_ML_).
    Teuchos::RefCountPtr<Epetra_RowMatrix> C_;
    //! Coarser-level operator as an ML_Operator.
    ML_Operator* C_ML_;
    //! Preconditioner that approximates the inverse of \c C_.
    Teuchos::RefCountPtr<MultiLevelPreconditioner> MLP_;

    //! Number of PDE equations
    int NumPDEEqns_;
    int NumMyBlockRows_;

    //! Time object.
    mutable Teuchos::RefCountPtr<Epetra_Time> Time_;
    mutable std::map<std::string, double> TimeTable;
    // @}

}; // class MatrixFreePreconditioner

} // namespace ML_Epetra

#endif // HAVE_ML_EPETRA
#endif // ML_MATRIX_FREE_PRECONDITIONER