This file is indexed.

/usr/include/trilinos/MueLu_Hierarchy_decl.hpp is in libtrilinos-muelu-dev 12.12.1-5.

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
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
// @HEADER
//
// ***********************************************************************
//
//        MueLu: A package for multigrid based preconditioning
//                  Copyright 2012 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
//                    Jonathan Hu       (jhu@sandia.gov)
//                    Andrey Prokopenko (aprokop@sandia.gov)
//                    Ray Tuminaro      (rstumin@sandia.gov)
//
// ***********************************************************************
//
// @HEADER
#ifndef MUELU_HIERARCHY_DECL_HPP
#define MUELU_HIERARCHY_DECL_HPP

#include <Teuchos_ParameterList.hpp>
#include <Teuchos_Ptr.hpp>

#include <Xpetra_ConfigDefs.hpp>  // global_size_t
#include <Xpetra_Matrix_fwd.hpp>
#include <Xpetra_MultiVector_fwd.hpp>
#include <Xpetra_MultiVectorFactory_fwd.hpp>
#include <Xpetra_Operator_fwd.hpp>

#include <Xpetra_Cloner.hpp>
#include <MueLu_SmootherCloner.hpp>
#include "MueLu_ConfigDefs.hpp"
#include "MueLu_BaseClass.hpp"
#include "MueLu_Hierarchy_fwd.hpp"

#include "MueLu_Types.hpp"

#include "MueLu_FactoryBase_fwd.hpp"
#include "MueLu_FactoryManager.hpp" // no fwd declaration because constructor of FactoryManager is used as a default parameter of Setup()
#include "MueLu_HierarchyUtils_fwd.hpp"
#include "MueLu_KeepType.hpp"
#include "MueLu_Level_fwd.hpp"
#include "MueLu_MasterList.hpp"
#include "MueLu_NoFactory.hpp"
#include "MueLu_PerfUtils_fwd.hpp"
#include "MueLu_PFactory_fwd.hpp"
#include "MueLu_RFactory_fwd.hpp"
#include "MueLu_SmootherBase_fwd.hpp"
#include "MueLu_SmootherFactoryBase_fwd.hpp"
#include "MueLu_SmootherFactory_fwd.hpp"
#include "MueLu_TwoLevelFactoryBase_fwd.hpp"
#include "MueLu_Utilities_fwd.hpp"

namespace MueLu {

  enum ReturnType {
    Converged,
    Unconverged,
    Undefined
  };

  /*!
    @class Hierarchy
    @brief Provides methods to build a multigrid hierarchy and apply multigrid cycles.

    Allows users to manually populate operators at different levels within
    a multigrid method and push them into the hierarchy via SetLevel()
    and/or to supply factories for automatically generating prolongators,
    restrictors, and coarse level discretizations.  Additionally, this class contains
    an apply method that supports V and W cycles.
  */
  template <class Scalar        = Xpetra::Operator<>::scalar_type,
            class LocalOrdinal  = typename Xpetra::Operator<Scalar>::local_ordinal_type,
            class GlobalOrdinal = typename Xpetra::Operator<Scalar, LocalOrdinal>::global_ordinal_type,
            class Node          = typename Xpetra::Operator<Scalar, LocalOrdinal, GlobalOrdinal>::node_type>
  class Hierarchy : public BaseClass {
#undef MUELU_HIERARCHY_SHORT
#include "MueLu_UseShortNames.hpp"

    typedef Teuchos::ScalarTraits<SC> STS;
    typedef typename STS::magnitudeType MagnitudeType;

    //! Data struct for defining stopping criteria of multigrid iteration
    struct ConvData {
      ConvData()                              : maxIts_(1),       tol_(-STS::magnitude(STS::one())) { }
      ConvData(LO maxIts)                     : maxIts_(maxIts),  tol_(-STS::magnitude(STS::one())) { }
      ConvData(MagnitudeType tol)             : maxIts_(10000),   tol_(tol) { }
      ConvData(std::pair<LO,MagnitudeType> p) : maxIts_(p.first), tol_(p.second) { }

      LO            maxIts_;
      MagnitudeType tol_;
    };

  public:

    //! @name Constructors/Destructors
    //@{

    //! Default constructor.
    Hierarchy();

    //! Constructor
    Hierarchy(const RCP<Matrix> & A);

    //! Destructor.
    virtual ~Hierarchy() { }

    //@}

    //! @name Set/Get Methods.
    //@{

    //!
    static CycleType             GetDefaultCycle()                                     { return MasterList::getDefault<std::string>("cycle type") == "V" ? VCYCLE : WCYCLE; }
    static bool                  GetDefaultImplicitTranspose()                         { return MasterList::getDefault<bool>("transpose: use implicit");  }
    static Xpetra::global_size_t GetDefaultMaxCoarseSize()                             { return MasterList::getDefault<int>("coarse: max size");   }
    static int                   GetDefaultMaxLevels()                                 { return MasterList::getDefault<int>("max levels");     }
    static bool                  GetDefaultPRrebalance()                               { return MasterList::getDefault<bool>("repartition: rebalance P and R");   }

    Xpetra::global_size_t        GetMaxCoarseSize() const                              { return maxCoarseSize_; }
    bool                         GetImplicitTranspose() const                          { return implicitTranspose_; }

    void                         SetMaxCoarseSize(Xpetra::global_size_t maxCoarseSize) { maxCoarseSize_ = maxCoarseSize; }
    void                         SetPRrebalance(bool doPRrebalance)                    { doPRrebalance_ = doPRrebalance; }
    void                         SetImplicitTranspose(const bool& implicit)            { implicitTranspose_ = implicit; }

    //@}

    //!

    template<class S2, class LO2, class GO2, class N2>
    friend class Hierarchy;

  private:
    int  LastLevelID()      const { return Levels_.size() - 1; }
    void DumpCurrentGraph() const;

  public:

    //! Add a level at the end of the hierarchy
    void AddLevel(const RCP<Level> & level);

    //! Add a new level at the end of the hierarchy
    void AddNewLevel();

    //! Retrieve a certain level from hierarchy.
    RCP<Level> & GetLevel(const int levelID = 0);

    int    GetNumLevels() const;
    int    GetGlobalNumLevels() const;

    MagnitudeType GetRate() const { return rate_; }

    // This function is global
    double GetOperatorComplexity() const;

    // This function is global
    double GetSmootherComplexity() const;

    //! Helper function
    void CheckLevel(Level& level, int levelID);

    //! Multi-level setup phase: build a new level of the hierarchy.
    /*!  This method is aimed to be used in a loop building the hierarchy level by level. See Hierarchy::Setup(manager, startLevel, numDesiredLevels) for an example of usage.
     *
     *   @param coarseLevelID ID of the level to be built.
     *   @param fineLevelManager defines how to build missing data of the fineLevel (example: aggregates)
     *   @param coarseLevelManager defines how to build the level
     *   @param nextLevelManager defines how the next coarse level will be built. This is used to post corresponding request before building the coarse level to keep useful data.

     CoarseLevel is considered to be the last level if:
      - input parameter isLastLevel == true
      or
      - Ac->getRowMap()->getGlobalNumElements() <= maxCoarseSize_
     Method return true if CoarseLevel is the last level.

     Pre-condition:
      * FineLevel:
         - must have kept useful data (TODO: not tested yet)
         - must be Teuchos::null when Setup is called for finest level (Setup then automatically calls Request for "Smoother" and "CoarseSolver")
      * CoarseLevel:
         - already allocated (using Hierarchy::AddLevel())
         - requests already posted
           (exception: for finest level (=fineLevelManager==null) requests are called within setup routine)
      * NextLevel:
         - do not need to be allocate but could (FIXME: will be deleted if lastlevel...).
         - should be null when Setup is called for last level

     Post-condition:
      * FineLevel:
         - temporary data have been used and released (this condition is not tested)
      * CoarseLevel:
         - built, requests have been used
         - if it is the last level (due to input parameter isLastLevel or getGlobalNumElements() <= maxCoarseSize_),
           then the coarse solver factory of the factory manager have been used instead of the smoother factory.
      * NextLevel:
        If input parameter isLastLevel == false:
         - have been allocated
         - requests already posted.
    */
    bool Setup(int coarseLevelID, const RCP<const FactoryManagerBase> fineLevelManager /* = Teuchos::null */, const RCP<const FactoryManagerBase> coarseLevelManager,
               const RCP<const FactoryManagerBase> nextLevelManager = Teuchos::null);

    //!
    void Setup(const FactoryManagerBase& manager = FactoryManager(), int startLevel = 0, int numDesiredLevels = GetDefaultMaxLevels());

    void SetupRe();

    //! Clear impermanent data from previous setup
    void Clear(int startLevel = 0);
    void ExpertClear();

    //! Returns multigrid cycle type (supports VCYCLE and WCYCLE)
    CycleType GetCycle()                 const { return Cycle_;  }

    //! Supports VCYCLE and WCYCLE types.
    void      SetCycle(CycleType Cycle)        { Cycle_ = Cycle; }

    //! Specify damping factor alpha such that x = x + alpha*P*c, where c is the coarse grid correction.
    void SetProlongatorScalingFactor(double scalingFactor) { scalingFactor_ = scalingFactor; }

    /*!
      @brief Apply the multigrid preconditioner.

      In theory, more general cycle types than just V- and W-cycles are possible.  However,
      the enumerated type CycleType would have to be extended.

      @param B right-hand side of linear problem
      @param X initial and final (approximate) solution of linear problem
      @param ConvData struct which stores convergence criteria (maximum number of multigrid iterations or stopping tolerance)
      @param InitialGuessIsZero Indicates whether the initial guess is zero
      @param startLevel index of starting level to build multigrid hierarchy (default = 0)
    */
    ReturnType Iterate(const MultiVector& B, MultiVector& X, ConvData conv = ConvData(),
                       bool InitialGuessIsZero = false, LO startLevel = 0);

    /*!
      @brief Print matrices in the multigrid hierarchy to file.

      @param[in] start start level
      @param[in] end   end level

      Default behavior is to print system and transfer matrices from the entire hierarchy.
      Files are named "A_0.m", "P_1.m", "R_1.m", etc, and are in matrix market coordinate format.
    */
    void Write(const LO &start=-1, const LO &end=-1, const std::string &suffix="");

    //@}

    //! @name Permanent storage
    //@{

    //! Call Level::Keep(ename, factory) for each level of the Hierarchy.
    void Keep(const std::string & ename, const FactoryBase* factory = NoFactory::get());

    //! Call Level::Delete(ename, factory) for each level of the Hierarchy.
    void Delete(const std::string& ename, const FactoryBase* factory = NoFactory::get());

    //! Call Level::AddKeepFlag for each level of the Hierarchy.
    void AddKeepFlag(const std::string & ename, const FactoryBase* factory = NoFactory::get(), KeepType keep = MueLu::Keep);

    //! Call Level::RemoveKeepFlag for each level of the Hierarchy
    void RemoveKeepFlag(const std::string & ename, const FactoryBase* factory, KeepType keep = MueLu::All);

    //@}

    //! @name Overridden from Teuchos::Describable
    //@{

    //! Return a simple one-line description of this object.
    std::string description() const; 

    /*! @brief Print the Hierarchy with some verbosity level to a FancyOStream object.

        @param[in] out The Teuchos::FancyOstream.
        @param[in] verbLevel Controls amount of output.
    */
    void describe(Teuchos::FancyOStream& out, const VerbLevel verbLevel = Default) const;
    void describe(Teuchos::FancyOStream& out, const Teuchos::EVerbosityLevel verbLevel = Teuchos::VERB_HIGH) const;

    // Hierarchy::print is local hierarchy function, thus the statistics can be different from global ones
    void print(std::ostream& out = std::cout, const VerbLevel verbLevel = (MueLu::Parameters | MueLu::Statistics0)) const;

    /*! Indicate whether the multigrid method is a preconditioner or a solver.

      This is used in conjunction with the verbosity level to determine whether the residuals can be printed.
    */
    void IsPreconditioner(const bool flag);

    //@}

    void EnableGraphDumping(const std::string& filename, int levelID = 1) {
      isDumpingEnabled_ = true;
      dumpLevel_ = levelID;
      dumpFile_  = filename;
    }

    template<class Node2>
    Teuchos::RCP< Hierarchy<Scalar, LocalOrdinal, GlobalOrdinal, Node2> >
    clone (const RCP<Node2> &node2) const;

    void setlib(Xpetra::UnderlyingLib inlib) { lib_ = inlib; }
    Xpetra::UnderlyingLib lib() { return lib_; }

    // force recreation of cached description_ next time description() is called: 
    void ResetDescription() {
      description_ = "";
    }
  protected:
    const RCP<const FactoryManagerBase>& GetLevelManager(const int levelID) const {
      return levelManagers_[levelID];
    }

  private:
    //! Copy constructor is not implemented.
    Hierarchy(const Hierarchy &h);

    //! Container for Level objects
    Array<RCP<Level> > Levels_;

    // We replace coordinates GIDs to make them consistent with matrix GIDs,
    // even if user does not do that.  Ideally, though, we should completely
    // remove any notion of coordinate GIDs, and deal only with LIDs, assuming
    // that they are consistent with matrix block IDs
    void ReplaceCoordinateMap(Level& level);

    // Minimum size of a matrix on any level. If we fall below that, we stop
    // the coarsening
    Xpetra::global_size_t maxCoarseSize_;

    // Potential speed up of the setup by skipping R construction, and using
    // transpose matrix-matrix product for RAP
    bool implicitTranspose_;

    // Potential speed up of the setup by skipping rebalancing of P and R, and
    // doing extra import during solve
    bool doPRrebalance_;

    // Hierarchy may be used in a standalone mode, or as a preconditioner
    bool isPreconditioner_;

    // V- or W-cycle
    CycleType Cycle_;

    // Scaling factor to be applied to coarse grid correction.
    double scalingFactor_;

    // Epetra/Tpetra mode
    Xpetra::UnderlyingLib lib_;

    // cache description to avoid recreating in each call to description() - use ResetDescription() to force recreation in Setup, SetupRe, etc.
    mutable std::string description_ = ""; // mutable so that we can lazily initialize in description(), which is declared const

    //! Graph dumping
    // If enabled, we dump the graph on a specified level into a specified file
    bool isDumpingEnabled_;
    int  dumpLevel_;
    std::string dumpFile_;

    //! Convergece rate
    MagnitudeType rate_;

    // Level managers used during the Setup
    Array<RCP<const FactoryManagerBase> > levelManagers_;

  }; //class Hierarchy

  template<class Scalar, class LocalOrdinal, class GlobalOrdinal, class Node>
  template<typename Node2>
  Teuchos::RCP<Hierarchy<Scalar, LocalOrdinal, GlobalOrdinal, Node2> >
  Hierarchy<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
  clone (const Teuchos::RCP<Node2> &node2) const {
    typedef Hierarchy<Scalar, LocalOrdinal, GlobalOrdinal, Node2>           New_H_Type;
    typedef Xpetra::Matrix<Scalar, LocalOrdinal, GlobalOrdinal, Node2>      CloneOperator;
    typedef MueLu::SmootherBase<Scalar, LocalOrdinal, GlobalOrdinal, Node2> CloneSmoother;

    Teuchos::RCP<New_H_Type> new_h = Teuchos::rcp(new New_H_Type());
    new_h->Levels_.resize(this->GetNumLevels());
    new_h->maxCoarseSize_     = maxCoarseSize_;
    new_h->implicitTranspose_ = implicitTranspose_;
    new_h->isPreconditioner_  = isPreconditioner_;
    new_h->isDumpingEnabled_  = isDumpingEnabled_;
    new_h->dumpLevel_         = dumpLevel_;
    new_h->dumpFile_          = dumpFile_;

    RCP<SmootherBase>  Pre, Post;
    RCP<CloneSmoother> clonePre, clonePost;
    RCP<CloneOperator> cloneA, cloneR, cloneP;
    RCP<Operator>      A, R, P;
    for (int i = 0; i < GetNumLevels(); i++) {
      RCP<Level> level      = this->Levels_[i];
      RCP<Level> clonelevel = rcp(new Level());

      if (level->IsAvailable("A")) {
        A      = level->template Get<RCP<Operator> >("A");
        cloneA = Xpetra::clone<Scalar, LocalOrdinal, GlobalOrdinal, Node, Node2>(*A, node2);
        clonelevel->template Set<RCP<CloneOperator> >("A", cloneA);
      }
      if (level->IsAvailable("R")){
        R      = level->template Get<RCP<Operator> >("R");
        cloneR = Xpetra::clone<Scalar, LocalOrdinal, GlobalOrdinal, Node, Node2>(*R, node2);
        clonelevel->template Set<RCP<CloneOperator> >("R", cloneR);
      }
      if (level->IsAvailable("P")){
        P      = level->template Get<RCP<Operator> >("P");
        cloneP = Xpetra::clone<Scalar, LocalOrdinal, GlobalOrdinal, Node, Node2>(*P,  node2);
        clonelevel->template Set<RCP<CloneOperator> >("P", cloneP);
      }
      if (level->IsAvailable("PreSmoother")){
        Pre      = level->template Get<RCP<SmootherBase> >("PreSmoother");
        clonePre = MueLu::clone<Scalar, LocalOrdinal, GlobalOrdinal, Node, Node2> (Pre, cloneA, node2);
        clonelevel->template Set<RCP<CloneSmoother> >("PreSmoother", clonePre);
      }
      if (level->IsAvailable("PostSmoother")){
        Post      = level->template Get<RCP<SmootherBase> >("PostSmoother");
        clonePost = MueLu::clone<Scalar, LocalOrdinal, GlobalOrdinal, Node, Node2> (Post, cloneA, node2);
        clonelevel-> template Set<RCP<CloneSmoother> >("PostSmoother", clonePost);
      }
      new_h->Levels_[i] = clonelevel;
    }

    return new_h;
  }

} //namespace MueLu

#define MUELU_HIERARCHY_SHORT
#endif // MUELU_HIERARCHY_DECL_HPP