This file is indexed.

/usr/include/trilinos/Rythmos_ImplicitRKStepper_decl.hpp is in libtrilinos-rythmos-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
//@HEADER
// ***********************************************************************
//
//                           Rythmos Package
//                 Copyright (2006) 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.
//
// This library is free software; you can redistribute it and/or modify
// it under the terms of the GNU Lesser General Public License as
// published by the Free Software Foundation; either version 2.1 of the
// License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
// USA
// Questions? Contact Todd S. Coffey (tscoffe@sandia.gov)
//
// ***********************************************************************
//@HEADER

#ifndef Rythmos_IMPLICIT_RK_STEPPER_DECL_H
#define Rythmos_IMPLICIT_RK_STEPPER_DECL_H

#include "Rythmos_Types.hpp"
#include "Rythmos_StepperBase.hpp"
#include "Rythmos_DataStore.hpp"
#include "Rythmos_SolverAcceptingStepperBase.hpp"
#include "Rythmos_RKButcherTableauAcceptingStepperBase.hpp"
#include "Rythmos_RKButcherTableauBase.hpp"
#include "Rythmos_StepControlStrategyAcceptingStepperBase.hpp"
#include "Rythmos_StepControlStrategyBase.hpp"

#include "Thyra_ModelEvaluator.hpp"
#include "Thyra_ProductVectorBase.hpp"
#include "Thyra_NonlinearSolverBase.hpp"

namespace Rythmos {


/** \brief . */
template<class Scalar>
class ImplicitRKStepper : 
  virtual public SolverAcceptingStepperBase<Scalar>,
  virtual public RKButcherTableauAcceptingStepperBase<Scalar>,
  virtual public StepControlStrategyAcceptingStepperBase<Scalar>
{
public:
  
  /** \brief . */
  typedef typename ScalarTraits<Scalar>::magnitudeType ScalarMag;
  
  /** \name Constructors, intializers, Misc. */
  //@{

  /** \brief . */
  ImplicitRKStepper();
  
  void set_W_factory( const RCP<Thyra::LinearOpWithSolveFactoryBase<Scalar> > &irk_W_factory );

  /** \brief . */
  RCP<const Thyra::LinearOpWithSolveFactoryBase<Scalar> > get_W_factory() const;
  
  /** \name Overridden from RKButcherTableauAcceptingStepperBase */
  //@{
  
  /** \brief . */
  void setRKButcherTableau( const RCP<const RKButcherTableauBase<Scalar> > &rkButcherTableau );

  /** \brief . */
  RCP<const RKButcherTableauBase<Scalar> > getRKButcherTableau() const;

  //@}

  /** \brief . */
  // This function is mostly for testing purposes to explicitely over-ride the
  // internal RKBT detection to allow testing of 1-stage RKBTs as both fully
  // implicit RK and as DIRK methods.
  void setDirk(bool isDirk);

  //@}
  
  /** \name Overridden from SolverAcceptingStepperBase */
  //@{

  /** \brief . */
  void setSolver(
    const RCP<Thyra::NonlinearSolverBase<Scalar> > &solver
    );

  /** \brief . */
  RCP<Thyra::NonlinearSolverBase<Scalar> >
  getNonconstSolver();

  /** \brief . */
  RCP<const Thyra::NonlinearSolverBase<Scalar> >
  getSolver() const;

  //@}

  /** \name Overridden from StepperBase */
  //@{

  /** \brief Returns true. */
  bool isImplicit() const;
 
  /** \brief Returns true. */
  bool supportsCloning() const;

  /** \brief . */
  RCP<StepperBase<Scalar> > cloneStepperAlgorithm() const;

  /** \brief . */
  void setModel(const RCP<const Thyra::ModelEvaluator<Scalar> >& model);

  /** \brief . */
  void setNonconstModel(const RCP<Thyra::ModelEvaluator<Scalar> >& model);
  
  /** \brief . */
  RCP<const Thyra::ModelEvaluator<Scalar> > getModel() const;

  /** \brief . */
  RCP<Thyra::ModelEvaluator<Scalar> > getNonconstModel();

  /** \brief . */
  void setInitialCondition(
    const Thyra::ModelEvaluatorBase::InArgs<Scalar> &initialCondition
    );

  /** \brief . */
  Thyra::ModelEvaluatorBase::InArgs<Scalar> getInitialCondition() const;

  /** \brief . */

  Scalar takeStep(Scalar dt, StepSizeType flag);
  
  /** \brief . */
  const StepStatus<Scalar> getStepStatus() const;
 
  /** \name Overridden from StepControlStrategyAcceptingStepperBase */
  //@{

  /** \brief . */
  void setStepControlStrategy(
      const RCP<StepControlStrategyBase<Scalar> >& stepControlStrategy
      );

  /** \brief . */
  RCP<StepControlStrategyBase<Scalar> > 
    getNonconstStepControlStrategy();
  
  /** \brief . */
  RCP<const StepControlStrategyBase<Scalar> >
    getStepControlStrategy() const;
  
  //@}

 
  //@}

  /** \name Overridden from InterpolationBufferBase */
  //@{

  /** \brief . */
  RCP<const Thyra::VectorSpaceBase<Scalar> >
  get_x_space() const;

  /** \brief . */
  void addPoints(
    const Array<Scalar>& time_vec,
    const Array<RCP<const Thyra::VectorBase<Scalar> > >& x_vec,
    const Array<RCP<const Thyra::VectorBase<Scalar> > >& xdot_vec
    );
  
  /** \brief . */
  TimeRange<Scalar> getTimeRange() const;
  
  /** \brief . */
  void getPoints(
    const Array<Scalar>& time_vec,
    Array<RCP<const Thyra::VectorBase<Scalar> > >* x_vec,
    Array<RCP<const Thyra::VectorBase<Scalar> > >* xdot_vec,
    Array<ScalarMag>* accuracy_vec
    ) const;
  
  /** \brief . */
  void getNodes(Array<Scalar>* time_vec) const;
  
  /** \brief . */
  void removeNodes(Array<Scalar>& time_vec);

  /** \brief . */
  int getOrder() const;

  //@}
  
  /** \name Overridden from Teuchos::ParameterListAcceptor */
  //@{

  /** \brief . */
  void setParameterList(RCP<ParameterList> const& paramList);
  
  /** \brief . */
  RCP<ParameterList> getNonconstParameterList();
  
  /** \brief . */
  RCP<ParameterList> unsetParameterList();
  
  /** \brief. */
  RCP<const ParameterList> getValidParameters() const;
 
  //@}

  /** \name Overridden from Teuchos::Describable */
  //@{
  
  /** \brief . */
  void describe(
    FancyOStream  &out,
    const Teuchos::EVerbosityLevel verbLevel
    ) const;

  //@}

  /** \brief . */
  bool isEmbeddedRK_ = false; // Sidafa

private:

  // ///////////////////////
  // Private date members

  bool isInitialized_;
  RCP<const Thyra::ModelEvaluator<Scalar> > model_;
  RCP<Thyra::NonlinearSolverBase<Scalar> > solver_;
  RCP<Thyra::LinearOpWithSolveFactoryBase<Scalar> > irk_W_factory_;
  RCP<ParameterList> paramList_;

  Thyra::ModelEvaluatorBase::InArgs<Scalar> basePoint_;
  RCP<Thyra::VectorBase<Scalar> > x_;
  RCP<Thyra::VectorBase<Scalar> > x_old_;
  RCP<Thyra::VectorBase<Scalar> > x_dot_;
  RCP<Thyra::VectorBase<Scalar> > oldSolution_; // Sidafa
  EStepLETStatus stepLETStatus_; // Local Error Test Status (Sidafa)
  RCP<Thyra::VectorBase<Scalar> > xhat_; // Embedded solution (Sidafa)
  RCP<Thyra::VectorBase<Scalar> > ee_; // error (Sidafa) 

  TimeRange<Scalar> timeRange_;

  RCP<Thyra::ModelEvaluator<Scalar> > irkModel_;
  RCP<const RKButcherTableauBase<Scalar> > irkButcherTableau_;

  bool isDirk_; // Used for Diagonal Implicit RK 
  bool isVariableStep_ = false;

  int numSteps_;
  Scalar LETvalue_;   // ck * e

  bool haveInitialCondition_;

  // Sidafa 9/4/15
  Thyra::SolveStatus<Scalar> nonlinearSolveStatus_;
  int rkNewtonConvergenceStatus_;
  RCP<Rythmos::StepControlStrategyBase<Scalar> > stepControl_;

  // Cache
  RCP<Thyra::ProductVectorBase<Scalar> > x_stage_bar_;

  // //////////////////////////
  // Private member functions

  void defaultInitializeAll_();
  void initialize_();

  Scalar takeVariableStep_(Scalar dt, StepSizeType flag);

  Scalar takeFixedStep_(Scalar dt, StepSizeType flag);

  

};


/** \brief Nonmember constructor.
 *
 * \relates ImplicitRKStepper
 */
template<class Scalar>
RCP<ImplicitRKStepper<Scalar> >
implicitRKStepper();

template<class Scalar>
RCP<ImplicitRKStepper<Scalar> >
implicitRKStepper(
  const RCP<const Thyra::ModelEvaluator<Scalar> >& model,
  const RCP<Thyra::NonlinearSolverBase<Scalar> >& solver,
  const RCP<Thyra::LinearOpWithSolveFactoryBase<Scalar> >& irk_W_factory,
  const RCP<const RKButcherTableauBase<Scalar> >& irkbt
  );


} // namespace Rythmos

#endif //Rythmos_IMPLICIT_RK_STEPPER_DECL_H