This file is indexed.

/usr/include/trilinos/LOCA_Stepper.H is in libtrilinos-nox-dev 12.10.1-3.

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
// $Id$
// $Source$

//@HEADER
// ************************************************************************
//
//            LOCA: Library of Continuation Algorithms Package
//                 Copyright (2005) 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.
//
// 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 Roger Pawlowski (rppawlo@sandia.gov) or
// Eric Phipps (etphipp@sandia.gov), Sandia National Laboratories.
// ************************************************************************
//  CVS Information
//  $Source$
//  $Author$
//  $Date$
//  $Revision$
// ************************************************************************
//@HEADER

#ifndef LOCA_STEPPER_H
#define LOCA_STEPPER_H

#include "Teuchos_RCP.hpp"

#include "LOCA_Abstract_Iterator.H"    // base class
#include "Teuchos_ParameterList.hpp"           // class data element
#include "NOX_Solver_Generic.H"           // class data element
#include "NOX_StatusTest_Generic.H"    // for enum StatusType
#include "NOX_Common.H"                // for <string> class
#include "LOCA_StatusTest_Abstract.H"  // for LOCA::StatusTest::Abstract

// taken fron /packages/isorropia/src/
#ifndef __deprecated
#if (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
#define __deprecated  __attribute__((__deprecated__))
#else
#define __deprecated
#endif /* __GNUC__ */
#endif /* __deprecated */


// forward declarations
namespace LOCA {
  class GlobalData;
  namespace MultiContinuation {
    class AbstractStrategy;
    class AbstractGroup;
    class ExtendedVector;
  }
  namespace MultiPredictor {
    class AbstractStrategy;
  }
  namespace Eigensolver {
    class AbstractStrategy;
  }
  namespace SaveEigenData {
    class AbstractStrategy;
  }
  namespace StepSize {
    class AbstractStrategy;
  }
  namespace Parameter {
    class SublistParser;
  }
}

namespace LOCA {

  /*!
   * \brief Implementation of LOCA::Abstract::Iterator for computing points
   * along a continuation curve.
   */
  /*!
   * The %Stepper class implements the pure virtual methods of the
   * LOCA::Abstract::Iterator for iteratively computing points along a
   * continuation curve.
   */

  class Stepper : public LOCA::Abstract::Iterator {

  public:

    //! Constructor with LOCA::StatusTest
    Stepper(const Teuchos::RCP<LOCA::GlobalData>& global_data,
        const Teuchos::RCP<LOCA::MultiContinuation::AbstractGroup>& initialGuess,
            const Teuchos::RCP<LOCA::StatusTest::Abstract>& lt,
        const Teuchos::RCP<NOX::StatusTest::Generic>& nt,
        const Teuchos::RCP<Teuchos::ParameterList>& p);

    //! Obsolete constructor without LOCA::StatusTest.
    //! @deprecated Use the constructor with LOCA::StatusTest instead.
//    __deprecated // TODO mark as deprecated as soon as all tests are implemented
    Stepper(const Teuchos::RCP<LOCA::GlobalData>& global_data,
            const Teuchos::RCP<LOCA::MultiContinuation::AbstractGroup>& initialGuess,
            const Teuchos::RCP<NOX::StatusTest::Generic>& nt,
            const Teuchos::RCP<Teuchos::ParameterList>& p);

    //! Destructor
    virtual ~Stepper();

    //! Reset the Stepper to start a new continuation run.
    //! Version with LOCA::StatusTest
    virtual bool
    reset(const Teuchos::RCP<LOCA::GlobalData>& global_data,
      const Teuchos::RCP<LOCA::MultiContinuation::AbstractGroup>& initialGuess,
          const Teuchos::RCP<LOCA::StatusTest::Abstract>& lt,
      const Teuchos::RCP<NOX::StatusTest::Generic>& nt,
      const Teuchos::RCP<Teuchos::ParameterList>& p);

    //! Reset the Stepper to start a new continuation run.
    //! Obsolete version without LOCA::StatusTest.
    //! @deprecated Use reset() with LOCA::StatusTest instead.
//    __deprecated // TODO mark as deprecated as soon as all tests are implemented
    virtual bool
    reset(const Teuchos::RCP<LOCA::GlobalData>& global_data,
          const Teuchos::RCP<LOCA::MultiContinuation::AbstractGroup>& initialGuess,
          const Teuchos::RCP<NOX::StatusTest::Generic>& nt,
          const Teuchos::RCP<Teuchos::ParameterList>& p);

    //! Replaces the eigensolver parameter list.
    bool
    eigensolverReset( Teuchos::RCP<Teuchos::ParameterList> & newEigensolverList );

    //! Return the current solution group.
    virtual Teuchos::RCP<const LOCA::MultiContinuation::AbstractGroup>
    getSolutionGroup() const;

    //! Return the current bifurcation group.
    /*!
     * If the current bifurcation method is "None", then the returned group
     * is the same as getSolutionGroup(), otherwise this method returns the
     * current bifurcation group (e.g., a turning point group).
     */
    virtual Teuchos::RCP<const LOCA::MultiContinuation::AbstractGroup>
    getBifurcationGroup() const;

    //! Return the output parameters from the stepper algorithm.
    virtual Teuchos::RCP<const Teuchos::ParameterList>
    getList() const;

    /*! @brief Return the current nonlinear solver pointer.
     *
     * Will throw an error if the solver does not exist yet.
     */
    virtual Teuchos::RCP<const NOX::Solver::Generic>
    getSolver() const;

    /*! @brief Return the current continuation parameter from the underlying LOCA::MultiContinuation::AbstractStrategy.
     *
     */
    virtual double
    getContinuationParameter() const;

  protected:

    //! Initialize iterator
    virtual LOCA::Abstract::Iterator::IteratorStatus start();

    //! Finalize iterator
    virtual LOCA::Abstract::Iterator::IteratorStatus
    finish(LOCA::Abstract::Iterator::IteratorStatus iteratorStatus);

    //! Preprocess step
    virtual LOCA::Abstract::Iterator::StepStatus
    preprocess(LOCA::Abstract::Iterator::StepStatus stepStatus);

    //! Compute step
    virtual LOCA::Abstract::Iterator::StepStatus
    compute(LOCA::Abstract::Iterator::StepStatus stepStatus);

    //! Postprocess step
    virtual LOCA::Abstract::Iterator::StepStatus
    postprocess(LOCA::Abstract::Iterator::StepStatus stepStatus);

    //! Wrapper method for stopping criteria checks
    virtual LOCA::Abstract::Iterator::IteratorStatus
    stop(LOCA::Abstract::Iterator::StepStatus stepStatus);

    //! Check stopping criteria using LOCA::StatusTest.
    LOCA::Abstract::Iterator::IteratorStatus
    stopLocaStatus(LOCA::Abstract::Iterator::StepStatus stepStatus);

    //! Check stopping criteria.
    //! Deprecated in Nov 2009 by the introduction of LOCA::StatusTest.
    LOCA::Abstract::Iterator::IteratorStatus
    stopDeprecated(LOCA::Abstract::Iterator::StepStatus stepStatus);

    //! Builds a constrained group is specified through parameter lists
    Teuchos::RCP<LOCA::MultiContinuation::AbstractGroup>
    buildConstrainedGroup(
      const Teuchos::RCP<LOCA::MultiContinuation::AbstractGroup>& grp);

    //! Compute a new step size based on results from the previous step
    LOCA::Abstract::Iterator::StepStatus
    computeStepSize(LOCA::Abstract::Iterator::StepStatus stepStatus,
            double& stepSize);

    //! Print to the screen the initialization information
    virtual void printInitializationInfo();

    //! Print to the screen information for the beginning of a new continuation step
    virtual void printStartStep();

    //! Print to the screen information for the end of a successful continuation step
    virtual void printEndStep(LOCA::Abstract::Iterator::StepStatus stepStatus);

    //! Print to the screen the concluding information
    virtual void printEndInfo();

    //! Checks to see if continuation parameter is within threshold of bound
    virtual bool withinThreshold();

  private:

    //! Private to prohibit copying
    Stepper(const Stepper&);

    //! Private to prohibit copying
    Stepper& operator = (const Stepper&);

    //! The old reset method without LOCA::StatusTest.
    //! Can be incorporated into the newer reset() method when the old
    //! reset() method does not have to be provided anymore.
    virtual bool
    resetExceptLocaStatusTest(const Teuchos::RCP<LOCA::GlobalData>& global_data,
                              const Teuchos::RCP<LOCA::MultiContinuation::AbstractGroup>& initialGuess,
                              const Teuchos::RCP<NOX::StatusTest::Generic>& nt,
                              const Teuchos::RCP<Teuchos::ParameterList>& p);

    void computeEigenData();

  protected:

    //! Global data
    Teuchos::RCP<LOCA::GlobalData> globalData;

    //! Parsed parameter list
    Teuchos::RCP<LOCA::Parameter::SublistParser> parsedParams;

    //! Predictor strategy
    Teuchos::RCP<LOCA::MultiPredictor::AbstractStrategy> predictor;

    //! Current continuation group
    Teuchos::RCP<LOCA::MultiContinuation::AbstractStrategy> curGroupPtr;

    //! Continuation group from previous step
    Teuchos::RCP<LOCA::MultiContinuation::AbstractStrategy> prevGroupPtr;

    //! Eigensolver for computing eigenvalues after each continuation step
    Teuchos::RCP<LOCA::Eigensolver::AbstractStrategy> eigensolver;

    //! Strategy for saving eigenvectors/values
    Teuchos::RCP<LOCA::SaveEigenData::AbstractStrategy> saveEigenData;

    //! Pointer to bifurcation group
    Teuchos::RCP<LOCA::MultiContinuation::AbstractGroup> bifGroupPtr;

    //! Pointer to the NOX status test.
    Teuchos::RCP<NOX::StatusTest::Generic> noxStatusTestPtr;

    //! Pointer to the LOCA status test.
    Teuchos::RCP<LOCA::StatusTest::Abstract> locaStatusTestPtr;

    //! Pointer to parameter list passed in constructor/reset method
    Teuchos::RCP<Teuchos::ParameterList> paramListPtr;

    //! Pointer to stepper parameters
    Teuchos::RCP<Teuchos::ParameterList> stepperList;

    //! Solver (a.k.a corrector)
    Teuchos::RCP<NOX::Solver::Generic> solverPtr;

    //! Current predictor direction
    Teuchos::RCP<LOCA::MultiContinuation::ExtendedVector> curPredictorPtr;

    //! previous predictor direction
    Teuchos::RCP<LOCA::MultiContinuation::ExtendedVector> prevPredictorPtr;

    //! Step size control strategy
    Teuchos::RCP<LOCA::StepSize::AbstractStrategy> stepSizeStrategyPtr;

    //! Name of continuation parameter
    std::string conParamName;

    //! Index of continuation parameter
    std::vector<int> conParamIDs;

    //! Starting value of continuation parameter, \f$\lambda_b \f$.
    double startValue;

    //! Largest allowable value of continuation parameter
    double maxValue;

    //! Smallest allowable value of continuation parameter
    double minValue;

    //! Current step size (change in the continuation parameter), \f$\Delta \lambda_i \f$.
    double stepSize;

    //! Maximum number of Newton iterations per continuation step,\f$ N_{max} \f$. Defaults to 15.
    int maxNonlinearSteps;

    //! Target parameter value for last step (either maxValue or minValue)
    double targetValue;

    //! Flag indicating if this is an extra step to hit target value
    bool isTargetStep;

    //! Flag indicating whether to do tangent factor step size scaling
    bool doTangentFactorScaling;

    //! Tangent factor
    double tangentFactor;

    //! Minimum tangent factor
    double minTangentFactor;

    //! Tangent factor exponent
    double tangentFactorExponent;

    //! Flag indicating whether to compute eigenvalues after each step
    bool calcEigenvalues;

    //! Flag indicating whether to return failed upon reaching max steps
    bool return_failed_on_max_steps;
  };
} // end namespace LOCA

#endif