This file is indexed.

/usr/include/trilinos/Rythmos_ExplicitRKStepper_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
//@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_ExplicitRK_STEPPER_DECL_H
#define Rythmos_ExplicitRK_STEPPER_DECL_H

#include "Rythmos_RKButcherTableauAcceptingStepperBase.hpp"
#include "Rythmos_RKButcherTableauBase.hpp"
#include "Rythmos_Types.hpp"
#include "Thyra_ModelEvaluator.hpp"

#include "Rythmos_StepControlStrategyAcceptingStepperBase.hpp"
#include "Rythmos_StepControlStrategyBase.hpp"

namespace Rythmos {

/** \brief . */
template<class Scalar>
class ExplicitRKStepper : virtual public RKButcherTableauAcceptingStepperBase<Scalar>,
  virtual public StepControlStrategyAcceptingStepperBase<Scalar>
{
  public:
    typedef Teuchos::ScalarTraits<Scalar> ST;
    typedef typename Teuchos::ScalarTraits<Scalar>::magnitudeType ScalarMag;
    
    /** \brief . */
    ExplicitRKStepper();

    /** \name Overridden from StepperBase */
    //@{
    
    /** \brief. */
    bool supportsCloning() const;

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

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

    /** \brief. */
    void setRKButcherTableau(const RCP<const RKButcherTableauBase<Scalar> > &rkbt);

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

    //@}

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

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

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

    /** \brief . */
    Teuchos::RCP<const Thyra::ModelEvaluator<Scalar> > getModel() const;

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

    /** \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;

    /** \brief . */
    void describe(
        Teuchos::FancyOStream &out,
        const Teuchos::EVerbosityLevel verbLevel
        ) const;

    /// Redefined from InterpolationBufferBase 
    /// Add points to buffer
    void addPoints(
      const Array<Scalar>& time_vec
      ,const Array<Teuchos::RCP<const Thyra::VectorBase<Scalar> > >& x_vec
      ,const Array<Teuchos::RCP<const Thyra::VectorBase<Scalar> > >& xdot_vec
      );

    /// Get values from buffer
    void getPoints(
      const Array<Scalar>& time_vec
      ,Array<RCP<const VectorBase<Scalar> > >* x_vec
      ,Array<RCP<const VectorBase<Scalar> > >* xdot_vec
      ,Array<ScalarMag>* accuracy_vec) const;

    /** \brief . */
    TimeRange<Scalar> getTimeRange() const;

    /// Get interpolation nodes
    void getNodes(Array<Scalar>* time_vec) const;

    /// Remove interpolation nodes
    void removeNodes(Array<Scalar>& time_vec);

    /// Get order of interpolation
    int getOrder() const;

    /// Redefined from Teuchos::ParameterListAcceptor
    /** \brief . */
    void setParameterList(Teuchos::RCP<Teuchos::ParameterList> const& paramList);

    /** \brief . */
    Teuchos::RCP<Teuchos::ParameterList> getNonconstParameterList();

    /** \brief . */
    Teuchos::RCP<Teuchos::ParameterList> unsetParameterList();
    
    /** \brief. */
    RCP<const Teuchos::ParameterList> getValidParameters() 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;
  
  //@}

  private:

    Teuchos::RCP<const Thyra::ModelEvaluator<Scalar> > model_;
    Teuchos::RCP<Thyra::VectorBase<Scalar> > solution_vector_;
    Teuchos::RCP<Thyra::VectorBase<Scalar> > solution_vector_old_;
    Array<Teuchos::RCP<Thyra::VectorBase<Scalar> > > k_vector_;
    Teuchos::RCP<Thyra::VectorBase<Scalar> > ktemp_vector_;
    Teuchos::RCP<Thyra::VectorBase<Scalar> > solution_hat_vector_;

    Thyra::ModelEvaluatorBase::InArgs<Scalar> basePoint_;

    RCP<const RKButcherTableauBase<Scalar> > erkButcherTableau_;

    Scalar t_;
    Scalar t_old_;
    Scalar dt_;
    int numSteps_;
    Scalar LETvalue_;   // ck * e

    Teuchos::RCP<Teuchos::ParameterList> parameterList_;
    RCP<Thyra::VectorBase<Scalar> > ee_; // error (Sidafa) 
    EStepLETStatus stepLETStatus_; // Local Error Test Status (Sidafa)
    TimeRange<Scalar> timeRange_;

    bool isInitialized_;

    bool haveInitialCondition_;

    // Private member functions:
    void defaultInitializeAll_();
    void initialize_();

  // Sidafa 9/4/15
  int rkNewtonConvergenceStatus_;
  RCP<Rythmos::StepControlStrategyBase<Scalar> > stepControl_;
  bool isVariableStep_ = false;

  Scalar takeVariableStep_(Scalar dt, StepSizeType flag);

  Scalar takeFixedStep_(Scalar dt, StepSizeType flag);

};

// Non-member constructors
template<class Scalar>
RCP<ExplicitRKStepper<Scalar> > explicitRKStepper();

template<class Scalar>
RCP<ExplicitRKStepper<Scalar> > explicitRKStepper(
    const Teuchos::RCP<Thyra::ModelEvaluator<Scalar> >& model 
    );

template<class Scalar>
RCP<ExplicitRKStepper<Scalar> > explicitRKStepper(
    const Teuchos::RCP<Thyra::ModelEvaluator<Scalar> >& model,
    const RCP<const RKButcherTableauBase<Scalar> >& rkbt 
    );

} // namespace Rythmos

#endif //Rythmos_ExplicitRK_STEPPER_DECL_H