This file is indexed.

/usr/include/trilinos/NOX_Epetra_MatrixFree.H is in libtrilinos-nox-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
//@HEADER
// ************************************************************************
//
//            NOX: An Object-Oriented Nonlinear Solver Package
//                 Copyright (2002) 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 NOX_EPETRA_MATRIXFREE_H
#define NOX_EPETRA_MATRIXFREE_H

#include "Epetra_Comm.h"

#include "Epetra_Operator.h"               // base class
#include "NOX_Epetra_Interface_Jacobian.H" // base class
#include "NOX_Utils.H"

#include "NOX_Common.H"
#include "Epetra_Import.h"
#include "NOX_Epetra_Vector.H"
#include "Teuchos_RCP.hpp"
#include "NOX_Solver_Generic.H"

// Forward Declarations
class Epetra_Comm;
class Epetra_Map;

namespace NOX {
  namespace Abstract {
    class Group;
  }
  namespace Epetra {
    namespace Interface {
      class Required;
    }
  }
}

namespace NOX {

namespace Epetra {

/*! \brief Concrete implementation for creating an Epetra_Operator Jacobian based on the Matrix-Free Newton-Krylov method.

Matrix-Free Newton-Krylov is a method that takes advantage of the fact the Newton Krylov solvers do not require an explicit Jacobian matrix.  Newton-Krylov solvers only require the matrix-vector product \f$Jy\f$ in the iteration sequence.  This product can approximated by the following:

\f[ Jy = \frac{F(x + \delta y) - F(x)}{\delta} \f]

where \f$J\f$ is the Jacobian, \f$F\f$ is the function evaluation, \f$x\f$ is the solution vector, \f$y\f$ is the vector to be operated on, and \f$\delta\f$ is a scalar perturbation calculated by:

\f[ \delta = \lambda * (\lambda + \frac{\| x\|}{\| y\|} ) \f]

where \f$ \lambda = 1.0e-6 \f$.
 */
class MatrixFree : public Epetra_Operator,
           public virtual NOX::Epetra::Interface::Jacobian {

 public:

  //! Define types for use of the perturbation parameter \f$ \delta\f$.
  enum DifferenceType {Forward, Backward, Centered};

  /*! \brief Constructor

    The vector \c x is used to clone the solution vector.
  */
  MatrixFree(Teuchos::ParameterList& printParams,
         const Teuchos::RCP<NOX::Epetra::Interface::Required>& i,
         const NOX::Epetra::Vector& cloneVector,
         bool useNewPerturbation = false);

  //! Pure virtual destructor
  virtual ~MatrixFree();

  //! If set true, transpose of this operator will be applied.
  /*! This flag allows the transpose of the given operator to be used implicitly.  Setting this flag
    affects only the Apply() and ApplyInverse() methods.  If the implementation of this interface
    does not support transpose use, this method should return a value of -1.
    \param     UseTranspose -If true, multiply by the transpose of operator, otherwise just use operator.

    \return Integer error code, set to 0 if successful.  Set to -1 if this implementation does not support transpose.
  */
  virtual int SetUseTranspose(bool UseTranspose);

  //! Returns the result of a Epetra_Operator applied to a Epetra_MultiVector X in Y.
  /*!
    \param     X - A Epetra_MultiVector of dimension NumVectors to multiply with matrix.
    \param     Y -A Epetra_MultiVector of dimension NumVectors containing result.

    \return Integer error code, set to 0 if successful.
  */
  virtual int Apply(const Epetra_MultiVector& X, Epetra_MultiVector& Y) const;

  //! Returns the result of a Epetra_Operator inverse applied to an Epetra_MultiVector X in Y.
  /*!
    \param     X - A Epetra_MultiVector of dimension NumVectors to solve for.
    \param     Y -A Epetra_MultiVector of dimension NumVectors containing result.

    \return Integer error code, set to 0 if successful.

    \warning In order to work with AztecOO, any implementation of this method must
    support the case where X and Y are the same object.
  */
  virtual int ApplyInverse(const Epetra_MultiVector& X, Epetra_MultiVector& Y) const;

  //! Returns the infinity norm of the global matrix.
  /* Returns the quantity \f$ \| A \|_\infty\f$ such that
     \f[\| A \|_\infty = \max_{1\lei\lem} \sum_{j=1}^n |a_{ij}| \f].

     \warning This method must not be called unless HasNormInf() returns true.    */
  virtual double NormInf() const;

  //! Returns a character std::string describing the operator
  virtual const char* Label () const;

  //! Returns the current UseTranspose setting.
  virtual bool UseTranspose() const;

  //! Returns true if the \e this object can provide an approximate Inf-norm, false otherwise.
  virtual bool HasNormInf() const;

  //! Returns a reference to the Epetra_Comm communicator associated with this operator.
  virtual const Epetra_Comm & Comm() const;

  //! Returns the Epetra_BlockMap object associated with the domain of this matrix operator.
  virtual const Epetra_Map& OperatorDomainMap () const;

  //! Returns the Epetra_BlockMap object associated with the range of this matrix operator.
  virtual const Epetra_Map& OperatorRangeMap () const;

  //! Compute Jacobian given the specified input vector, x.  Returns true if computation was successful.
  virtual bool computeJacobian(const Epetra_Vector& x, Epetra_Operator& Jac);

  //! Set the type of perturbation method used (default is Forward)
  virtual void setDifferenceMethod( DifferenceType type );

  //! Allows the user to change the value of \f$ \lambda \f$ in the perturbation calculation.
  void setLambda(double lambda_);

  //! Flag that toggles whether MatrixFree should compute the perturbation parameter \f$ \eta \f$ or use a value supplied by the user through setPerturbation().
  void setComputePerturbation(bool bVal);

  //! Set the perturbation parameter \f$ \eta \f$.
  void setPerturbation(double eta_);

  //! Returns the most recently used value of the perturbation parameter \f$ \eta \f$.
  double getPerturbation() const;

  //! Clone a NOX::Abstract::Group derived object and use the computeF() method of that group for the perturbation instead of the NOX::Epetra::Interface::Required::computeF() method.  This is required for LOCA to get the operators correct during homotopy.
  void setGroupForComputeF(const NOX::Abstract::Group& group);

  //! Save a RCP to a solver, and use the Solver's current Group's computeF() in the computeJacobian call, which can save a function call by respecting the isValid flag
  void setSolverForComputeJacobian(const Teuchos::RCP<NOX::Solver::Generic>& slvr);


protected:

  //! Label for matrix
  std::string label;

  //! User provided interface function
  Teuchos::RCP<NOX::Epetra::Interface::Required> interface;

  //! The current solution vector
  NOX::Epetra::Vector currentX;

  //! Perturbed solution vector
  mutable NOX::Epetra::Vector perturbX;

  //! Function evaluation at currentX
  mutable NOX::Epetra::Vector fo;

  //! Function evaluation at perturbX
  mutable NOX::Epetra::Vector fp;

  //! Optional pointer to function evaluation at -perturbX - needed only for centered finite differencing
  mutable Teuchos::RCP<NOX::Epetra::Vector> fmPtr;

  //! Epetra_Map object used in the returns of the Epetra_Operator derived methods.
  /*! If the user is using Epetra_BlockMaps, then NOX::Epetra::MatrixFree must create an equivalent Epetra_Map from the Epetra_BlockMap that can be used as the return object of the OperatorDomainMap() and OperatorRangeMap() methods.
   */
  Teuchos::RCP<const Epetra_Map> epetraMap;

  //! Define types for use of the perturbation parameter \f$ \delta\f$.
  DifferenceType diffType;

  //! Scale factor for eta calculation
  double lambda;

  //! Perturbation value to use in the directional derivative
  mutable double eta;

  //! User specified perturbation value to use in the directional derivative.  Set by setPerturbation().
  double userEta;

  //! Flag that determines if we should calculate eta or use a value set by the user.
  bool computeEta;

  //! Flag to enables the use of a group instead of the interface for the computeF() calls in the directional difference calculation.
  bool useGroupForComputeF;

  //! Flag to enables the use of Solver's Group instead of the interface for the computeF() calls in the directional difference calculation, to make use of isValid flags
  bool useSolverForComputeJacobian;

  //! A new perturbation formulation developed by C. T. Kelley and A. G. Salinger can be used by the constructor flag useNewPerturbation = true.
  bool useNewPerturbation;

  //! Pointer to the group for possible use in computeF() calls.
  Teuchos::RCP<NOX::Abstract::Group> groupPtr;

  //! Pointer to the Solver for possible use in computeF() calls.
  Teuchos::RCP<NOX::Solver::Generic> slvrPtr;

  //! Printing utilities.
  NOX::Utils utils;

};
} // namespace Epetra
} // namespace NOX

#endif /* NOX_EPETRA_MATRIXFREE_H */