This file is indexed.

/usr/include/trilinos/Teko_NeumannSeriesPreconditionerFactory.hpp is in libtrilinos-teko-dev 12.4.2-2.

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
/*
// @HEADER
// 
// ***********************************************************************
// 
//      Teko: A package for block and physics based preconditioning
//                  Copyright 2010 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 Eric C. Cyr (eccyr@sandia.gov)
// 
// ***********************************************************************
// 
// @HEADER

*/

#ifndef __Teko_NeumannSeriesPreconditionerFactory_hpp__
#define __Teko_NeumannSeriesPreconditionerFactory_hpp__

#include "Teko_NeumannSeriesPreconditionerFactoryDecl.hpp"

#include "Thyra_DefaultPreconditioner.hpp"
#include "Thyra_DefaultPreconditioner.hpp"
#include "Thyra_DefaultScaledAdjointLinearOp.hpp"
#include "Thyra_DefaultAddedLinearOp.hpp"
#include "Thyra_DefaultMultipliedLinearOp.hpp"
#include "Thyra_DefaultIdentityLinearOp.hpp"

#include "Teuchos_Array.hpp"
#include "Teuchos_StandardParameterEntryValidators.hpp"

namespace Teko {

using Teuchos::RCP;
using Teuchos::rcp;

static RCP<Teuchos::StringToIntegralParameterEntryValidator<Teko::DiagonalType> > scalingTypeVdtor;

template <typename ScalarT>
NeumannSeriesPreconditionerFactory<ScalarT>::NeumannSeriesPreconditionerFactory()
   : numberOfTerms_(1), scalingType_(Teko::NotDiag)
{
}

//! is this operator compatiable with the preconditioner factory?
template <typename ScalarT>
bool NeumannSeriesPreconditionerFactory<ScalarT>::isCompatible(const Thyra::LinearOpSourceBase<ScalarT> &fwdOpSrc) const
{
   return true;
}

//! create an instance of the preconditioner
template <typename ScalarT>
RCP<Thyra::PreconditionerBase<ScalarT> > NeumannSeriesPreconditionerFactory<ScalarT>::createPrec() const
{
   return rcp(new Thyra::DefaultPreconditioner<ScalarT>()); 
}

/** \brief initialize a newly created preconditioner object
  *
  * Initialize a newly created preconditioner object. 
  *
  * \param[in] fwdOpSrc Forward operator to be preconditioned
  * \param[in,out] precOp Return location for the preconditioner
  * \param[in] supportSolveUse Thyra information (?)
  */
template <typename ScalarT>
void NeumannSeriesPreconditionerFactory<ScalarT>::initializePrec(const RCP<const Thyra::LinearOpSourceBase<ScalarT> > & fwdOpSrc,
                    Thyra::PreconditionerBase<ScalarT> * prec,
                    const Thyra::ESupportSolveUse supportSolveUse) const
{
   using Thyra::scale;
   using Thyra::add;
   using Thyra::multiply;

   RCP<const Thyra::LinearOpBase<ScalarT> > M; // left-preconditioner
   RCP<const Thyra::LinearOpBase<ScalarT> > A = fwdOpSrc->getOp();
   if(scalingType_!=Teko::NotDiag) {
      M = Teko::getInvDiagonalOp(A,scalingType_);
      A = Thyra::multiply(M,A); 
   }

   RCP<const Thyra::LinearOpBase<ScalarT> > id = Thyra::identity<ScalarT>(A->range()); // I
   RCP<const Thyra::LinearOpBase<ScalarT> > idMA = add(id,scale(-1.0,A)); // I - A
 

   RCP<const Thyra::LinearOpBase<ScalarT> > precOp;
   if(numberOfTerms_==1) {
      // no terms requested, just return identity matrix
      precOp = id;
   }
   else {
      int iters = numberOfTerms_-1;
      // use Horner's method to computed higher order polynomials
      precOp = add(scale(2.0,id),scale(-1.0,A)); // I + (I - A)
      for(int i=0;i<iters;i++)
         precOp = add(id,multiply(idMA,precOp)); // I + (I - A) * p
   }

   // multiply by the preconditioner if it exists
   if(M!=Teuchos::null)
      precOp = Thyra::multiply(precOp,M);
   
   // must first cast that to be initialized
   Thyra::DefaultPreconditioner<ScalarT> & dPrec = Teuchos::dyn_cast<Thyra::DefaultPreconditioner<ScalarT> >(*prec);

   // this const-cast is unfortunate...needs to be fixed (larger than it seems!) ECC FIXME!
   dPrec.initializeUnspecified(Teuchos::rcp_const_cast<Thyra::LinearOpBase<ScalarT> >(precOp));
}

//! wipe clean a already initialized preconditioner object
template <typename ScalarT>
void NeumannSeriesPreconditionerFactory<ScalarT>::uninitializePrec(Thyra::PreconditionerBase<ScalarT> * prec, 
                      RCP<const Thyra::LinearOpSourceBase<ScalarT> > * fwdOpSrc,
                      Thyra::ESupportSolveUse *supportSolveUse) const
{
   Thyra::DefaultPreconditioner<ScalarT> & dPrec = Teuchos::dyn_cast<Thyra::DefaultPreconditioner<ScalarT> >(*prec);
 
   // wipe out any old preconditioner
   dPrec.uninitialize();
}

// for ParameterListAcceptor

//! \brief Set parameters from a parameter list
template <typename ScalarT>
void NeumannSeriesPreconditionerFactory<ScalarT>::setParameterList(const RCP<Teuchos::ParameterList> & paramList)
{
   TEUCHOS_TEST_FOR_EXCEPT(paramList==Teuchos::null);
 
   // check the parameters are correct
   paramList->validateParametersAndSetDefaults(*getValidParameters(),0);

   // store the parameter list
   paramList_ = paramList;

   numberOfTerms_ = paramList_->get<int>("Number of Terms");

   // get the scaling type
   scalingType_ = Teko::NotDiag;
   const Teuchos::ParameterEntry * entry = paramList_->getEntryPtr("Scaling Type");
   if(entry!=NULL)
      scalingType_ = scalingTypeVdtor->getIntegralValue(*entry);
}

/** \brief Get the valid parameters */
template <typename ScalarT>
RCP<const Teuchos::ParameterList> NeumannSeriesPreconditionerFactory<ScalarT>::getValidParameters() const
{
   static RCP<Teuchos::ParameterList> validPL;

   // only fill valid parameter list once
   if(validPL==Teuchos::null) {
      RCP<Teuchos::ParameterList> pl = rcp(new Teuchos::ParameterList());
   
      // build the validator for scaling type
      scalingTypeVdtor = Teuchos::stringToIntegralParameterEntryValidator<DiagonalType>(
            Teuchos::tuple<std::string>("Diagonal","Lumped","AbsRowSum","None"),
            Teuchos::tuple<Teko::DiagonalType>(Teko::Diagonal,Teko::Lumped,Teko::AbsRowSum,Teko::NotDiag),
            "Scaling Type");

      pl->set<int>("Number of Terms",1,
                   "The number of terms to use in the Neumann series expansion.");
      pl->set("Scaling Type","None","The number of terms to use in the Neumann series expansion.",
              scalingTypeVdtor);

      validPL = pl;
   }

   return validPL;
}

//! Unset the parameter list that was set using setParameterList(). 
template <typename ScalarT>
RCP<Teuchos::ParameterList> NeumannSeriesPreconditionerFactory<ScalarT>::unsetParameterList()
{
  Teuchos::RCP<Teuchos::ParameterList> oldList = paramList_;
  paramList_ = Teuchos::null;
  return oldList;
}

//! Get the parameter list that was set using setParameterList().
template <typename ScalarT>
RCP<const Teuchos::ParameterList> NeumannSeriesPreconditionerFactory<ScalarT>::getParameterList() const
{
  return paramList_;
}

//! Get the parameter list that was set using setParameterList().
template <typename ScalarT>
RCP<Teuchos::ParameterList> NeumannSeriesPreconditionerFactory<ScalarT>::getNonconstParameterList()
{
   return paramList_;
}

template <typename ScalarT>
std::string NeumannSeriesPreconditionerFactory<ScalarT>::description() const
{
  std::ostringstream oss;
  oss << "Teko::NeumannSeriesPreconditionerFactory";
  return oss.str();
}

} // end namespace Teko

#endif