This file is indexed.

/usr/include/trilinos/EpetraExt_TCrsGraph_MapColoringIndex.h is in libtrilinos-epetraext-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
//@HEADER
// ***********************************************************************
//
//     EpetraExt: Epetra Extended - Linear Algebra Services Package
//                 Copyright (2011) 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 Michael A. Heroux (maherou@sandia.gov)
//
// ***********************************************************************
//@HEADER

#ifndef EpetraExt_TCRSGRAPH_MAPCOLORINGINDEX_H
#define EpetraExt_TCRSGRAPH_MAPCOLORINGINDEX_H

#include <EpetraExt_Transform.h>
#include <Epetra_GIDTypeVector.h>
#include <Epetra_MapColoring.h>

#include <vector>
#include <map>

class Epetra_CrsGraph;
class Epetra_IntVector;

namespace EpetraExt {

///
/** Generates a std::vector of Epetra_IntVector's to be used to map perturbation
 * contributions to a CrsGraph/CrsMatrix from a perturbed vector.
 */

template<typename int_type>
class TCrsGraph_MapColoringIndex
: public StructuralTransform< Epetra_CrsGraph,std::vector<typename Epetra_GIDTypeVector<int_type>::impl> > {

  const Epetra_MapColoring & ColorMap_;

 protected:

  ///
  /** Destructor
   */
  ~TCrsGraph_MapColoringIndex() {}

  ///
  /** Constructor
   * input param ColorMap defines the perturbation coloring
   */
  TCrsGraph_MapColoringIndex( const Epetra_MapColoring & ColorMap )
  : ColorMap_( ColorMap )
  {}
public:
  typedef StructuralTransform< Epetra_CrsGraph,std::vector<typename Epetra_GIDTypeVector<int_type>::impl> > Base;
  ///
  /** Generates a std::vector<Epetra_IntVector> from the input Epetra_CrsGraph
   */
  typedef typename Base::NewTypeRef NewTypeRef;
  typedef typename Base::OriginalTypeRef OriginalTypeRef;
  NewTypeRef operator()( OriginalTypeRef orig );
};

//////// Implementations ////////

template<typename int_type>
typename TCrsGraph_MapColoringIndex<int_type>::NewTypeRef
TCrsGraph_MapColoringIndex<int_type>::
operator()( OriginalTypeRef orig )
{
  if(!orig.RowMap(). template GlobalIndicesIsType<int_type>())
    throw "EpetraExt::TCrsGraph_MapColoringIndex::operator(): Global indices mismatch.";

  Base::origObj_ = &orig;

  const Epetra_BlockMap & RowMap = orig.RowMap();
  int nRows = RowMap.NumMyElements();

  int NumColors = ColorMap_.NumColors();
  int * ListOfColors = ColorMap_.ListOfColors();

  std::map<int,int> MapOfColors;
  for( int i = 0; i < NumColors; ++i ) MapOfColors[ ListOfColors[i] ] = i;

  //initial setup of stl vector of IntVectors for indexing
  std::vector<int_type> dummy( nRows, -1 );
  typename Base::NewTypePtr IndexVec = new typename Base::NewType( NumColors, typename Epetra_GIDTypeVector<int_type>::impl( Copy, RowMap, &dummy[0] ) );

  int MaxNumIndices = orig.MaxNumIndices();
  int NumIndices;
  std::vector<int_type> Indices( MaxNumIndices );

  for( int i = 0; i < nRows; ++i )
  {
    orig.ExtractGlobalRowCopy( (int_type) orig.GRID64(i), MaxNumIndices, NumIndices, &Indices[0] );

    for( int j = 0; j < NumIndices; ++j )
     (*IndexVec)[ MapOfColors[ColorMap_(Indices[j])] ][i] = Indices[j];
  }

  Base::newObj_ = IndexVec;

  return *IndexVec;
}

} //namespace EpetraExt

#endif // EpetraExt_TCRSGRAPH_MAPCOLORINGINDEX_H