This file is indexed.

/usr/include/trilinos/Stokhos_LanczosPCEBasis.hpp is in libtrilinos-stokhos-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
// @HEADER
// ***********************************************************************
// 
//                           Stokhos Package
//                 Copyright (2009) 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 Eric T. Phipps (etphipp@sandia.gov).
// 
// ***********************************************************************
// @HEADER

#ifndef STOKHOS_LANCZOSPCEBASIS_HPP
#define STOKHOS_LANCZOSPCEBASIS_HPP

#include "Teuchos_RCP.hpp"
#include "Teuchos_Array.hpp"
#include "Teuchos_SerialDenseVector.hpp"

#include "Stokhos_RecurrenceBasis.hpp"
#include "Stokhos_OrthogPolyApprox.hpp"
#include "Stokhos_Quadrature.hpp"
#include "Stokhos_Lanczos.hpp"

namespace Stokhos {

  template <typename ord_type, typename val_type>
  class DiagonalOperator {
  public:
    typedef ord_type ordinal_type;
    typedef val_type value_type;
    typedef Teuchos::SerialDenseVector<ordinal_type, value_type> vector_type;

    DiagonalOperator(const vector_type& A_): A(A_), n(A.length()) {}
    
    void 
    apply(const vector_type& u, vector_type& v) const {
      for (ordinal_type j=0; j<n; j++)
        v[j] = A[j]*u[j];
    }

  protected:

    const vector_type& A;
    ordinal_type n;

  };


  /*! 
   * \brief Generates three-term recurrence using the Lanczos 
   * procedure applied to a polynomial chaos expansion in another basis.
   */
  template <typename ordinal_type, typename value_type>
  class LanczosPCEBasis : 
    public RecurrenceBasis<ordinal_type, value_type> {
  public:

    //! Constructor
    /*!
     * \param p order of the basis
     * \param pce polynomial chaos expansion defining new density function
     * \param quad quadrature data for basis of PC expansion
     */
    LanczosPCEBasis(
      ordinal_type p,
      const Teuchos::RCP< const Stokhos::OrthogPolyApprox<ordinal_type, value_type> >& pce,
      const Teuchos::RCP< const Stokhos::Quadrature<ordinal_type, value_type> >& quad,
      bool normalize,
      bool limit_integration_order);

    //! Destructor
    ~LanczosPCEBasis();

    //! \name Implementation of Stokhos::OneDOrthogPolyBasis methods
    //@{

    //! Get Gauss quadrature points, weights, and values of basis at points
    virtual void 
    getQuadPoints(ordinal_type quad_order,
		  Teuchos::Array<value_type>& points,
		  Teuchos::Array<value_type>& weights,
		  Teuchos::Array< Teuchos::Array<value_type> >& values) const;

    /*! 
     * \brief Clone this object with the option of building a higher order
     * basis.
     */
    /*!
     * This method is following the Prototype pattern (see Design Pattern's textbook).
     * The slight variation is that it allows the order of the polynomial to be modified,
     * otherwise an exact copy is formed. The use case for this is creating basis functions
     * for column indices in a spatially varying adaptive refinement context.
     */
    virtual Teuchos::RCP<OneDOrthogPolyBasis<ordinal_type,value_type> > cloneWithOrder(ordinal_type p) const;

    //@}

    //! Get new coefficients in this new basis
    value_type getNewCoeffs(ordinal_type i) const;

    //! Map expansion coefficients from this basis to original
    void transformCoeffsFromLanczos(const value_type *in, 
				      value_type *out) const;

  protected:

    //! \name Implementation of Stokhos::RecurrenceBasis methods
    //@{ 

    //! Compute recurrence coefficients
    virtual bool
    computeRecurrenceCoefficients(ordinal_type n,
				  Teuchos::Array<value_type>& alpha,
				  Teuchos::Array<value_type>& beta,
				  Teuchos::Array<value_type>& delta,
				  Teuchos::Array<value_type>& gamma) const;

    //! Setup basis after computing recurrence coefficients
    virtual void setup();

    //@}

    //! Copy constructor with specified order
    LanczosPCEBasis(ordinal_type p, const LanczosPCEBasis& basis);

  private:

    // Prohibit copying
    LanczosPCEBasis(const LanczosPCEBasis&);

    // Prohibit Assignment
    LanczosPCEBasis& operator=(const LanczosPCEBasis& b);

  protected:

    typedef WeightedVectorSpace<ordinal_type,value_type> vectorspace_type;
    typedef DiagonalOperator<ordinal_type,value_type> operator_type;
    typedef Stokhos::Lanczos<vectorspace_type, operator_type> lanczos_type;
    typedef typename lanczos_type::matrix_type matrix_type;
    typedef typename lanczos_type::vector_type vector_type;
    
    //! PCE Lanczos procedure is based on
    Teuchos::RCP< const Stokhos::OrthogPolyApprox<ordinal_type, value_type> > pce;

    //! Quadrature object
    Teuchos::RCP< const Stokhos::Quadrature<ordinal_type, value_type> > quad;

    //! Flag indicating whether to limit the integration order
    bool limit_integration_order;

    //! Number of quadrature points
    ordinal_type nqp;

    //! Quadrature weights
    vector_type pce_weights;

    //! Values of PCE at quadrature points
    vector_type pce_vals;

    //! Initial Lanczos vector
    vector_type u0;

    //! Lanczos vectors
    mutable matrix_type lanczos_vecs;

    //! Matrix mapping coefficients in Stieltjes basis back to original basis
    matrix_type fromStieltjesMat;

    //! Projection of pce in new basis
    vector_type new_pce;

  }; // class LanczosPCEBasis

} // Namespace Stokhos

// Include template definitions
#include "Stokhos_LanczosPCEBasisImp.hpp"

#endif