This file is indexed.

/usr/include/trilinos/Stokhos_MonomialGramSchmidtPCEBasisImp.hpp is in libtrilinos-stokhos-dev 12.10.1-3.

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
// @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

#include "Stokhos_SDMUtils.hpp"
#include "Stokhos_OrthogonalizationFactory.hpp"

template <typename ordinal_type, typename value_type>
Stokhos::MonomialGramSchmidtPCEBasis<ordinal_type, value_type>::
MonomialGramSchmidtPCEBasis(
  ordinal_type max_p,
  const Teuchos::Array< Stokhos::OrthogPolyApprox<ordinal_type, value_type> >& pce,
  const Teuchos::RCP<const Stokhos::Quadrature<ordinal_type, value_type> >& quad,
  const Teuchos::ParameterList& params) :
  GSReducedPCEBasisBase<ordinal_type,value_type>(max_p, pce, quad, params),
  name("Monomial Gram Schmidt PCE Basis")
{
  this->setup(max_p, pce, quad);
}

template <typename ordinal_type, typename value_type>
Stokhos::MonomialGramSchmidtPCEBasis<ordinal_type, value_type>::
~MonomialGramSchmidtPCEBasis()
{
}

template <typename ordinal_type, typename value_type>
const std::string&
Stokhos::MonomialGramSchmidtPCEBasis<ordinal_type, value_type>::
getName() const
{
  return name;
}

template <typename ordinal_type, typename value_type>
ordinal_type
Stokhos::MonomialGramSchmidtPCEBasis<ordinal_type, value_type>::
buildReducedBasis(
  ordinal_type max_p, 
  value_type threshold, 
  const Teuchos::SerialDenseMatrix<ordinal_type,value_type>& A, 
  const Teuchos::SerialDenseMatrix<ordinal_type,value_type>& F,
  const Teuchos::Array<value_type>& weights, 
  Teuchos::Array< Stokhos::MultiIndex<ordinal_type> >& terms_,
  Teuchos::Array<ordinal_type>& num_terms_,
  Teuchos::SerialDenseMatrix<ordinal_type,value_type>& Qp_, 
  Teuchos::SerialDenseMatrix<ordinal_type,value_type>& Q_)
{
  // Compute basis terms -- 2-D array giving powers for each linear index
  ordinal_type max_sz;
  CPBUtils::compute_terms(max_p, this->d, max_sz, terms_, num_terms_);

  // Compute B matrix -- monomials in F
  // for i=0,...,nqp-1
  //   for j=0,...,sz-1
  //      B(i,j) = F(i,1)^terms_[j][1] * ... * F(i,d)^terms_[j][d]
  // where sz is the total size of a basis up to order p and terms_[j] 
  // is an array of powers for each term in the total-order basis
  ordinal_type nqp = weights.size();
  SDM B(nqp, max_sz);
  for (ordinal_type i=0; i<nqp; i++) {
    for (ordinal_type j=0; j<max_sz; j++) {
      B(i,j) = 1.0;
      for (ordinal_type k=0; k<this->d; k++)
	B(i,j) *= std::pow(F(i,k), terms_[j][k]);
    }
  }

  // Rescale columns of B to have unit norm
  for (ordinal_type j=0; j<max_sz; j++) {
    value_type nrm = 0.0;
    for (ordinal_type i=0; i<nqp; i++)
      nrm += B(i,j)*B(i,j)*weights[i];
    nrm = std::sqrt(nrm);
    for (ordinal_type i=0; i<nqp; i++)
      B(i,j) /= nrm;
  }

  // Compute our new basis -- each column of Q is the new basis evaluated
  // at the original quadrature points.  Constraint pivoting so first d+1
  // columns and included in Q.
  SDM R;
  Teuchos::Array<ordinal_type> piv(max_sz);
  for (int i=0; i<this->d+1; i++)
    piv[i] = 1;
  typedef Stokhos::OrthogonalizationFactory<ordinal_type,value_type> SOF;
   ordinal_type sz_ = SOF::createOrthogonalBasis(
    this->orthogonalization_method, threshold, this->verbose, B, weights, 
    Q_, R, piv);

  // Compute Qp = A^T*W*Q
  SDM tmp(nqp, sz_);
  Qp_.reshape(this->pce_sz, sz_);
  for (ordinal_type i=0; i<nqp; i++)
    for (ordinal_type j=0; j<sz_; j++)
      tmp(i,j) = Q_(i,j)*weights[i];
  ordinal_type ret = 
    Qp_.multiply(Teuchos::TRANS, Teuchos::NO_TRANS, 1.0, A, tmp, 0.0);
  TEUCHOS_ASSERT(ret == 0);

  // It isn't clear that Qp is orthogonal, but if you derive the projection
  // matrix from the original space to the reduced, you end up with 
  // Q^T*W*A = Qp^T

  return sz_;
}