This file is indexed.

/usr/include/deal.II/numerics/derivative_approximation.h is in libdeal.ii-dev 8.5.1-3.

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
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
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
// ---------------------------------------------------------------------
//
// Copyright (C) 2000 - 2017 by the deal.II authors
//
// This file is part of the deal.II library.
//
// The deal.II library is free software; you can use it, redistribute
// it, and/or modify it under the terms of the GNU Lesser General
// Public License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
// The full text of the license can be found in the file LICENSE at
// the top level of the deal.II distribution.
//
// ---------------------------------------------------------------------

#ifndef dealii__derivative_approximation_h
#define dealii__derivative_approximation_h

#include <deal.II/base/config.h>
#include <deal.II/base/exceptions.h>
#include <deal.II/base/std_cxx11/tuple.h>
#include <deal.II/base/synchronous_iterator.h>
#include <deal.II/fe/fe_update_flags.h>
#include <deal.II/fe/mapping.h>
#include <deal.II/lac/vector.h>
#include <deal.II/grid/filtered_iterator.h>
#ifdef _MSC_VER
#  include <deal.II/dofs/dof_accessor.h>
#endif
#include <utility>

DEAL_II_NAMESPACE_OPEN

/**
 * This namespace provides functions that compute a cell-wise approximation of
 * the norm of a derivative of a finite element field by taking difference
 * quotients between neighboring cells. This is a rather simple but efficient
 * form to get an error indicator, since it can be computed with relatively
 * little numerical effort and yet gives a reasonable approximation.
 *
 * The way the difference quotients are computed on cell $K$ is the following
 * (here described for the approximation of the gradient of a finite element
 * field, but see below for higher derivatives): let $K'$ be a neighboring
 * cell, and let $y_{K'}=x_{K'}-x_K$ be the distance vector between the
 * centers of the two cells, then $ \frac{u_h(x_{K'}) - u_h(x_K)}{ \|y_{K'}\|
 * }$ is an approximation of the directional derivative $ \nabla u(x_K) \cdot
 * \frac{y_{K'}}{ \|y_{K'}\| }.$ By multiplying both terms by $\frac{y_{K'}}{
 * \|y_{K'}\| }$ from the left and summing over all neighbors $K'$, we obtain
 * $ \sum_{K'} \left( \frac{y_{K'}}{ \|y_{K'}\|} \frac{y_{K'}^T}{ \|y_{K'}\| }
 * \right) \nabla u(x_K) \approx \sum_{K'} \left( \frac{y_{K'}}{ \|y_{K'}\|}
 * \frac{u_h(x_{K'}) - u_h(x_K)}{ \|y_{K'}\| }  \right).$
 *
 * Thus, if the matrix $ Y =  \sum_{K'} \left( \frac{y_{K'}}{\|y_{K'}\|}
 * \frac{y_{K'}^T}{ \|y_{K'}\| } \right)$ is regular (which is the case when
 * the vectors $y_{K'}$ to all neighbors span the whole space), we can obtain
 * an approximation to the true gradient by $ \nabla u(x_K) \approx Y^{-1}
 * \sum_{K'} \left( \frac{y_{K'}}{\|y_{K'}\|} \frac{u_h(x_{K'}) - u_h(x_K)}{
 * \|y_{K'}\| } \right).$ This is a quantity that is easily computed. The
 * value returned for each cell when calling the @p approximate_gradient
 * function of this class is the $l_2$ norm of this approximation to the
 * gradient. To make this a useful quantity, you may want to scale each
 * element by the correct power of the respective cell size.
 *
 * The computation of this quantity must fail if a cell has only neighbors for
 * which the direction vectors $y_K$ do not span the whole space, since then
 * the matrix $Y$ is no longer invertible. If this happens, you will get an
 * error similar to this one:
 * @code
 * --------------------------------------------------------
 * An error occurred in line <749> of file <source/numerics/derivative_approximation.cc> in function
 *     void DerivativeApproximation::approximate(const Mapping<dim,spacedim>&, const DoFHandlerType<dim,spacedim>&, const InputVector&, unsigned int, const
 *  std::pair<unsigned int, unsigned int>&, Vector<float>&) [with DerivativeDescription = DerivativeApproximation::Gradient<3>, int
 * dim = 3, DoFHandlerType = DoFHandler, InputVector = Vector<double>]
 * The violated condition was:
 *     determinant(Y) != 0
 * The name and call sequence of the exception was:
 *     ExcInsufficientDirections()
 * Additional Information:
 * (none)
 * --------------------------------------------------------
 * @endcode
 * As can easily be verified, this can only happen on very coarse grids, when
 * some cells and all their neighbors have not been refined even once. You
 * should therefore only call the functions of this class if all cells are at
 * least once refined. In practice this is not much of a restriction.
 *
 *
 * <h3>Approximation of higher derivatives</h3>
 *
 * Similar to the reasoning above, approximations to higher derivatives can be
 * computed in a similar fashion. For example, the tensor of second
 * derivatives is approximated by the formula $ \nabla^2 u(x_K) \approx Y^{-1}
 * \sum_{K'} \left( \frac{y_{K'}}{\|y_{K'}\|} \otimes \frac{\nabla u_h(x_{K'})
 * - \nabla u_h(x_K)}{ \|y_{K'}\| } \right), $ where $\otimes$ denotes the
 * outer product of two vectors. Note that unlike the true tensor of second
 * derivatives, its approximation is not necessarily symmetric. This is due to
 * the fact that in the derivation, it is not clear whether we shall consider
 * as projected second derivative the term $\nabla^2 u y_{KK'}$ or $y_{KK'}^T
 * \nabla^2 u$. Depending on which choice we take, we obtain one approximation
 * of the tensor of second derivatives or its transpose. To avoid this
 * ambiguity, as result we take the symmetrized form, which is the mean value
 * of the approximation and its transpose.
 *
 * The returned value on each cell is the spectral norm of the approximated
 * tensor of second derivatives, i.e. the largest eigenvalue by absolute
 * value. This equals the largest curvature of the finite element field at
 * each cell, and the spectral norm is the matrix norm associated to the $l_2$
 * vector norm.
 *
 * Even higher than the second derivative can be obtained along the same lines
 * as exposed above.
 *
 *
 * <h3>Refinement indicators based on the derivatives</h3>
 *
 * If you would like to base a refinement criterion upon these approximation
 * of the derivatives, you will have to scale the results of this class by an
 * appropriate power of the mesh width. For example, since $\|u-u_h\|^2_{L_2}
 * \le C h^2 \|\nabla u\|^2_{L_2}$, it might be the right thing to scale the
 * indicators as $\eta_K = h \|\nabla u\|_K$, i.e. $\eta_K = h^{1+d/2}
 * \|\nabla u\|_{\infty;K}$, i.e. the right power is $1+d/2$.
 *
 * Likewise, for the second derivative, one should choose a power of the mesh
 * size $h$ one higher than for the gradient.
 *
 *
 * <h3>Implementation</h3>
 *
 * The formulae for the computation of approximations to the gradient and to
 * the tensor of second derivatives shown above are very much alike. The basic
 * difference is that in one case the finite difference quotient is a scalar,
 * while in the other case it is a vector. For higher derivatives, this would
 * be a tensor of even higher rank. We then have to form the outer product of
 * this difference quotient with the distance vector $y_{KK'}$, symmetrize it,
 * contract it with the matrix $Y^{-1}$ and compute its norm. To make the
 * implementation simpler and to allow for code reuse, all these operations
 * that are dependent on the actual order of the derivatives to be
 * approximated, as well as the computation of the quantities entering the
 * difference quotient, have been separated into auxiliary nested classes
 * (names @p Gradient and @p SecondDerivative) and the main algorithm is
 * simply passed one or the other data types and asks them to perform the
 * order dependent operations. The main framework that is independent of this,
 * such as finding all active neighbors, or setting up the matrix $Y$ is done
 * in the main function @p approximate.
 *
 * Due to this way of operation, the class may be easily extended for higher
 * oder derivatives than are presently implemented. Basically, only an
 * additional class along the lines of the derivative descriptor classes @p
 * Gradient and @p SecondDerivative has to be implemented, with the respective
 * typedefs and functions replaced by the appropriate analogues for the
 * derivative that is to be approximated.
 *
 * @ingroup numerics
 * @author Wolfgang Bangerth, 2000
 */
namespace DerivativeApproximation
{
  /**
   * This function is used to obtain an approximation of the gradient. Pass it
   * the DoF handler object that describes the finite element field, a nodal
   * value vector, and receive the cell-wise Euclidean norm of the
   * approximated gradient.
   *
   * The last parameter denotes the solution component, for which the gradient
   * is to be computed. It defaults to the first component. For scalar
   * elements, this is the only valid choice; for vector-valued ones, any
   * component between zero and the number of vector components can be given
   * here.
   *
   * In a parallel computation the @p solution vector needs to contain the
   * locally relevant unknowns.
   */
  template <int dim, template <int, int> class DoFHandlerType, class InputVector, int spacedim>
  void
  approximate_gradient (const Mapping<dim,spacedim>        &mapping,
                        const DoFHandlerType<dim,spacedim> &dof,
                        const InputVector                  &solution,
                        Vector<float>                      &derivative_norm,
                        const unsigned int                  component = 0);

  /**
   * Call the @p interpolate function, see above, with
   * <tt>mapping=MappingQGeneric@<dim@>(1)</tt>.
   */
  template <int dim, template <int, int> class DoFHandlerType, class InputVector, int spacedim>
  void
  approximate_gradient (const DoFHandlerType<dim,spacedim> &dof,
                        const InputVector                  &solution,
                        Vector<float>                      &derivative_norm,
                        const unsigned int                  component = 0);

  /**
   * This function is the analogue to the one above, computing finite
   * difference approximations of the tensor of second derivatives. Pass it
   * the DoF handler object that describes the finite element field, a nodal
   * value vector, and receive the cell-wise spectral norm of the approximated
   * tensor of second derivatives. The spectral norm is the matrix norm
   * associated to the $l_2$ vector norm.
   *
   * The last parameter denotes the solution component, for which the gradient
   * is to be computed. It defaults to the first component. For scalar
   * elements, this is the only valid choice; for vector-valued ones, any
   * component between zero and the number of vector components can be given
   * here.
   *
   * In a parallel computation the @p solution vector needs to contain the
   * locally relevant unknowns.
   */
  template <int dim, template <int, int> class DoFHandlerType, class InputVector, int spacedim>
  void
  approximate_second_derivative (const Mapping<dim,spacedim>        &mapping,
                                 const DoFHandlerType<dim,spacedim> &dof,
                                 const InputVector                  &solution,
                                 Vector<float>                      &derivative_norm,
                                 const unsigned int                  component = 0);

  /**
   * Call the @p interpolate function, see above, with
   * <tt>mapping=MappingQGeneric@<dim@>(1)</tt>.
   */
  template <int dim, template <int, int> class DoFHandlerType, class InputVector, int spacedim>
  void
  approximate_second_derivative (const DoFHandlerType<dim,spacedim> &dof,
                                 const InputVector                  &solution,
                                 Vector<float>                      &derivative_norm,
                                 const unsigned int                  component = 0);

  /**
   * This function calculates the <tt>order</tt>-th order approximate
   * derivative and returns the full tensor for a single cell.
   *
   * The last parameter denotes the solution component, for which the gradient
   * is to be computed. It defaults to the first component. For scalar
   * elements, this is the only valid choice; for vector-valued ones, any
   * component between zero and the number of vector components can be given
   * here.
   *
   * In a parallel computation the @p solution vector needs to contain the
   * locally relevant unknowns.
   */
  template <typename DoFHandlerType, class InputVector, int order>
  void
  approximate_derivative_tensor
  (const Mapping<DoFHandlerType::dimension, DoFHandlerType::space_dimension>  &mapping,
   const DoFHandlerType                                                       &dof,
   const InputVector                                                          &solution,
#ifndef _MSC_VER
   const typename DoFHandlerType::active_cell_iterator                        &cell,
#else
   const TriaActiveIterator <dealii::DoFCellAccessor<DoFHandlerType, false> > &cell,
#endif
   Tensor<order, DoFHandlerType::dimension>                                   &derivative,
   const unsigned int                                                         component = 0);

  /**
   * Same as above, with <tt>mapping=MappingQGeneric@<dim@>(1)</tt>.
   */
  template <typename DoFHandlerType, class InputVector, int order>
  void
  approximate_derivative_tensor
  (const DoFHandlerType                                &dof,
   const InputVector                                   &solution,
#ifndef _MSC_VER
   const typename DoFHandlerType::active_cell_iterator &cell,
#else
   const TriaActiveIterator<dealii::DoFCellAccessor<DoFHandlerType, false> > &cell,
#endif
   Tensor<order, DoFHandlerType::dimension>            &derivative,
   const unsigned int                                   component = 0);

  /**
   * Return the norm of the derivative.
   */
  template <int dim, int order>
  double
  derivative_norm (const Tensor<order,dim> &derivative);

  /**
   * Exception
   */
  DeclException2 (ExcVectorLengthVsNActiveCells,
                  int, int,
                  << "The output vector needs to have a size equal "
                  "to the number of active cells of your triangulation "
                  "but has length " << arg1 << "There are "
                  << arg2 << " active cells in your triangulation.");
  /**
   * Exception
   */
  DeclExceptionMsg (ExcInsufficientDirections,
                    "We have encountered a cell on which the number of linearly "
                    "independent directions that span the matrix Y (discussed "
                    "in the documentation of the DerivativeApproximation "
                    "class) is not equal to dim. The matrix Y then is "
                    "rank deficient and can not be inverted.");
}



DEAL_II_NAMESPACE_CLOSE

#endif