This file is indexed.

/usr/include/dolfin/nls/PETScSNESSolver.h is in libdolfin-dev 2016.2.0-2.

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
// Copyright (C) 2012 Patrick E. Farrell
//
// This file is part of DOLFIN.
//
// DOLFIN is free software: you can 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 3 of the License, or
// (at your option) any later version.
//
// DOLFIN is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
//
// Modified by Corrado Maurini, 2013.

#ifndef __PETSC_SNES_SOLVER_H
#define __PETSC_SNES_SOLVER_H

#ifdef HAS_PETSC

#include <map>
#include <memory>
#include <petscsnes.h>

#include <dolfin/common/MPI.h>
#include <dolfin/la/PETScObject.h>
#include <dolfin/nls/NewtonSolver.h>
#include <dolfin/parameter/Parameters.h>

namespace dolfin
{

  /// Forward declarations
  class PETScVector;

  /// This class implements methods for solving nonlinear systems via
  /// PETSc's SNES interface. It includes line search and trust region
  /// techniques for globalising the convergence of the nonlinear
  /// iteration.

  class PETScSNESSolver : public PETScObject
  {
  public:

    /// Create SNES solver
    explicit PETScSNESSolver(MPI_Comm comm);

    /// Create SNES solver for a particular method
    PETScSNESSolver(std::string nls_type="default");

    /// Destructor
    virtual ~PETScSNESSolver();

    /// Solve a nonlinear variational inequality with bound constraints
    ///
    /// *Arguments*
    ///     nonlinear_function (_NonlinearProblem_)
    ///         The nonlinear problem.
    ///     x (_GenericVector_)
    ///         The vector.
    ///     lb (_GenericVector_)
    ///         The lower bound.
    ///     ub (_GenericVector_)
    ///         The upper bound.
    ///
    /// *Returns*
    ///     std::pair<std::size_t, bool>
    ///         Pair of number of Newton iterations, and whether
    ///         iteration converged)
    std::pair<std::size_t, bool> solve(NonlinearProblem& nonlinear_problem,
                                       GenericVector& x,
                                       const GenericVector& lb,
                                       const GenericVector& ub);

    /// Solve abstract nonlinear problem :math:`F(x) = 0` for given
    /// :math:`F` and Jacobian :math:`\dfrac{\partial F}{\partial x}`.
    ///
    /// *Arguments*
    ///     nonlinear_function (_NonlinearProblem_)
    ///         The nonlinear problem.
    ///     x (_GenericVector_)
    ///         The vector.
    ///
    /// *Returns*
    ///     std::pair<std::size_t, bool>
    ///         Pair of number of Newton iterations, and whether
    ///         iteration converged)
    std::pair<std::size_t, bool> solve(NonlinearProblem& nonlinear_function,
                                       GenericVector& x);

    /// Set up the SNES object, but don't do anything yet, in case the
    /// user wants to access the SNES object directly
    void init(NonlinearProblem& nonlinear_problem, GenericVector& x);

    /// Set options from the PETSc options database
    void set_from_options() const;

    /// Sets the prefix used by PETSc when searching the PETSc options
    /// database
    void set_options_prefix(std::string options_prefix);

    /// Returns the prefix used by PETSc when searching the PETSc
    /// options database
    std::string get_options_prefix() const;

    /// Return the MPI communicator
    MPI_Comm mpi_comm() const;

    /// Return a list of available solver methods
    static std::vector<std::pair<std::string, std::string>> methods();

    /// Default parameter values
    static Parameters default_parameters();

    Parameters parameters;

    /// Return PETSc SNES pointer
    SNES snes() const
    { return _snes; }

  private:

    struct snes_ctx_t
    {
      // Constructor
      snes_ctx_t() : nonlinear_problem(NULL), x(NULL), f_tmp(NULL), xl(NULL),
                     xu(NULL) {}

      // Destructor
      ~snes_ctx_t()
      {
        if (f_tmp)
          VecDestroy(&f_tmp);
      }

      NonlinearProblem* nonlinear_problem;
      PETScVector* x;
      Vec f_tmp;
      const PETScVector* xl;
      const PETScVector* xu;
    };

    // PETSc solver pointer
    SNES _snes;

    // Update the linear solver parameters
    void set_linear_solver_parameters();

    // Available solvers
    static const std::map<std::string,
      std::pair<std::string, const SNESType>> _methods;

    // The callback for PETSc to compute F, the nonlinear residual
    static PetscErrorCode FormFunction(SNES snes, Vec x, Vec f, void* ctx);

    // The callback for PETSc to compute A, the Jacobian
    static PetscErrorCode FormJacobian(SNES snes, Vec x, Mat A, Mat B,
                                       void* ctx);

    static PetscErrorCode FormObjective(SNES snes, Vec x, PetscReal* out,
                                        void* ctx);

    // Set the bounds on the problem from the parameters, if desired
    // Here, x is passed in as a model vector from which we make our
    // Vecs that tell PETSc the bounds if the "sign" parameter is
    // used.
    void set_bounds(GenericVector& x);

    // Check if the problem is a variational inequality
    bool is_vi() const;

    // Upper and lower bounds for bound-constrained solvers
    std::shared_ptr<const PETScVector> lb;
    std::shared_ptr<const PETScVector> ub;

    // Flag to indicate if explicit bounds are set
    bool _has_explicit_bounds;

    // SNES context
    struct snes_ctx_t _snes_ctx;
  };

}

#endif

#endif