This file is indexed.

/usr/include/dolfin/fem/SystemAssembler.h is in libdolfin-dev 1.4.0+dfsg-4.

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
// Copyright (C) 2008-2013 Kent-Andre Mardal and Garth N. Wells
//
// 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 Anders Logg 2008-2011
//
// First added:  2009-06-22
// Last changed: 2013-04-23

#ifndef __SYSTEM_ASSEMBLER_H
#define __SYSTEM_ASSEMBLER_H

#include <map>
#include <vector>
#include <boost/array.hpp>
#include <memory>
#include "DirichletBC.h"
#include "AssemblerBase.h"

namespace ufc
{
  class cell_integral;
}

namespace dolfin
{

  // Forward declarations
  class Cell;
  class Facet;
  class Form;
  class GenericMatrix;
  class GenericVector;
  template<typename T> class MeshFunction;
  class UFC;

  /// This class provides an assembler for systems of the form
  /// Ax = b. It differs from the default DOLFIN assembler in that it
  /// applies boundary conditions at the time of assembly, which
  /// preserves any symmetries in A.

  class SystemAssembler : public AssemblerBase
  {
  public:

    /// Constructor
    SystemAssembler(const Form& a, const Form& L);

    /// Constructor
    SystemAssembler(const Form& a, const Form& L, const DirichletBC& bc);

    /// Constructor
    SystemAssembler(const Form& a, const Form& L,
                    const std::vector<const DirichletBC*> bcs);

    /// Constructor
    SystemAssembler(std::shared_ptr<const Form> a,
                    std::shared_ptr<const Form> L);

    /// Constructor
    SystemAssembler(std::shared_ptr<const Form> a,
                    std::shared_ptr<const Form> L,
                    const DirichletBC& bc);

    /// Constructor
    SystemAssembler(std::shared_ptr<const Form> a,
                    std::shared_ptr<const Form> L,
                    const std::vector<const DirichletBC*> bcs);

    /// Assemble system (A, b)
    void assemble(GenericMatrix& A, GenericVector& b);

    /// Assemble matrix A
    void assemble(GenericMatrix& A);

    /// Assemble vector b
    void assemble(GenericVector& b);

    /// Assemble system (A, b) for (negative) increment dx, where
    /// x = x0 - dx is solution to system a == -L subject to bcs.
    /// Suitable for use inside a (quasi-)Newton solver.
    void assemble(GenericMatrix& A, GenericVector& b, const GenericVector& x0);

    /// Assemble rhs vector b for (negative) increment dx, where
    /// x = x0 - dx is solution to system a == -L subject to bcs.
    /// Suitable for use inside a (quasi-)Newton solver.
    void assemble(GenericVector& b, const GenericVector& x0);

  private:

    // Check form arity
    static void check_arity(std::shared_ptr<const Form> a,
                            std::shared_ptr<const Form> L);

    // Assemble system
    void assemble(GenericMatrix* A, GenericVector* b,
                  const GenericVector* x0);

    // Bilinear and linear forms
    std::shared_ptr<const Form> _a, _l;

    // Boundary conditions
    std::vector<const DirichletBC*> _bcs;

    class Scratch;

    static void
      cell_wise_assembly(boost::array<GenericTensor*, 2>& tensors,
                         boost::array<UFC*, 2>& ufc,
                         Scratch& data,
                         const DirichletBC::Map& boundary_values,
                         const MeshFunction<std::size_t>* cell_domains,
                       const MeshFunction<std::size_t>* exterior_facet_domains);

    static void
    facet_wise_assembly(boost::array<GenericTensor*, 2>& tensors,
                        boost::array<UFC*, 2>& ufc,
                        Scratch& data,
                        const DirichletBC::Map& boundary_values,
                        const MeshFunction<std::size_t>* cell_domains,
                        const MeshFunction<std::size_t>* exterior_facet_domains,
                       const MeshFunction<std::size_t>* interior_facet_domains);

    static void apply_bc(double* A, double* b,
                         const DirichletBC::Map& boundary_values,
                         const std::vector<dolfin::la_index>& global_dofs0,
                         const std::vector<dolfin::la_index>& global_dofs1);

    // Return true if cell has an Dirichlet/essential boundary
    // condition applied
    static bool has_bc(const DirichletBC::Map& boundary_values,
                       const std::vector<dolfin::la_index>& dofs);

    // Return true if element matrix is required
    static bool cell_matrix_required(const GenericTensor* A,
                                     const void* integral,
                                     const DirichletBC::Map& boundary_values,
                                     const std::vector<dolfin::la_index>& dofs);

    // Class to hold temporary data
    class Scratch
    {
    public:

      Scratch(const Form& a, const Form& L);

      ~Scratch();

      void zero_cell();

      boost::array<std::vector<double>, 2> Ae;

    };

  };

}

#endif