This file is indexed.

/usr/share/pyshared/dolfin/fem/adaptivesolving.py is in python-dolfin 1.0.0-7.

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
"""This module provides a Python layer on top of the C++
Adaptive*VariationalSolver classes"""

# Copyright (C) 2011 Marie E. Rognes
#
# 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 2011
#
# First added:  2011-06-27
# Last changed: 2011-11-14

__all__ = ["AdaptiveLinearVariationalSolver",
           "AdaptiveNonlinearVariationalSolver",
           "generate_error_control",
           "generate_error_control_forms"]

import dolfin.cpp as cpp

from dolfin.fem.form import Form
from dolfin.fem.solving import LinearVariationalProblem
from dolfin.fem.solving import NonlinearVariationalProblem

from dolfin.fem.errorcontrolgenerator import DOLFINErrorControlGenerator

class AdaptiveLinearVariationalSolver(cpp.AdaptiveLinearVariationalSolver):

    # Reuse doc-string
    __doc__ = cpp.AdaptiveLinearVariationalSolver.__doc__

    def __init__(self, problem):
        """
        Create AdaptiveLinearVariationalSolver

        *Arguments*

            problem (:py:class:`LinearVariationalProblem <dolfin.fem.solving.LinearVariationalProblem>`)

        """

        # Store problem
        self.problem = problem

        # Initialize C++ base class
        cpp.AdaptiveLinearVariationalSolver.__init__(self, problem)

    def solve(self, tol, goal):
        """
        Solve such that the estimated error in the functional 'goal'
        is less than the given tolerance 'tol'

        *Arguments*

            tol (float)

                The error tolerance

            goal (:py:class:`Form <dolfin.fem.form.Form>`)

                The goal functional

        """

        # Generate error control object
        ec = generate_error_control(self.problem, goal)

        # Compile goal functional separately
        p = self.problem.form_compiler_parameters
        M = Form(goal, form_compiler_parameters=p)

        # Call cpp.AdaptiveLinearVariationalSolver.solve with ec
        cpp.AdaptiveLinearVariationalSolver.solve(self, tol, M, ec)

class AdaptiveNonlinearVariationalSolver(cpp.AdaptiveNonlinearVariationalSolver):

    # Reuse doc-string
    __doc__ = cpp.AdaptiveNonlinearVariationalSolver.__doc__

    def __init__(self, problem):
        """
        Create AdaptiveLinearVariationalSolver

        *Arguments*

            problem (:py:class:`NonlinearVariationalProblem <dolfin.fem.solving.NonlinearVariationalProblem>`)

        """

        # Store problem
        self.problem = problem

        # Initialize C++ base class
        cpp.AdaptiveNonlinearVariationalSolver.__init__(self, problem)

    def solve(self, tol, goal):
        """
        Solve such that the estimated error in the functional 'goal'
        is less than the given tolerance 'tol'.

        *Arguments*

            tol (float)

                The error tolerance

            goal (:py:class:`Form <dolfin.fem.form.Form>`)

                The goal functional

        """

        # Generate error control object
        ec = generate_error_control(self.problem, goal)

        # Compile goal functional separately
        p = self.problem.form_compiler_parameters
        M = Form(goal, form_compiler_parameters=p)

        # Call cpp.AdaptiveNonlinearVariationlSolver.solve with ec
        cpp.AdaptiveNonlinearVariationalSolver.solve(self, tol, M, ec)

def generate_error_control(problem, goal):
    """
    Create suitable ErrorControl object from problem and the goal

    *Arguments*

        problem (:py:class:`LinearVariationalProblem <dolfin.fem.solving.LinearVariationalProblem>` or :py:class:`NonlinearVariationalProblem <dolfin.fem.solving.NonlinearVariationalProblem>`)

            The (primal) problem

        goal (:py:class:`Form <dolfin.fem.form.Form>`)

            The goal functional

    *Returns*

        :py:class:`ErrorControl <dolfin.cpp.ErrorControl>`

    """

    # Generate UFL forms to be used for error control
    (ufl_forms, is_linear) = generate_error_control_forms(problem, goal)

    # Compile generated forms
    p = problem.form_compiler_parameters
    forms = [Form(form, form_compiler_parameters=p) for form in ufl_forms]

    # Create cpp.ErrorControl object
    forms += [is_linear]  # NOTE: Lingering design inconsistency.
    ec = cpp.ErrorControl(*forms)

    # Return generated ErrorControl
    return ec

def generate_error_control_forms(problem, goal):
    """
    Create UFL forms required for initializing an ErrorControl object

    *Arguments*

        problem (:py:class:`LinearVariationalProblem <dolfin.fem.solving.LinearVariationalProblem>` or :py:class:`NonlinearVariationalProblem <dolfin.fem.solving.NonlinearVariationalProblem>`)

            The (primal) problem

        goal (:py:class:`Form <dolfin.fem.form.Form>`)

            The goal functional

    *Returns*

        (tuple of forms, bool)

    """

    msg = "Generating forms required for error control. This can take time..."
    cpp.info(msg)

    # Extract primal forms from problem
    is_linear = True
    if isinstance(problem, LinearVariationalProblem):
        primal = (problem.a_ufl, problem.L_ufl)
    elif isinstance(problem, NonlinearVariationalProblem):
        is_linear = False
        primal = problem.F_ufl
    else:
        cpp.dolfin_error("adaptivesolving.py",
                         "generate forms required for error control"
                         "Unknown problem type (\"%s\")" % str(problem))

    # Extract unknown Function from problem
    u = problem.u_ufl

    # Get DOLFIN's error control generator to generate all forms
    generator = DOLFINErrorControlGenerator(primal, goal, u)
    forms = generator.generate_all_error_control_forms()

    return (forms, is_linear)