This file is indexed.

/usr/share/pyshared/dolfin/fem/assembling.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
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
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
"""This module provides functionality for form assembly in Python,
corresponding to the C++ assembly and PDE classes.

The C++ :py:class:`assemble <dolfin.cpp.assemble>` function
(renamed to cpp_assemble) is wrapped with an additional
preprocessing step where code is generated using the
FFC JIT compiler.

The C++ PDE classes are reimplemented in Python since the C++ classes
rely on the dolfin::Form class which is not used on the Python side."""

# Copyright (C) 2007-2008 Anders Logg
#
# 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 Martin Sandve Alnaes, 2008.
# Modified by Johan Hake, 2008-2009.
# Modified by Garth N. Wells, 2008-2009.
#
# First added:  2007-08-15
# Last changed: 2010-11-04

__all__ = ["assemble", "assemble_system"]

import types

# UFL modules
from ufl import interval, triangle, tetrahedron

# Import SWIG-generated extension module (DOLFIN C++)
import dolfin.cpp as cpp

# Local imports
from dolfin.fem.form import *

# JIT assembler
def assemble(form,
             tensor=None,
             mesh=None,
             coefficients=None,
             function_spaces=None,
             cell_domains=None,
             exterior_facet_domains=None,
             interior_facet_domains=None,
             reset_sparsity=True,
             add_values=False,
             finalize_tensor=True,
             backend=None,
             form_compiler_parameters=None):
    """
    Assemble the given form and return the corresponding tensor.

    *Arguments*
        Depending on the input form, which may be a functional, linear
        form, bilinear form or higher rank form, a scalar value, a vector,
        a matrix or a higher rank tensor is returned.

    In the simplest case, no additional arguments are needed. However,
    additional arguments may and must in some cases be provided as
    outlined below.

    The ``form`` can be either an FFC form or a precompiled UFC
    form. If a precompiled or 'pure' UFC form is given, then
    ``coefficients`` and ``function_spaces`` have to be provided
    too. The coefficient functions should be provided as a 'dict'
    using the FFC functions as keys. The function spaces should be
    provided either as a list where the number of function spaces must
    correspond to the number of basis functions in the form, or as a
    single argument, implying that the same FunctionSpace is used for
    all test/trial spaces.

    If the form defines integrals over different subdomains,
    :py:class:`MeshFunctions <dolfin.cpp.MeshFunction>` over the
    corresponding topological entities defining the subdomains can be
    provided. An instance of a :py:class:`SubDomain
    <dolfin.cpp.SubDomain>` can also be passed for each subdomain.

    The implementation of the returned tensor is determined by the
    default linear algebra backend. This can be overridden by
    specifying a different backend.

    Each call to assemble() will create a new tensor. If the
    ``tensor`` argument is provided, this will be used instead. If
    ``reset_sparsity`` is set to True, the provided tensor will not be
    reset to zero before assembling (adding) values to the tensor.

    Specific form compiler parameters can be provided by the
    ``form_compiler_parameters`` argument. Form compiler parameters
    can also be controlled using the global parameters stored in
    parameters["form_compiler"].

    *Examples of usage*
        The standard stiffness matrix ``A`` and a load vector ``b``
        can be assembled as follows:

        .. code-block:: python

            A = assemble(inner(grad(u),grad(v))*dx)
            b = assemble(f*v*dx)

        It is possible to explicitly prescribe the domains over which
        integrals wll be evaluated using the arguments
        ``cell_domains``, ``exterior_facet_domains`` and
        ``interior_facet_domains``. For instance, using a mesh
        function marking parts of the boundary:

        .. code-block:: python

            # MeshFunction marking boundary parts
            boundary_parts = MeshFunction("uint", mesh, mesh.topology().dim()-1)

            # Sample variational forms
            a = inner(grad(u), grad(v))*dx + p*u*v*ds(0)
            L = f*v*dx - g*v*ds(1) + p*q*v*ds(0)

            A = assemble(a, exterior_facet_domains=boundary_parts)
            b = assemble(L, exterior_facet_domains=boundary_parts)

        To ensure that the assembled matrix has the right type, one may use
        the ``tensor`` argument:

        .. code-block:: python

            A = PETScMatrix()
            assemble(a, tensor=A)

        The form ``a`` is now assembled into the PETScMatrix ``A``.

    """

    # Extract common cell from mesh (may be missing in form definition)
    common_cell = None
    if mesh is not None:
        dim = mesh.topology().dim()
        common_cell = {1: interval, 2: triangle, 3: tetrahedron}[dim]

    # Wrap form
    dolfin_form = Form(form,
                       function_spaces=function_spaces,
                       coefficients=coefficients,
                       form_compiler_parameters=form_compiler_parameters,
                       common_cell=common_cell)

    # Set mesh if specified (important for functionals without a function spaces)
    if mesh is not None:
        dolfin_form.set_mesh(mesh)

    # Create tensor
    tensor = _create_tensor(form, dolfin_form.rank(), backend, tensor)

    # Extract domains
    cell_domains, exterior_facet_domains, interior_facet_domains = \
        _extract_domains(dolfin_form.mesh(),
                         cell_domains,
                         exterior_facet_domains,
                         interior_facet_domains)

    # Call C++ assemble function
    cpp.assemble(tensor,
                 dolfin_form,
                 cell_domains,
                 exterior_facet_domains,
                 interior_facet_domains,
                 reset_sparsity,
                 add_values,
                 finalize_tensor)

    # Convert to float for scalars
    if dolfin_form.rank() == 0:
        tensor = tensor.getval()

    # Return value
    return tensor

# JIT system assembler
def assemble_system(A_form,
                    b_form,
                    bcs=None,
                    x0=None,
                    A_coefficients=None,
                    b_coefficients=None,
                    A_function_spaces=None,
                    b_function_spaces=None,
                    cell_domains=None,
                    exterior_facet_domains=None,
                    interior_facet_domains=None,
                    reset_sparsity=True,
                    add_values=False,
                    finalize_tensor=True,
                    A_tensor=None,
                    b_tensor=None,
                    backend=None,
                    form_compiler_parameters=None):
    """
    Assemble form(s) and apply any given boundary conditions in a
    symmetric fashion and return tensor(s).

    The standard application of boundary conditions does not
    necessarily preserve the symmetry of the assembled matrix. In
    order to perserve symmetry in a system of equations with boundary
    conditions, one may use the alternative assemble_system instead of
    multiple calls to :py:func:`assemble
    <dolfin.fem.assembling.assemble>`.

    *Examples of usage*

       For instance, the statements

       .. code-block:: python

           A = assemble(a)
           b = assemble(L)
           bc.apply(A, b)

       can alternatively be carried out by

       .. code-block:: python

           A, b = assemble_system(a, L, bc)

       The statement above is valid even if ``bc`` is a list of
       :py:class:`DirichletBC <dolfin.fem.bcs.DirichletBC>`
       instances. For more info and options, see :py:func:`assemble
       <dolfin.fem.assembling.assemble>`.

    """

    # Extract subdomains
    subdomains = { "cell": cell_domains,
                   "exterior_facet": exterior_facet_domains,
                   "interior_facet": interior_facet_domains}

    # Wrap forms
    A_dolfin_form = Form(A_form, A_function_spaces, A_coefficients,
                         subdomains, form_compiler_parameters)
    b_dolfin_form = Form(b_form, b_function_spaces, b_coefficients,
                         subdomains, form_compiler_parameters)

    # Create tensors
    A_tensor = _create_tensor(A_form, A_dolfin_form.rank(), backend, A_tensor)
    b_tensor = _create_tensor(b_form, b_dolfin_form.rank(), backend, b_tensor)

    # Extract domains
    cell_domains, exterior_facet_domains, interior_facet_domains = \
        _extract_domains(A_dolfin_form.mesh(),
                         cell_domains,
                         exterior_facet_domains,
                         interior_facet_domains)

    # Check bcs
    if not isinstance(bcs,(types.NoneType,list,cpp.DirichletBC)):
        raise TypeError, "expected a 'list', or a 'DirichletBC' as bcs argument"
    if bcs is None:
        bcs = []
    elif isinstance(bcs,cpp.DirichletBC):
        bcs = [bcs]

    # Call C++ assemble function
    cpp.assemble_system(A_tensor,
                        b_tensor,
                        A_dolfin_form,
                        b_dolfin_form,
                        bcs,
                        cell_domains,
                        exterior_facet_domains,
                        interior_facet_domains,
                        x0,
                        reset_sparsity,
                        add_values,
                        finalize_tensor)

    return A_tensor, b_tensor

def _create_tensor(form, rank, backend, tensor):
    "Create tensor for form"

    # Check if tensor is supplied by user
    if tensor is not None:
        return tensor

    # Check backend argument
    if (not backend is None) and (not isinstance(backend, cpp.LinearAlgebraFactory)):
        raise TypeError, "Provide a LinearAlgebraFactory as 'backend'"

    # Create tensor
    if rank == 0:
        tensor = cpp.Scalar()
    elif rank == 1:
        if backend: tensor = backend.create_vector()
        else:       tensor = cpp.Vector()
    elif rank == 2:
        if backend: tensor = backend.create_matrix()
        else:       tensor = cpp.Matrix()
    else:
        raise RuntimeError, "Unable to create tensors of rank %d." % rank

    return tensor

def _extract_domains(mesh,
                     cell_domains,
                     exterior_facet_domains,
                     interior_facet_domains):

    def check_domain_type(domain,domain_type):
        if not isinstance(domain,(cpp.SubDomain,cpp.MeshFunctionUInt,types.NoneType)):
            raise TypeError, "expected a 'SubDomain', 'MeshFunction' of 'UInt' or 'None', for the '%s'"%domain_type

    def build_mf(subdomain, dim):
        " Builds a MeshFunction from a SubDomain"
        mf = cpp.MeshFunction("uint", mesh, dim)
        mf.set_all(1)
        subdomain.mark(mf,0)
        return mf

    # Type check of input
    check_domain_type(cell_domains,"cell_domains")
    check_domain_type(exterior_facet_domains,"exterior_facet_domains")
    check_domain_type(interior_facet_domains,"interior_facet_domains")

    # The cell dimension
    cell_dim = mesh.topology().dim()

    # Get cell_domains
    if isinstance(cell_domains, cpp.SubDomain):
        cell_domains = build_mf(cell_domains, cell_dim)

    # Get exterior_facet_domains (may be stored as part of the mesh)
    if exterior_facet_domains is None:
        exterior_facet_domains = mesh.data().mesh_function("exterior facet domains")
    elif isinstance(exterior_facet_domains, cpp.SubDomain):
        exterior_facet_domains = build_mf(exterior_facet_domains, cell_dim-1)

    # Get interior_facet_domains
    if isinstance(interior_facet_domains, cpp.SubDomain):
        interior_facet_domains = build_mf(interior_facet_domains, cell_dim-1)

    return cell_domains, exterior_facet_domains, interior_facet_domains