Added periodic homog example + changes in process files for including zip and notebooks

doc/conf.py

@@ -24,8 +24,9 @@ sys.path.insert(0, os.path.abspath('..'))
 #sys.path.insert(0, os.path.abspath('../examples</'))
 
 sys.path.append(os.getcwd())
-import rstprocess
-rstprocess.process()
+import process_sources
+process_sources.process()
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -35,13 +36,17 @@ rstprocess.process()
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx',
-              'sphinx.ext.mathjax', 'sphinx.ext.napoleon']
+              'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'nbsphinx']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
+source_parsers = {
+   '.md': 'recommonmark.parser.CommonMarkParser',
+}
+
 # The suffix of source filenames.
-source_suffix = '.rst'#,'.txt']
+source_suffix = ['.rst','.md']#,'.txt']
 
 # The encoding of source files.
 #source_encoding = 'utf-8-sig'
@@ -58,9 +63,9 @@ copyright = u'2016, Jeremy Bleyer'
 # built documents.
 #
 # The short X.Y version.
-version = '1.0'
+version = 'master'
 # The full version, including alpha/beta/rc tags.
-release = '1.0'
+release = 'master'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -74,7 +79,7 @@ release = '1.0'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ['_build', '**.ipynb_checkpoints']
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -186,6 +191,7 @@ html_static_path = ['_static']
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'NumericaltoursofcontinuummechanicsusingFEniCSdoc'
 
+html_short_title = "Numerical tours of continuum mechanics using FEniCS"
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -204,7 +210,7 @@ latex_elements = {
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', 'NumericaltoursofcontinuummechanicsusingFEniCS.tex', u'Numerical tours of continuum mechanics using FEniCS Documentation',
+  ('index', 'NumericaltoursofcontinuummechanicsusingFEniCS.tex', u'Numerical tours of continuum mechanics using FEniCS',
    u'Jeremy Bleyer', 'manual'),
 ]
 
@@ -216,6 +222,7 @@ latex_documents = [
 # not chapters.
 #latex_use_parts = False
 
+
 # If true, show page references after internal links.
 #latex_show_pagerefs = False
 
@@ -234,7 +241,7 @@ latex_documents = [
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'numericaltoursofcontinuummechanicsusingfenics', u'Numerical tours of continuum mechanics using FEniCS Documentation',
+    ('index', 'numericaltoursofcontinuummechanicsusingfenics', u'Numerical tours of continuum mechanics using FEniCS',
      [u'Jeremy Bleyer'], 1)
 ]
 
@@ -248,7 +255,7 @@ man_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'NumericaltoursofcontinuummechanicsusingFEniCS', u'Numerical tours of continuum mechanics using FEniCS Documentation',
+  ('index', 'NumericaltoursofcontinuummechanicsusingFEniCS', u'Numerical tours of continuum mechanics using FEniCS',
    u'Jeremy Bleyer', 'NumericaltoursofcontinuummechanicsusingFEniCS', 'One line description of project.',
    'Miscellaneous'),
 ]
@@ -264,3 +271,19 @@ texinfo_documents = [
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
+#nbsphinx_prolog = """
+#Go there: https://example.org/notebooks/{{ env.doc2path(env.docname, base=None) }}
+#
+#----
+#"""
+
+#{% set docname = env.doc2path(env.docname, base='doc') %}
+nbsphinx_prolog = r"""
+{% set docname = env.docname.split("/")[-1] %}
+.. role:: raw-html(raw)
+ :format: html
+.. nbinfo::
+ The corresponding files can be obtained from:
+
+ - Jupyter Notebook: :download:`{{docname+".ipynb"}}`
+ - Python script: :download:`{{docname+".py"}}`"""
\ No newline at end of file

doc/homogenization.rst

+.. Numerical tours of continuum mechanics using FEniCS documentation master file, created by
+   sphinx-quickstart on Wed Jun  8 21:25:10 2016.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Homogenization of heterogeneous materials
+=========================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 1
+
+   demo/periodic_homog_elas/periodic_homog_elas.ipynb
+
+
+

doc/index.rst

@@ -13,6 +13,7 @@ Contents:
 
    intro
    linear_problems
+   homogenization
    nonlinear_problems
    demo/reissner_mindlin/reissner_mindlin.rst
    tips_and_tricks

doc/nonlinear_problems.rst

@@ -10,7 +10,7 @@ Contents:
 .. toctree::
    :maxdepth: 1
 
-   demo/nonlinear_materials/vonMises_plasticity.py.rst
+   demo/2D_plasticity/vonMises_plasticity.py.rst
 
 
 

doc/rstprocess.py → doc/process_sources.py

@@ -19,9 +19,11 @@
 import sys
 import os
 import shutil
+import zipfile
 
 # extensions of files which must be copied with the demo when building docs
 file_extensions = [".png",".gif", ".geo", ".xml", ".msh", ".pdf"]
+zipfile_extensions = [".geo", ".msh", ".xml", ".py", ".ipynb"]
 
 def process():
     """Copy demo rst files (C++ and Python) from the DOLFIN source tree
@@ -36,7 +38,7 @@ def process():
 
     # Directories to scan
     subdirs = ["../examples"]
-
+    retval = os.getcwd()
     # Iterate over subdirectories containing demos
     for subdir in subdirs:
 
@@ -55,28 +57,51 @@ def process():
                 if not os.path.isdir(version_path):
                     continue
 
-                # Build list of rst files in demo source directory
-                rst_files = [f for f in os.listdir(version_path) if os.path.splitext(f)[1] == ".rst" ]
-
                 # Create directory in documentation tree for demo
-                demo_dir = os.path.join('./demo/', demo, version)
+                demo_dir = os.path.join('./demo/', demo)
                 if not os.path.exists(demo_dir):
                     os.makedirs(demo_dir)
 
+                ipynb_files =  [f for f in os.listdir(version_path) if f.endswith("ipynb") ]
+                for f in ipynb_files:
+                    ff = os.path.join(path, f)
+                    shutil.copy(ff, demo_dir)
+                    ret = os.system("jupyter-nbconvert --to script %s --output %s" % (ff,  os.path.join("../../doc",demo_dir, os.path.splitext(f)[0])))
+                    if not ret == 0:
+                        raise RuntimeError("Unable to convert ipynb file to a .py ({})".format(f))
+
+                # Build list of rst files in demo source directory
+                rst_files = [f for f in os.listdir(version_path) if f.endswith("rst") ]
+
                 # Copy rst files into documentation demo directory and process with Pylit
                 for f in rst_files:
                     shutil.copy(os.path.join(version_path, f), demo_dir)
 
                     # Run pylit on cpp.rst and py.rst files (file with 'double extensions')
-                    if os.path.splitext(os.path.splitext(f)[0])[1] in (".py"):
+                    if "py" in f.split("."):
                         rst_file = os.path.join(demo_dir, f)
                         command = pylit_parser + " " + rst_file
                         ret = os.system("python "+command)
                         if not ret == 0:
                             raise RuntimeError("Unable to convert rst file to a .py ({})".format(f))
 
+
+
                 tocopy_files = [f for f in os.listdir(version_path) if os.path.splitext(f)[1] in file_extensions ]
                 for f in tocopy_files:
                     source = os.path.join(version_path, f)
-                    print("Copying {} to {}".format(source, demo_dir)) 
+                    print("Copying {} to {}".format(source, demo_dir))
                     shutil.copy(source, demo_dir)
+
+                for f in ipynb_files + rst_files:
+                    cwd = os.getcwd()
+                    os.chdir(demo_dir)
+                    files = os.listdir(".")
+                    zip_files = []
+                    for ff in files:
+                        if any([ff.endswith(ext) for ext in zipfile_extensions]):
+                            zip_files.append(ff)
+                    with zipfile.ZipFile(f.split(".")[0]+".zip", 'w') as myzip:
+                        for a in zip_files:
+                            myzip.write(a, compress_type=zipfile.ZIP_DEFLATED)
+                    os.chdir(cwd)

examples/nonlinear_materials/vonMises_plasticity.py.rst → examples/2D_plasticity/vonMises_plasticity.py.rst

@@ -2,28 +2,28 @@
 .. _vonMisesPlasticity:
 
 ==================================================
-Elasto-plastic analysis of a 2D von Mises material 
+Elasto-plastic analysis of a 2D von Mises material
 ==================================================
 
 -------------
 Introduction
 -------------
 
-This example is concerned with the incremental analysis of an elasto-plastic 
+This example is concerned with the incremental analysis of an elasto-plastic
 von Mises material. The structure response is computed using an iterative
 predictor-corrector return mapping algorithm embedded in a Newton-Raphson global
 loop for restoring equilibrium. Due to the simple expression of the von Mises criterion,
 the return mapping procedure is completely analytical (with linear isotropic
-hardening). The corresponding file can be obtained from :download:`vonMises_plasticity.py`.
+hardening). The corresponding sources can be obtained from :download:`vonMises_plasticity.zip`.
 Another implementation of von Mises plasticity can also be found at
 https://bitbucket.org/fenics-apps/fenics-solid-mechanics.
 
 We point out that the 2D nature of the problem will impose keeping
 track of the out-of-plane :math:`\varepsilon_{zz}^p` plastic strain and dealing with
-representations of stress/strain states including the :math:`zz` component. Note 
+representations of stress/strain states including the :math:`zz` component. Note
 also that are not concerned with the issue of volumetric locking induced by
-incompressible plastic deformations since quadratic triangles in 2D is enough 
-to mitigate the locking phenomenon. 
+incompressible plastic deformations since quadratic triangles in 2D is enough
+to mitigate the locking phenomenon.
 
 The plastic strain evolution during the cylinder expansion will look like this:
 
@@ -35,12 +35,12 @@ The plastic strain evolution during the cylinder expansion will look like this:
 Problem position
 -----------------
 
-In FEniCS 2017.2, the FEniCS Form Compiler ``ffc`` now uses ``uflacs`` as a default 
+In FEniCS 2017.2, the FEniCS Form Compiler ``ffc`` now uses ``uflacs`` as a default
 representation instead of the old ``quadrature`` representation. However, using
 ``Quadrature`` elements generates some bugs in this representation and we therefore
 need to revert to the old representation. Deprecation warning messages are also disabled.
 See `this post <https://www.allanswered.com/post/lknbq/assemble-quadrature-representation-vs-uflacs/>`_
-and the corresponding `issue <https://bitbucket.org/fenics-project/ffc/issues/146/uflacs-generates-undefined-variable-for>`_ 
+and the corresponding `issue <https://bitbucket.org/fenics-project/ffc/issues/146/uflacs-generates-undefined-variable-for>`_
 for more information.::
 
  from __future__ import print_function
@@ -64,9 +64,9 @@ can also be related to a tangent elastic modulus :math:`E_t = \dfrac{EH}{E+H}`.
 
 
 The considered problem is that of a plane strain hollow cylinder of internal (resp. external)
-radius :math:`R_i` (resp. :math:`R_e`) under internal uniform pressure :math:`q`. 
+radius :math:`R_i` (resp. :math:`R_e`) under internal uniform pressure :math:`q`.
 Only a quarter of cylinder is generated using ``Gmsh`` and converted to ``.xml`` format. ::
- 
+
  # elastic parameters
  E = Constant(70e3)
  nu = Constant(0.3)
@@ -80,7 +80,7 @@ Only a quarter of cylinder is generated using ``Gmsh`` and converted to ``.xml``
  mesh = Mesh("thick_cylinder.xml")
  facets = MeshFunction("size_t", mesh, "thick_cylinder_facet_region.xml")
  ds = Measure('ds')[facets]
- 
+
 Function spaces will involve a standard CG space for the displacement whereas internal
 state variables such as plastic strains will be represented using a **Quadrature** element.
 This choice will make it possible to express the complex non-linear material constitutive
@@ -99,16 +99,16 @@ of Gauss points will be determined by the required degree of the Quadrature elem
  W = FunctionSpace(mesh, We)
  W0e = FiniteElement("Quadrature", mesh.ufl_cell(), degree=deg_stress, quad_scheme='default')
  W0 = FunctionSpace(mesh, W0e)
- 
+
 .. note::
  In older versions, it was possible to define Quadrature function spaces directly
  using ``FunctionSpace(mesh, "Quadrature", 1)``. This is no longer the case since
- FEniCS 2016.1 (see `this issue <https://bitbucket.org/fenics-project/dolfin/issues/757/functionspace-mesh-quadrature-1-broken-in>`_). Instead, Quadrature elements must first be defined 
+ FEniCS 2016.1 (see `this issue <https://bitbucket.org/fenics-project/dolfin/issues/757/functionspace-mesh-quadrature-1-broken-in>`_). Instead, Quadrature elements must first be defined
  by specifying the associated degree and quadrature scheme before defining the
  associated FunctionSpace.
- 
- 
- 
+
+
+
 Various functions are defined to keep track of the current internal state and
 currently computed increments::
 
@@ -124,21 +124,21 @@ currently computed increments::
  u_ = TestFunction(V)
 
 Boundary conditions correspond to symmetry conditions on the bottom and left
-parts (resp. numbered 1 and 3). Loading consists of a uniform pressure on the 
+parts (resp. numbered 1 and 3). Loading consists of a uniform pressure on the
 internal boundary (numbered 4). It will be progressively increased from 0 to
 :math:`q_{lim}=\dfrac{2}{\sqrt{3}}\sigma_0\log\left(\dfrac{R_e}{R_i}\right)`
 which is the analytical collapse load for a perfectly-plastic material (no hardening)::
 
  bc = [DirichletBC(V.sub(1), 0, facets, 1), DirichletBC(V.sub(0), 0, facets, 3)]
 
- 
+
  n = FacetNormal(mesh)
  q_lim = float(2/sqrt(3)*ln(Re/Ri)*sig0)
  loading = Expression("-q*t", q=q_lim, t=0, degree=2)
 
  def F_ext(v):
      return loading*dot(n, v)*ds(4)
- 
+
 -----------------------------
 Constitutive relation update
 -----------------------------
@@ -147,7 +147,7 @@ Before writing the variational form, we now define some useful functions which
 will enable performing the constitutive relation update using a return mapping
 procedure. This step is quite classical in FEM plasticity for a von Mises criterion
 with isotropic hardening and follow notations from [BON2014]_. First, the strain
-tensor will be represented in a 3D fashion by appending zeros on the out-of-plane 
+tensor will be represented in a 3D fashion by appending zeros on the out-of-plane
 components since, even if the problem is 2D, the plastic constitutive relation will
 involve out-of-plane plastic strains. The elastic consitutive relation is also defined
 and a function ``as_3D_tensor`` will enable to represent a 4 dimensional vector
@@ -166,35 +166,35 @@ containing respectively :math:`xx, yy, zz` and :math:`xy` components as a 3D ten
                        [0, 0, X[2]]])
 
 The return mapping procedure consists in finding a new stress :math:`\boldsymbol{\sigma}_{n+1}`
-and internal variable :math:`p_{n+1}` state verifying the current plasticity condition 
-from a previous stress :math:`\boldsymbol{\sigma}_{n}` and internal variable :math:`p_n` state  and 
+and internal variable :math:`p_{n+1}` state verifying the current plasticity condition
+from a previous stress :math:`\boldsymbol{\sigma}_{n}` and internal variable :math:`p_n` state  and
 an increment of total deformation :math:`\Delta \boldsymbol{\varepsilon}`. An elastic
-trial stress :math:`\boldsymbol{\sigma}_{\text{elas}} = \boldsymbol{\sigma}_{n} + \mathbf{C}\Delta \boldsymbol{\varepsilon}` 
-is first computed. The plasticity criterion is then evaluated with the previous plastic strain 
-:math:`f_{\text{elas}} = \sigma^{eq}_{\text{elas}} - \sigma_0 - H p_n` where 
+trial stress :math:`\boldsymbol{\sigma}_{\text{elas}} = \boldsymbol{\sigma}_{n} + \mathbf{C}\Delta \boldsymbol{\varepsilon}`
+is first computed. The plasticity criterion is then evaluated with the previous plastic strain
+:math:`f_{\text{elas}} = \sigma^{eq}_{\text{elas}} - \sigma_0 - H p_n` where
 :math:`\sigma^{eq}_{\text{elas}} = \sqrt{\frac{3}{2}\boldsymbol{s}:\boldsymbol{s}}`
 with the deviatoric elastic stress :math:`\boldsymbol{s} = \operatorname{dev}\boldsymbol{\sigma}_{\text{elas}}`.
 If :math:`f_{\text{elas}} < 0`, no plasticity occurs during this time increment and
-:math:`\Delta p,\Delta  \boldsymbol{\varepsilon}^p =0`. 
+:math:`\Delta p,\Delta  \boldsymbol{\varepsilon}^p =0`.
 
 Otherwise, plasticity
 occurs and the increment of plastic strain is given by :math:`\Delta p = \dfrac{f_{\text{elas}}}{3\mu+H}`.
 Hence, both elastic and plastic evolution can be accounted for by defining the
-plastic strain increment as follows: 
+plastic strain increment as follows:
 
 .. math::
  \Delta p = \dfrac{\langle f_{\text{elas}}\rangle_+}{3\mu+H}
 
 where :math:`\langle \star \rangle_+` represents the positive part of :math:`\star`
 and is obtained by function ``ppos``. Plastic evolution also requires the computation
-of the normal vector to the final yield surface given by 
+of the normal vector to the final yield surface given by
 :math:`\boldsymbol{n}_{\text{elas}} = \boldsymbol{s}/\sigma_{\text{elas}}^{eq}`. In the following,
-this vector must be zero in case of elastic evolution. Hence, we multiply it by 
+this vector must be zero in case of elastic evolution. Hence, we multiply it by
 :math:`\dfrac{\langle f_{\text{elas}}\rangle_+}{ f_{\text{elas}}}` to tackle
-both cases in a single expression. The final stress state is corrected by the 
-plastic strain as follows :math:`\boldsymbol{\sigma}_{n+1} = \boldsymbol{\sigma}_{\text{elas}} - 
-\beta \boldsymbol{s}` with :math:`\beta = \dfrac{3\mu}{\sigma_{\text{elas}}^{eq}}\Delta p`. 
-It can be observed that the last term vanishes in case of elastic evolution so 
+both cases in a single expression. The final stress state is corrected by the
+plastic strain as follows :math:`\boldsymbol{\sigma}_{n+1} = \boldsymbol{\sigma}_{\text{elas}} -
+\beta \boldsymbol{s}` with :math:`\beta = \dfrac{3\mu}{\sigma_{\text{elas}}^{eq}}\Delta p`.
+It can be observed that the last term vanishes in case of elastic evolution so
 that the final stress is indeed the elastic predictor. ::
 
  ppos = lambda x: (x+abs(x))/2.
@@ -202,7 +202,7 @@ that the final stress is indeed the elastic predictor. ::
      sig_n = as_3D_tensor(old_sig)
      sig_elas = sig_n + sigma(deps)
      s = dev(sig_elas)
-     sig_eq = sqrt(3/2.*inner(s, s)) 
+     sig_eq = sqrt(3/2.*inner(s, s))
      f_elas = sig_eq - sig0 - H*old_p
      dp = ppos(f_elas)/(3*mu+H)
      n_elas = s/sig_eq*ppos(f_elas)/f_elas
@@ -212,7 +212,7 @@ that the final stress is indeed the elastic predictor. ::
             as_vector([n_elas[0, 0], n_elas[1, 1], n_elas[2, 2], n_elas[0, 1]]), \
             beta, dp
 
-.. note:: 
+.. note::
  We could have used conditionals to write more explicitly the difference
  between elastic and plastic evolution.
 
@@ -224,10 +224,10 @@ need to derive the algorithmic consistent tangent matrix given by:
  \boldsymbol{n}_{\text{elas}} \otimes \boldsymbol{n}_{\text{elas}} - 2\mu\beta\mathbf{DEV}
 
 where :math:`\mathbf{DEV}` is the 4th-order tensor associated with the deviatoric
-operator (note that :math:`\mathbf{C}_{\text{tang}}^{\text{alg}}=\mathbf{C}` for 
-elastic evolution). Contrary to what is done in the FEniCS book, we do not store it as the components 
-of a 4th-order tensor but it will suffice keeping track of the normal vector and 
-the :math:`\beta` parameter related to the plastic strains. We instead define a function 
+operator (note that :math:`\mathbf{C}_{\text{tang}}^{\text{alg}}=\mathbf{C}` for
+elastic evolution). Contrary to what is done in the FEniCS book, we do not store it as the components
+of a 4th-order tensor but it will suffice keeping track of the normal vector and
+the :math:`\beta` parameter related to the plastic strains. We instead define a function
 computing the tangent stress :math:`\boldsymbol{\sigma}_\text{tang} = \mathbf{C}_{\text{tang}}^{\text{alg}}
 \boldsymbol{\varepsilon}` as follows::
 
@@ -242,26 +242,26 @@ Global problem and Newton-Raphson procedure
 
 We are now in position to derive the global problem with its associated
 Newton-Raphson procedure. Each iteration will require establishing equilibrium