yade-dev team mailing list archive

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------------------------------------------------------------
revno: 4028
committer: bchareyre <bruno.chareyre@xxxxxxxxxxxxxxx>
timestamp: Mon 2017-03-27 18:01:35 +0200
message:
  small updates in doc, fixing compile errors and some warnings
modified:
  doc/sphinx/amazonEC2.rst
  doc/sphinx/book/confBook.py
  doc/sphinx/book/confManual.py
  doc/sphinx/book/confReference.py
  doc/sphinx/book/confTheory.py
  doc/sphinx/conf.py
  doc/sphinx/index-toctree-theory.rst
  doc/sphinx/introduction.rst
  doc/yade-articles.bib


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=== modified file 'doc/sphinx/amazonEC2.rst'
--- doc/sphinx/amazonEC2.rst	2017-03-22 19:40:46 +0000
+++ doc/sphinx/amazonEC2.rst	2017-03-27 16:01:35 +0000
@@ -4,9 +4,6 @@
 Using YADE with cloud computing on Amazon EC2
 =============================================
 
-.. role:: math(raw)
-	:format: html latex
-
 (Note: we thank Robert Caulk for preparing and sharing this guide)
 
 Summary
@@ -31,14 +28,15 @@
 
 	Amazon Web Services (AWS) Console
 
+
 Start by signing into the console on `Amazon
 EC2 <https://aws.amazon.com/?nc2=h_lgl>`__. This will require an
 existing or new Amazon account. Once you’ve signed in, you should find
 the EC2 console by clicking on ‘services’ in the upper left hand corner
 of the AWS homepage. Start by clicking on the \`\`launch an instance“
-blue button (Fig. :ref:`fig-console`). Select the Amazon
+blue button (Fig. `fig-console`_). Select the Amazon
 Machine Image (AMI): \`\`Ubuntu Server 16.04 LTS\`\` (Fig.
-:ref:`fig-ubuntu`).
+`fig-ubuntu`_).
 
 .. _fig-ubuntu:
 .. figure:: fig/ubunut.*
@@ -58,7 +56,7 @@
 selection. The \`\`Compute Optimized" instances are necessary for most
 YADE simulations because they provide access to high performing
 processors and guaranteed computing power. The C3.2xlarge (Fig.
-:ref:`fig-type`) is equivalent to an 8 core 2.8ghz Xeon E5
+`fig-type`_) is equivalent to an 8 core 2.8ghz Xeon E5
 with 25 mb of cache, which is likely the best option for medium-large
 scale YADE simulations.
 
@@ -90,7 +88,7 @@
 a java based terminal on the AWS website. You can find the necessary
 information by navigating to \`\`Instances" in the left menu of the AWS
 console. Right click on the instance as shown in Fig.
-:ref:`fig-connect` and click connect.
+`fig-connect`_ and click connect.
 
 
 .. _fig-connect:
@@ -101,7 +99,7 @@
 	Connecting to the instance
 
 You will be presented with the public DNS, which should look something
-like Fig. :ref:`fig-dns`.
+like Fig. `fig-dns`_.
 
 
 .. _fig-dns:
@@ -121,13 +119,13 @@
 
 ::
 
-	#install yadedaily 
+	#install yadedaily
 	sudo bash -c 'echo "deb http://www.yade-dem.org/packages/ xenial/" >> /etc/apt/sources.list'
 	wget -O - http://www.yade-dem.org/packages/yadedev_pub.gpg | sudo apt-key add -
 	sudo apt-get update
 	sudo apt-get install -y yadedaily
 
-	# install python 
+	# install python
 	sudo apt-get -y install python
 	sudo apt-get -y install python-pip python-dev build-essential
 
@@ -152,7 +150,7 @@
 
 ::
 
-	yadedaily nameOfSimulation.py 
+	yadedaily nameOfSimulation.py
 
 In order to retrieve the output files (folder titled ‘out’ below) for
 post processing purposes, you will use the same command that you used to

=== modified file 'doc/sphinx/book/confBook.py'
--- doc/sphinx/book/confBook.py	2017-03-08 12:27:22 +0000
+++ doc/sphinx/book/confBook.py	2017-03-27 16:01:35 +0000
@@ -670,7 +670,7 @@
 
 # -- Options for LaTeX output --------------------------------------------------
 
-my_maketitle=u'''
+my_maketitle=r'''
 \begin{titlepage}
 
 \begin{flushright}
@@ -706,16 +706,16 @@
  \item \text{\sffamily\bfseries\normalsize Sergei Dorofeenko}\\ \text{\sffamily\small IPCP RAS, Chernogolovka}
  \item \text{\sffamily\bfseries\normalsize J\'er\^ome Duriez}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR}
  \item \text{\sffamily\bfseries\normalsize Nolan Dyck}\\ \text{\sffamily\small Univ. of Western Ontario}
- \item \text{\sffamily\bfseries\normalsize Jan Eliáš}\\ \text{\sffamily\small Brno University of Technology}
+ \item \text{\sffamily\bfseries\normalsize Eli\'{a}\v{s}}\\ \text{\sffamily\small Brno University of Technology}
  \item \text{\sffamily\bfseries\normalsize Burak Er}\\ \text{\sffamily\small Bursa Technical University}
  \item \text{\sffamily\bfseries\normalsize Alexander Eulitz}\\ \text{\sffamily\small TU Berlin / Institute for Machine Tools}\\ \text{\sffamily\small and Factory Management}
  \item \text{\sffamily\bfseries\normalsize Anton Gladky}\\ \text{\sffamily\small TU Bergakademie Freiberg}
  \item \text{\sffamily\bfseries\normalsize Ning Guo}\\ \text{\sffamily\small Hong Kong Univ. of Science and Tech.}
  \item \text{\sffamily\bfseries\normalsize Christian Jakob}\\ \text{\sffamily\small TU Bergakademie Freiberg}
- \item \text{\sffamily\bfseries\normalsize François Kneib}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR / Irstea Grenoble}
+ \item \text{\sffamily\bfseries\normalsize Fran\c{c}ois Kneib}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR / Irstea Grenoble}
  \item \text{\sffamily\bfseries\normalsize Janek Kozicki}\\ \text{\sffamily\small Gdansk University of Technology}
  \item \text{\sffamily\bfseries\normalsize Donia Marzougui}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR}
- \item \text{\sffamily\bfseries\normalsize Raphaël Maurin}\\ \text{\sffamily\small Irstea Grenoble}
+ \item \text{\sffamily\bfseries\normalsize Rapha\"el Maurin}\\ \text{\sffamily\small Irstea Grenoble}
  \item \text{\sffamily\bfseries\normalsize Chiara Modenese}\\ \text{\sffamily\small University of Oxford}
  \item \text{\sffamily\bfseries\normalsize Luc Scholt\`{e}s}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR}
  \item \text{\sffamily\bfseries\normalsize Luc Sibille}\\ \text{\sffamily\small University of Nantes, lab. GeM}

=== modified file 'doc/sphinx/book/confManual.py'
--- doc/sphinx/book/confManual.py	2017-03-08 12:27:22 +0000
+++ doc/sphinx/book/confManual.py	2017-03-27 16:01:35 +0000
@@ -661,7 +661,7 @@
 
 # -- Options for LaTeX output --------------------------------------------------
 
-my_maketitle=u'''
+my_maketitle=r'''
 \begin{titlepage}
 
 \begin{flushright}

=== modified file 'doc/sphinx/book/confReference.py'
--- doc/sphinx/book/confReference.py	2017-03-08 12:27:22 +0000
+++ doc/sphinx/book/confReference.py	2017-03-27 16:01:35 +0000
@@ -661,7 +661,7 @@
 
 # -- Options for LaTeX output --------------------------------------------------
 
-my_maketitle=u'''
+my_maketitle=r'''
 \begin{titlepage}
 
 \begin{flushright}
@@ -676,7 +676,7 @@
 \vspace{20 mm}
 %\vspace{70 mm}
 \begin{sffamily}\bfseries\Large
-V\'{a}clav \v{S}milauer, Emanuele Catalano, Bruno Chareyre, Sergei Dorofeenko, J\'er\^ome Duriez, Nolan Dyck, Jan Eliáš, Burak Er, Alexander Eulitz, Anton Gladky, Christian Jakob, Fran\c{c}ois Kneib, Janek Kozicki, Donia Marzougui, Rapha\"el Maurin, Chiara Modenese, Luc Scholt\`{e}s, Luc Sibille, Jan Str\'{a}nsk\'{y}, Thomas Sweijen, Klaus Thoeni, Chao Yuan
+V\'{a}clav \v{S}milauer, Emanuele Catalano, Bruno Chareyre, Sergei Dorofeenko, J\'er\^ome Duriez, Nolan Dyck, Jan Eli\'{a}\v{s}, Burak Er, Alexander Eulitz, Anton Gladky, Christian Jakob, Fran\c{c}ois Kneib, Janek Kozicki, Donia Marzougui, Rapha\"el Maurin, Chiara Modenese, Luc Scholt\`{e}s, Luc Sibille, Jan Str\'{a}nsk\'{y}, Thomas Sweijen, Klaus Thoeni, Chao Yuan
 \end{sffamily}
 \vspace{20 mm}
 \hrule{}

=== modified file 'doc/sphinx/book/confTheory.py'
--- doc/sphinx/book/confTheory.py	2017-03-08 12:27:22 +0000
+++ doc/sphinx/book/confTheory.py	2017-03-27 16:01:35 +0000
@@ -661,7 +661,7 @@
 
 # -- Options for LaTeX output --------------------------------------------------
 
-my_maketitle=u'''
+my_maketitle=r'''
 \begin{titlepage}
 
 \begin{flushright}

=== modified file 'doc/sphinx/conf.py'
--- doc/sphinx/conf.py	2017-03-08 12:27:22 +0000
+++ doc/sphinx/conf.py	2017-03-27 16:01:35 +0000
@@ -661,7 +661,7 @@
 
 # -- Options for LaTeX output --------------------------------------------------
 
-my_maketitle=u'''
+my_maketitle=r'''
 \begin{titlepage}
 
 \begin{flushright}
@@ -699,16 +699,16 @@
  \item \text{\sffamily\bfseries\normalsize Sergei Dorofeenko} \text{\sffamily\small IPCP RAS, Chernogolovka}
  \item \text{\sffamily\bfseries\normalsize J\'er\^ome Duriez} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR}
  \item \text{\sffamily\bfseries\normalsize Nolan Dyck} \text{\sffamily\small Univ. of Western Ontario}
- \item \text{\sffamily\bfseries\normalsize Jan Eliáš} \text{\sffamily\small Brno University of Technology}
+ \item \text{\sffamily\bfseries\normalsize Jan Eli\'{a}\v{s}} \text{\sffamily\small Brno University of Technology}
  \item \text{\sffamily\bfseries\normalsize Burak Er} \text{\sffamily\small Bursa Technical University}
  \item \text{\sffamily\bfseries\normalsize Alexander Eulitz} \text{\sffamily\small TU Berlin / Institute for Machine Tools}\\ \text{\sffamily\small and Factory Management}
  \item \text{\sffamily\bfseries\normalsize Anton Gladky} \text{\sffamily\small TU Bergakademie Freiberg}
  \item \text{\sffamily\bfseries\normalsize Ning Guo} \text{\sffamily\small Hong Kong Univ. of Science and Tech.}
  \item \text{\sffamily\bfseries\normalsize Christian Jakob} \text{\sffamily\small TU Bergakademie Freiberg}
- \item \text{\sffamily\bfseries\normalsize François Kneib} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR / Irstea Grenoble}
+ \item \text{\sffamily\bfseries\normalsize Fran\c{c}ois Kneib} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR / Irstea Grenoble}
  \item \text{\sffamily\bfseries\normalsize Janek Kozicki} \text{\sffamily\small Gdansk University of Technology}
  \item \text{\sffamily\bfseries\normalsize Donia Marzougui} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR}
- \item \text{\sffamily\bfseries\normalsize Raphaël Maurin} \text{\sffamily\small Irstea Grenoble}
+ \item \text{\sffamily\bfseries\normalsize Rapha\"el Maurin} \text{\sffamily\small Irstea Grenoble}
  \item \text{\sffamily\bfseries\normalsize Chiara Modenese} \text{\sffamily\small University of Oxford}
  \item \text{\sffamily\bfseries\normalsize Luc Scholt\`{e}s} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR}
  \item \text{\sffamily\bfseries\normalsize Luc Sibille} \text{\sffamily\small University of Nantes, lab. GeM}
@@ -751,8 +751,8 @@
 latex_documents = [
    ('index-toctree', 'Yade.tex', u'Yade Documentation',
    u'Václav Šmilauer', 'manual'),
-   ('index-toctree_manuals', 'YadeManuals.tex', u'Yade Tutorial and Manuals',
-   u'Václav Šmilauer', 'manual'),
+   #('index-toctree_manuals', 'YadeManuals.tex', u'Yade Tutorial and Manuals',
+   #u'Václav Šmilauer', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of

=== modified file 'doc/sphinx/index-toctree-theory.rst'
--- doc/sphinx/index-toctree-theory.rst	2015-11-20 22:46:24 +0000
+++ doc/sphinx/index-toctree-theory.rst	2017-03-27 16:01:35 +0000
@@ -6,4 +6,4 @@
   :maxdepth: 2
   
   formulation.rst
-  fullPublications.rst
+  publications.rst

=== modified file 'doc/sphinx/introduction.rst'
--- doc/sphinx/introduction.rst	2016-06-07 18:48:04 +0000
+++ doc/sphinx/introduction.rst	2017-03-27 16:01:35 +0000
@@ -485,7 +485,7 @@
 hides 3 internal dispatchers within the :yref:`InteractionLoop` engine; they all operate on interactions and are, for performance reasons, put together:
 
 :yref:`IGeomDispatcher`
-	uses the first set of functors (``Ig2``), which are dispatched based on combination of ``2`` :yref:`Shapes<Shapes>` objects. Dispatched functor resolves exact collision configuration and creates :yref:`IGeom<Interaction::geom>` (whence ``Ig`` in the name) associated with the interaction, if there is collision. The functor might as well fail on approximate interactions, indicating there is no real contact between the bodies, even if they did overlap in the approximate collision detection.
+	uses the first set of functors (``Ig2``), which are dispatched based on combination of ``2`` :yref:`Shapes<Shape>` objects. Dispatched functor resolves exact collision configuration and creates :yref:`IGeom<Interaction::geom>` (whence ``Ig`` in the name) associated with the interaction, if there is collision. The functor might as well fail on approximate interactions, indicating there is no real contact between the bodies, even if they did overlap in the approximate collision detection.
 
 	#. The first functor, :yref:`Ig2_Sphere_Sphere_ScGeom`, is called on interaction of 2 :yref:`Spheres<Sphere>` and creates :yref:`ScGeom` instance, if appropriate.
 
@@ -509,7 +509,7 @@
 .. figure:: fig/dispatch-loop.*
 	:width: 13cm
 
-	Chain of functors producing and accepting certain types. In the case shown, the ``Ig2`` functors produce :yref:`ScfGeom` instances from all handled :yref:`Shape` combinations; the ``Ig2`` functor produces :yref:`FrictMat`. The constitutive law functor ``Law2`` accepts the combination of types produced. Note that the types are stated in the functor's class names.
+	Chain of functors producing and accepting certain types. In the case shown, the ``Ig2`` functors produce :yref:`ScGeom` instances from all handled :yref:`Shape` combinations; the ``Ig2`` functor produces :yref:`FrictMat`. The constitutive law functor ``Law2`` accepts the combination of types produced. Note that the types are stated in the functor's class names.
 
 .. note::
 	When Yade starts, O.engines is filled with a reasonable default list, so that it is not strictly necessary to redefine it when trying simple things. The default scene will handle spheres, boxes, and facets with :yref:`frictional<FrictMat>` properties correctly, and adjusts the timestep dynamically. You can find an example in simple-scene-default-engines.py.

=== modified file 'doc/yade-articles.bib'
--- doc/yade-articles.bib	2017-03-08 18:07:25 +0000
+++ doc/yade-articles.bib	2017-03-27 16:01:35 +0000
@@ -619,7 +619,7 @@
 	pages={1-13}
 }
 
-@Article{Maurin2015,
+@Article{Maurin2015b,
    author = {Maurin, R. and Chauchat, J. and Chareyre, B. and Frey, P.},
    title = {A minimal coupled fluid-discrete element model for bedload transport},
    journal = {Physics of Fluids},
@@ -644,7 +644,7 @@
 
 @article{Montella2016,
   title = {Localized fluidization in granular materials: Theoretical and numerical study},
-  author = {Montell\`a, E. P. and Toraldo, M. and Chareyre, B. and Sibille, L.},
+  author = {Montellà, E. P. and Toraldo, M. and Chareyre, B. and Sibille, L.},
   journal = {Phys. Rev. E},
   volume = {94},
   issue = {5},
@@ -707,7 +707,7 @@
 
 @article{Papachristos2017,
   title={Intensity and volumetric characterizations of hydraulically driven fractures by hydro-mechanical simulations},
-  author={Papachristos, E and Scholt{\`e}s, L and Donz{\'e}, FV and Chareyre, B},
+  author={Papachristos, E and Scholtès, L and Donzé, F.V and Chareyre, B},
   journal={International Journal of Rock Mechanics and Mining Sciences},
   volume={93},
   pages={163--178},