Tutorials maintenance

.pylintrc

@@ -68,6 +68,7 @@ disable=all
 # it should appear only once). See also the "--disable" option for examples.
 enable=dangerous-default-value, # W0102
        wildcard-import, # W0401
+       assert-on-tuple, # W0199
        unused-import, # W0611
        unused-variable, # W0612
        unused-argument, # W0613

doc/sphinx/constraints.rst

@@ -28,11 +28,18 @@ Shapes define geometries which can be used in |es| either as
 constraints in particle interactions or as a boundary for a
 lattice-Boltzmann fluid.
 
-To avoid unexpected behavior make sure all parts of your shape are
+To avoid unexpected behavior, make sure all parts of your shape are
 within the central box since the distance to the shape is calculated only
-within the central box. If parts of the shape are placed
-outside of the central box these parts are truncated by the box boundaries. This may
-or may not be desired as for example in the case of a cylinder without or with cylinder cover.
+within the central box. If parts of the shape are placed outside of the
+central box, these parts are truncated by the box boundaries. This may
+be desired as for example in the case of a cylinder shape whose end caps
+could extend outside the box boundaries to create an infinite rod.
+
+In addition, particles will not interact with periodic images of shapes,
+therefore make sure the shapes are not too close to any of the six sides
+of the box. If the distance between the shape and the nearest box boundary
+is less than the interaction cutoff, the potential will be discontinuous
+when the particle crosses that periodic boundary.
 
 A shape is instantiated by calling its constructor. If you wanted to
 create a wall shape you could do::

doc/sphinx/introduction.rst

@@ -291,15 +291,15 @@ physical systems. You can also find the tutorials and related scripts in the
 directory :file:`/doc/tutorials` or `online on GitHub <https://github.com/espressomd/espresso/blob/python/doc/tutorials/>`_.
 Currently, the following tutorials are available:
 
-* :file:`01-lennard_jones`: Modelling of a single-component and a two-component Lennard-Jones liquid.
-* :file:`02-charged_system`: Modelling of charged systems such as ionic crystals.
-* :file:`04-lattice_boltzmann`: Simulations including hydrodynamic interactions using the lattice-Boltzmann method.
-* :file:`05-raspberry_electrophoresis`: Extended objects in a lattice-Boltzmann fluid, raspberry particles.
-* :file:`06-active_matter`: Modelling of self-propelling particles.
-* :file:`07-electrokinetics`: Modelling electrokinetics together with hydrodynamic interactions.
-* :file:`08-visualization`: Using the online visualizers of |es|.
-* :file:`11-ferrofluid`: Modelling a colloidal suspension of magnetic particles.
-* :file:`12-constant_pH`: Modelling the titration of a weak acid using the constant pH method
+* :file:`lennard_jones`: Modelling of a single-component and a two-component Lennard-Jones liquid.
+* :file:`visualization`: Using the online visualizers of |es|.
+* :file:`charged_system`: Modelling of ion condensation around a charged rod.
+* :file:`ferrofluid`: Modelling a colloidal suspension of magnetic particles.
+* :file:`lattice_boltzmann`: Simulations including hydrodynamic interactions using the lattice-Boltzmann method.
+* :file:`raspberry_electrophoresis`: Extended objects in a lattice-Boltzmann fluid, raspberry particles.
+* :file:`active_matter`: Modelling of self-propelling particles.
+* :file:`electrokinetics`: Modelling electrokinetics together with hydrodynamic interactions.
+* :file:`constant_pH`: Modelling the titration of a weak acid using the constant pH method
 
 .. _Sample scripts:
 

doc/sphinx/zrefs.bib

@@ -197,6 +197,17 @@ @ARTICLE{dao03
   pages = {2259-2280},
 }
 
+@article{debuyl18a,
+  author = {de Buyl, Pierre},
+  title = {tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations},
+  journal = {Journal of Open Source Software},
+  volume = {3},
+  number = {28},
+  pages = {877},
+  year = {2018},
+  doi = {10.21105/joss.00877},
+}
+
 @ARTICLE{degraaf16,
   author = {de Graaf, Joost and Menke, Henri and Mathijssen, Arnold J.T.M. and Fabritius, Marc and Holm, Christian and Shendruk, Tyler N.},
   title = {Lattice-Boltzmann Hydrodynamics of Anisotropic Active Matter},