doc: Apply summer school feedback

Explain the effect of the lattice offset on shape-base boundaries. Replace PhD dissertation by the corresponding textbook. Add ELC tutorial to the GitHub Pages website.
RudolfWeeber · Oct 13, 2023 · 99f4275 · 99f4275
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diff --git a/doc/bibliography.bib b/doc/bibliography.bib
@@ -673,21 +673,14 @@ @Article{kolb99a
   doi = {10.1063/1.479208},
 }
 
-@PhdThesis{kruger11a,
-author = {Kr\"{u}ger, Timm},
-title = {Computer simulation study of collective phenomena in dense suspensions of red blood cells under shear},
-school = {Universit\"{a}t Bochum},
-year = {2011}
-}
-
 @Book{kruger12a,
-author={Kr\"{u}ger, Timm},
-title={Computer simulation study of collective phenomena in dense suspensions of red blood cells under shear},
-year={2012},
-publisher={Vieweg+Teubner Verlag},
-address={Wiesbaden},
-isbn={978-3-8348-2376-2},
-doi={10.1007/978-3-8348-2376-2},
+  author    = {Kr{\"u}ger, Timm},
+  title     = {Computer Simulation Study of Collective Phenomena in Dense Suspensions of Red Blood Cells under Shear},
+  year      = {2012},
+  publisher = {Vieweg+Teubner Verlag},
+  isbn      = {978-3-8348-2376-2},
+  doi       = {10.1007/978-3-8348-2376-2},
+  address   = {Wiesbaden},
 }
 
 @Book{kruger17a,

diff --git a/doc/sphinx/advanced_methods.rst b/doc/sphinx/advanced_methods.rst
@@ -272,7 +272,7 @@ Please contact the Biofluid Simulation and Modeling Group at the
 University of Bayreuth if you plan to use this feature.
 
 With the Immersed Boundary Method (IBM), soft particles are considered as an infinitely
-thin shell filled with liquid (see e.g. :cite:`peskin02a,crowl10a,kruger11a`). When the
+thin shell filled with liquid (see e.g. :cite:`peskin02a,crowl10a,kruger12a`). When the
 shell is deformed by an external flow, it responds with elastic restoring
 forces which are transmitted into the fluid. In the present case, the
 inner and outer liquid are of the same type and are simulated using
@@ -281,7 +281,7 @@ lattice-Boltzmann.
 Numerically, the shell is discretized by a set of marker points
 connected by triangles. The marker points are advected with *exactly*
 the local fluid velocity, i.e., they do not possess a mass nor a
-friction coefficient (this is different from the Object-in-Fluid method
+friction coefficient (this is different from the :ref:`Object-in-Fluid` method
 below). We implement these marker points as virtual tracer
 particles which are not integrated using the usual velocity-Verlet
 scheme, but instead are propagated using a simple Euler algorithm with

diff --git a/doc/sphinx/lb.rst b/doc/sphinx/lb.rst
@@ -473,6 +473,13 @@ This allows the user to quickly set up a system with boundary conditions
 that simultaneously act on the fluid and particles. For a complete
 description of all available shapes, refer to :mod:`espressomd.shapes`.
 
+When using shapes, keep in mind the lattice origin is offset by half a grid
+size from the box origin. For illustration purposes, assuming ``agrid=1``,
+setting a wall constraint with ``dist=1`` and a normal vector pointing along
+the x-axis will set all LB nodes in the left side of the box as boundary
+nodes with thickness 1. The same outcome is obtained with ``dist=1.49``,
+but with ``dist=1.51`` the thickness will be 2.
+
 .. _Prototyping new LB methods:
 
 Prototyping new LB methods

diff --git a/doc/tutorials/Readme.md b/doc/tutorials/Readme.md
@@ -59,6 +59,10 @@ physical systems.
 * **Electrokinetics**  
   Modelling electrokinetics together with hydrodynamic interactions.  
   [Guide](electrokinetics/electrokinetics.ipynb)
+* **Electrodes**  
+  Modelling electrodes and measuring differential capacitance with the ELC method.  
+  [Part 1](electrodes/electrodes_part1.ipynb) |
+  Part 2 (work in progress)
 * **Constant pH method**  
   Modelling an acid dissociation curve using the constant pH method.  
   [Guide](constant_pH/constant_pH.ipynb)

diff --git a/doc/tutorials/electrodes/CMakeLists.txt b/doc/tutorials/electrodes/CMakeLists.txt
@@ -22,5 +22,5 @@ configure_tutorial_target(TARGET tutorial_electrodes DEPENDS
 
 nb_export(TARGET tutorial_electrodes SUFFIX "1" FILE "electrodes_part1.ipynb"
           HTML_RUN)
-nb_export(TARGET tutorial_electrodes SUFFIX "2" FILE "electrodes_part2.ipynb"
-          HTML_RUN)
+# TODO: fix time step issues (#4798) before adding HTML_RUN back
+nb_export(TARGET tutorial_electrodes SUFFIX "2" FILE "electrodes_part2.ipynb")
diff --git a/doc/tutorials/lattice_boltzmann/lattice_boltzmann_sedimentation.ipynb b/doc/tutorials/lattice_boltzmann/lattice_boltzmann_sedimentation.ipynb
@@ -79,9 +79,9 @@
     "espressomd.assert_features([\"LENNARD_JONES\", \"WALBERLA\"])\n",
     "\n",
     "# imports for data handling, plotting, and progress bar\n",
+    "import tqdm\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import tqdm"
+    "import matplotlib.pyplot as plt"
    ]
   },
   {