Merge branch 'python' into cellsystem

Readme.md

@@ -1,9 +1,3 @@
-# Invitation to the ESPResSo Summer School 2023
-
-[![CECAM Flagship School registration link](https://img.shields.io/badge/CECAM%20Flagship%20School-Register%20Now-blue?style=for-the-badge)](https://www.cecam.org/workshop-details/1229)
-
-The summer school "Simulating energy materials with ESPResSo and waLBerla" will take place on October 9-13, 2023, in Stuttgart. Registration is now open on [CECAM](https://www.cecam.org/workshop-details/1229).
-
 # ESPResSo
 
 [![GitLab CI](https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/badges/python/pipeline.svg)](https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/-/commits/python)

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,

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

doc/sphinx/installation.rst

@@ -8,10 +8,10 @@ This chapter will describe how to get, compile and run the software.
 |es| releases are available as source code packages from the homepage [1]_.
 This is where new users should get the code. The code within release packages
 is tested and known to run on a number of platforms.
-Alternatively, people that want to use the newest features of |es| or that
-want to start contributing to the software can instead obtain the
+Alternatively, people who want to use the newest features of |es| or
+start contributing to the software can instead obtain the
 current development code via the version control system software  [2]_
-from |es|'s project page at Github  [3]_. This code might be not as well
+from |es|'s project page at GitHub  [3]_. This code might be not as well
 tested and documented as the release code; it is recommended to use this
 code only if you have already gained some experience in using |es|.
 
@@ -93,7 +93,7 @@ To compile |es| on Ubuntu 22.04 LTS, install the following dependencies:
 .. code-block:: bash
 
     sudo apt install build-essential cmake cython3 python3-pip python3-numpy \
-      libboost-all-dev openmpi-common fftw3-dev libhdf5-dev libhdf5-openmpi-dev \
+      libboost-all-dev openmpi-common fftw3-dev libfftw3-mpi-dev libhdf5-dev libhdf5-openmpi-dev \
       python3-scipy python3-opengl libgsl-dev freeglut3
 
 Optionally the ccmake utility can be installed for easier configuration:
@@ -221,7 +221,7 @@ To use Jupyter Notebook, install the following packages:
 
 .. code-block:: bash
 
-    pip3 install --user nbformat notebook 'jupyter_contrib_nbextensions==0.5.1'
+    pip3 install --user 'nbformat==5.1.3' 'nbconvert==6.4.5' 'notebook==6.4.8' 'jupyter_contrib_nbextensions==0.5.1'
     jupyter contrib nbextension install --user
     jupyter nbextension enable rubberband/main
     jupyter nbextension enable exercise2/main

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

doc/tutorials/CMakeLists.txt

@@ -114,6 +114,7 @@ add_subdirectory(visualization)
 add_subdirectory(ferrofluid)
 add_subdirectory(constant_pH)
 add_subdirectory(widom_insertion)
+add_subdirectory(electrodes)
 
 configure_file(Readme.md ${CMAKE_CURRENT_BINARY_DIR} COPYONLY)
 configure_file(convert.py ${CMAKE_CURRENT_BINARY_DIR})

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)

doc/tutorials/electrodes/CMakeLists.txt

@@ -0,0 +1,26 @@
+#
+# Copyright (C) 2020-2022 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# ESPResSo 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+configure_tutorial_target(TARGET tutorial_electrodes DEPENDS
+                          electrodes_part1.ipynb electrodes_part2.ipynb)
+
+nb_export(TARGET tutorial_electrodes SUFFIX "1" FILE "electrodes_part1.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")

doc/tutorials/electrodes/NotesForTutor.md

@@ -0,0 +1,32 @@
+# Simulations of electrodes in ESPResSO
+
+## Physics learning goals
+
+### Part 1
+
+* Give a short recap about image charges, dielectric media, ...
+* Nano-confinement can exhibit a broad variety of interesting effects that can
+  be studied with computer simulations!
+* Electrostatics in nano-confinement: concept of a Green's function
+* Discrete image charges: ICC\*
+
+### Part 2
+
+* Nano-confined charged liquids as super-capacitors
+* Advanced Poisson-Boltzmann theory: Gouy-Chapman, Graham equation
+* Limits of PB: finite ion size, correlations, ...
+* Coarse-grained view: Surface charge density via ELC-IC
+* How to apply a potential difference in the simulation.
+
+After the tutorial, students should be able to:
+
+* Explain how ESPResSo implements 2D periodic electrostatics.
+* What are the limitations of the mean-field PB description.
+* How to evaluate the differential capacitance from simulations.
+* The basic idea of super-ionic states.
+
+## ESPResSo learning goals
+
+* Setting up ELC, ICC and ELC-IC simulations
+* Why is choosing the ELC-gap a crucial parameter?
+* Setting up observables and accumulators for the density profiles.