Split LB tutorial and create polymers tutorial (espressomd#3939)

schlaicha · Dec 17, 2020 · 342c368 · 342c368
1 parent 9f17307
commit 342c368
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Showing 13 changed files with 596 additions and 593 deletions.
diff --git a/doc/tutorials/CMakeLists.txt b/doc/tutorials/CMakeLists.txt
@@ -101,6 +101,7 @@ add_custom_target(tutorials_python)
 # Here: add new directory
 add_subdirectory(lennard_jones)
 add_subdirectory(charged_system)
+add_subdirectory(polymers)
 add_subdirectory(lattice_boltzmann)
 add_subdirectory(raspberry_electrophoresis)
 add_subdirectory(active_matter)

diff --git a/doc/tutorials/lattice_boltzmann/CMakeLists.txt b/doc/tutorials/lattice_boltzmann/CMakeLists.txt
@@ -1,14 +1,9 @@
 configure_tutorial_target(
   TARGET tutorial_lb DEPENDS lattice_boltzmann_part1.ipynb
-  lattice_boltzmann_part2.ipynb lattice_boltzmann_part3.ipynb
-  lattice_boltzmann_part4.ipynb figures/latticeboltzmann-grid.png
+  lattice_boltzmann_part2.ipynb figures/latticeboltzmann-grid.png
   figures/latticeboltzmann-momentumexchange.png)
 
 nb_export(TARGET tutorial_lb SUFFIX "1" FILE "lattice_boltzmann_part1.ipynb"
           HTML_RUN)
 nb_export(TARGET tutorial_lb SUFFIX "2" FILE "lattice_boltzmann_part2.ipynb"
-          HTML_RUN)
-nb_export(TARGET tutorial_lb SUFFIX "3" FILE "lattice_boltzmann_part3.ipynb"
-          HTML_RUN VAR_SUBST "STEPS=200;BOX_L=16;N_MONOMERS=[6,8,10,12,14]")
-nb_export(TARGET tutorial_lb SUFFIX "4" FILE "lattice_boltzmann_part4.ipynb"
-          HTML_RUN)
+          HTML_RUN)
diff --git a/doc/tutorials/lattice_boltzmann/NotesForTutor.md b/doc/tutorials/lattice_boltzmann/NotesForTutor.md
@@ -1,4 +1,4 @@
-# Part 1: Lattice-Boltzmann
+# Part 1: The Lattice-Boltzmann method
 
 ## Physical learning goals
 
@@ -8,33 +8,7 @@
 
 * Learning the LB interface in ESPResSo
 
-# Part 2: Brownian motion of a sphere in a fluid
-
-## Physical learning goals
-
-* Getting a short introduction to the Flory theory of polymers
-* Learning the basics of Brownian motion
-* Modeling the Brownian motion of a spherical object
-* Calculating the diffusion coefficient of a spherical object
-
-# Part 3: Brownian motion of a polymer in a fluid
-
-## Physical learning goals
-
-* Modeling the Brownian motion of a polymer
-* Learning about the hydrodynamic radius, radius of gyration, end-to-end distance
-* Reproducing theoretical results of the Flory theory of polymers
-* Using the Green-Kubo relation to calculate the diffusion coefficient of a polymer
-* Estimating the correlation-corrected standard error of the mean of a time series
-* Observing the effect of implicit hydrodynamics vs. LB hydrodynamics on polymer diffusion
-
-## Espresso learning goals
-
-* Creating linear polymers with ESPResSo functions
-* Using tools from the analysis module not based on the Observable framework
-* Setting up correlators for various operations, with compression
-
-# Part 4: Planar Poiseuille flow
+# Part 2: Planar Poiseuille flow
 
 ## Physical learning goals