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Electrokinetics tutorial #4782

Merged
merged 3 commits into from
Oct 2, 2023
Merged

Electrokinetics tutorial #4782

merged 3 commits into from
Oct 2, 2023

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reinaual
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@reinaual reinaual commented Sep 4, 2023 •
edited by jngrad
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Write diffusion-advection-reaction tutorial.

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christophlohrmann
christophlohrmann suggested changes Sep 6, 2023
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The physics in the tutorial semms good, especially the reaction in turbulent flow looks fantastic. Obviously, the exercises are still missing.
The language/style of the descriptive text needs to be improved, but that's something I could do

doc/tutorials/electrokinetics/electrokinetics.ipynb Outdated
" ext_efield=[0., 0., 0.], tau=TAU)\n",
"system.ekcontainer.add(species)\n",
"\n",
"species[BOX_L[0] // 2, BOX_L[1] // 2, 0].density = 1.0"
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I would put 1/agrid**3 here to make sure there is one unit of material in the system.
Alternatively would using a gaussian as the starting condition reduce numerical errors connected to discretised gradients?

doc/tutorials/electrokinetics/electrokinetics.ipynb Outdated Show resolved Hide resolved
doc/tutorials/electrokinetics/electrokinetics.ipynb Outdated Show resolved Hide resolved
christophlohrmann
christophlohrmann reviewed Sep 14, 2023
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Exercises are a bit short (especially in the summer school context where we need people to do stuff for 90mins) but cover the essentials.
Text still needs some polishing. I could take it from here

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@jngrad @reinaual ready for review

@reinaual reinaual marked this pull request as ready for review September 25, 2023 07:47
christophlohrmann
christophlohrmann approved these changes Sep 27, 2023
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can I approve my own changes?

@jngrad
Rework electrokinetics tutorial
d330457 
Write tests to check for analytical solutions and turbulent flow.
Improve matplotlib figures, ffmpeg videos and png figure captions.
Fix undefined behavior during integration (missing LB thermostat).
@jngrad jngrad added this to the ESPResSo 4.3.0 milestone Oct 2, 2023
@jngrad jngrad added Documentation automerge Merge with kodiak labels Oct 2, 2023
@kodiakhq kodiakhq bot merged commit 52efe9d into espressomd:python Oct 2, 2023
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@reinaual @christophlohrmann @jngrad