Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Electrokinetics tutorial #4782

Merged
merged 3 commits into from
Oct 2, 2023

Conversation

reinaual
Copy link
Contributor

@reinaual reinaual commented Sep 4, 2023

Write diffusion-advection-reaction tutorial.

@review-notebook-app
Copy link

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.


Powered by ReviewNB

Copy link
Contributor

@christophlohrmann christophlohrmann left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

" 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"
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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doc/tutorials/electrokinetics/electrokinetics.ipynb Outdated Show resolved Hide resolved
doc/tutorials/electrokinetics/electrokinetics.ipynb Outdated Show resolved Hide resolved
Copy link
Contributor

@christophlohrmann christophlohrmann left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

@christophlohrmann
Copy link
Contributor

@jngrad @reinaual ready for review

@reinaual reinaual marked this pull request as ready for review September 25, 2023 07:47
Copy link
Contributor

@christophlohrmann christophlohrmann left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

can I approve my own changes?

@jngrad jngrad force-pushed the tutorial_electrokinetics branch from 497b651 to b7617a3 Compare October 2, 2023 12:56
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 force-pushed the tutorial_electrokinetics branch from b7617a3 to d330457 Compare October 2, 2023 13:59
@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
5 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants