Adds an updated version of the Jupyter notebook tutorial for the onse… #5533

ljhwang · 2023-12-19T19:02:55Z

Back at the 2017 hack in Georgia, the original onset of convection tutorials were converted to Jupyter notebooks.

This adds an updated version of the notebook to the cookbook directory that the tutorial is related to.

Updates include:

modifications to the prm files. Note that between versions the structure changed.
modifications to the Nusselt-Rayleigh number relationship exercise. Note with the substantial improvements to the solver, the results changed. I have left the previous numbers in for historic reasons and arbitrarily reset the end times. Feel free to suggest a different set of parameters.
corrected a bug in plotting the Nusselt-Rayleigh number plot. Verification by the reviewer that this is now correct is warranted.

The updated version is designed to work using the ASPECT Jupyterlab environment on geodynamics.org: https://geodynamics.org/resources/aspectnotebook

The instructions to run in the old Docker container and the old parameter files are retained. This could be removed if a new docker container is made or this is confusing.

tjhei · 2023-12-27T02:49:44Z

Can you please remove all the checkpoint files you accidentally added?

ljhwang · 2023-12-27T17:50:16Z

@tjhei Thanks for the catch on the hidden files. Hopefully this is clean now.

bangerth · 2024-01-09T05:07:52Z

You'll have to merge the two commits (squash or fix-up) to ensure these large files are not in one commit and then removed in the next, leaving them as large (but unnecessary) additions to the repository.

bangerth · 2024-01-09T05:08:16Z

cookbooks/convection-box/tutorial-onset-of-convection/README.md

+
+## Running on your desktop
+
+If you run in your local JupyetrLab environment, note the following dependencies:


Suggested change

If you run in your local JupyetrLab environment, note the following dependencies:

If you run in your local JupyterLab environment, note the following dependencies:

bangerth · 2024-01-09T05:09:20Z

...torial-onset-of-convection/model_input/.ipynb_checkpoints/convection-box2-old-checkpoint.prm

@@ -0,0 +1,161 @@
+# A description of convection in a 2d box. See the manual for more information.


Out of curiosity, why leave old stuff around? Documentation should document the current state of a code base; it is not helpful to anyone to document a previous version.

Always a good question. The reason to keep this around is that there is not a new docker container with the most recent code.

ljhwang · 2024-01-19T18:12:37Z

@bangerth. Both of your comments have been addressed and this should be ready to be merged. Once merged, I will remove the old prm files and update the README to be consistent. ty.

tjhei

Hi Lorraine, thank you for putting this together. This is great to have as a resource. I think we need to discuss a couple of things first, though.

tjhei · 2024-01-24T05:25:19Z

cookbooks/convection-box/tutorial-onset-of-convection/README.md

+
+The current version is verified to run within the ASPECT Jupyter Notebooks tool which can be launched from the CIG website:
+
+https://geodynamics.org/resources/aspectnotebook


This is not documented here or on the page linked here: It seems that you have to add $ASPECT_DIR to the path manually before you can start "aspect". @gassmoeller is that true or am I missing something?

I believe this is in the default path for the notebook container.

@tjhei: Lorraine is correct, $ASPECT_DIR is already set inside the tool. No need for the user to set it.

If I click on https://geodynamics.org/resources/aspectnotebook, then 'launch tool', "new terminal" I get:

timoheister@geodynamics_1099_6:~$ aspect bash: aspect: command not found

while $ASPECT_DIR/bin/aspect works.

tjhei · 2024-01-24T05:26:43Z

cookbooks/convection-box/tutorial-onset-of-convection/README.md

+A. Install Docker
+
+B. Download the docker image
+> docker pull tjhei/aspect-jupyter


Should we maybe update this image first instead of trying to be compatible with it? This image is from 2017 and contains ASPECT 2.0.0-pre. If we don't update it, we should remove these instructions.

The plan is to remove these files and clean-up the README.md file after this pull request is merged. This way we have a record of it somewhere in the commit history if needed.

tjhei · 2024-01-24T05:27:17Z

...torial-onset-of-convection/model_input/.ipynb_checkpoints/convection-box2-old-checkpoint.prm

+# A description of convection in a 2d box. See the manual for more information.
+
+
+# At the top, we define the number of space dimensions we would like to


This and many other files are in a folder .ipynb_checkpoints/. I think this temporary folder should not be part of your PR.

Oh drats, you did find more. Do you mind if i clean this up when i get rid of the "old" files?

tjhei · 2024-01-24T05:29:37Z

cookbooks/convection-box/tutorial-onset-of-convection/tutorial_main.ipynb

@@ -0,0 +1,111 @@
+{
+ "cells": [


why is this file not in the notebooks folder?

True. The philosophy here is to put the "obvious" starting point at the top level. Agnostic about this. what do others think?

tjhei · 2024-01-24T05:30:29Z

cookbooks/convection-box/tutorial-onset-of-convection/README.md

+
+# Introduction to ASPECT
+
+This notebook is based on tutorials by J. Dannberg that provide a basic introduction to ASPECT.


Do we have a better place to put notebooks/tutorials? It seems weird to me to hide them inside the convection-box folder.

This was part of a broader discussion to keep notebooks as close as possible to the related prm's such that they stay current.

gassmoeller · 2024-01-26T19:45:19Z

I removed the checkpoint files.

bangerth · 2024-03-09T01:07:59Z

It fails the indentation check with these diffs:

diff --git a/cookbooks/convection-box/tutorial-onset-of-convection/README.md b/cookbooks/convection-box/tutorial-onset-of-convection/README.md
index a1d0535..1668690 100644
--- a/cookbooks/convection-box/tutorial-onset-of-convection/README.md
+++ b/cookbooks/convection-box/tutorial-onset-of-convection/README.md
@@ -29,11 +29,11 @@ If you run in your local JupyterLab environment, note the following dependencies
  * ipympl
  * scipy
  * glob
- 
- 
- 
+
+
+
 ## Packages install
- 
+
 The heat flux slider requires the installation of two additional packages.
 
 **Adding Jupyter widgets**
@@ -43,5 +43,3 @@ You should have added this in Step 3 above:
 
 **Installing tables**
 > conda install tables
- 
- 
\ No newline at end of file
diff --git a/cookbooks/convection-box/tutorial-onset-of-convection/model_input/tutorial.prm b/cookbooks/convection-box/tutorial-onset-of-convection/model_input/tutorial.prm
index d6f0ff2..3686151 100644
--- a/cookbooks/convection-box/tutorial-onset-of-convection/model_input/tutorial.prm
+++ b/cookbooks/convection-box/tutorial-onset-of-convection/model_input/tutorial.prm
@@ -[14](https://github.com/geodynamics/aspect/actions/runs/7674802326/job/20920049230?pr=5533#step:6:15)7,4 +147,3 @@ subsection Postprocess
     set Data output format = vtu
   end
 end
-

bangerth · 2024-03-09T01:09:23Z

The other failures seem to come from the fact that the root of the branch is at a point in time where we had the GMG failures.

…t of convection

…vious incompatible version

gassmoeller · 2024-03-15T20:53:26Z

I indented, rebased and fixed a number of remaining typos, this should be good to go @ljhwang.

bangerth reviewed Jan 9, 2024

View reviewed changes

ljhwang force-pushed the tutorial-convection branch from 16c4239 to d77075c Compare January 19, 2024 17:26

tjhei reviewed Jan 24, 2024

View reviewed changes

tjhei approved these changes Jan 28, 2024

View reviewed changes

ljhwang and others added 5 commits March 15, 2024 13:13

Adds an updated version of the Jupyter notebook tutorial for the onse…

bb9ba71

…t of convection

Remove checkpoints

d94a659

remove old files that no longer work with current version of ASPECT

78f61cf

Removes reference to how to run using the Docker container with a pre…

563683f

…vious incompatible version

Indent

3f0edc7

gassmoeller force-pushed the tutorial-convection branch from a84e412 to 3f0edc7 Compare March 15, 2024 17:14

gassmoeller added 2 commits March 15, 2024 13:48

Fix typos

6de840b

Add readme to documentation

88b3995

gassmoeller force-pushed the tutorial-convection branch from f2d0c13 to 88b3995 Compare March 15, 2024 18:00

gassmoeller merged commit 6d2e1af into geodynamics:main Mar 28, 2024
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Adds an updated version of the Jupyter notebook tutorial for the onse… #5533

Adds an updated version of the Jupyter notebook tutorial for the onse… #5533

ljhwang commented Dec 19, 2023

tjhei commented Dec 27, 2023

ljhwang commented Dec 27, 2023

bangerth commented Jan 9, 2024

bangerth Jan 9, 2024

bangerth Jan 9, 2024

ljhwang Jan 10, 2024

ljhwang commented Jan 19, 2024

tjhei left a comment

tjhei Jan 24, 2024

ljhwang Jan 24, 2024

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tjhei Jan 28, 2024

tjhei Jan 24, 2024

ljhwang Jan 24, 2024

tjhei Jan 24, 2024

ljhwang Jan 24, 2024

tjhei Jan 24, 2024

ljhwang Jan 24, 2024

tjhei Jan 24, 2024

ljhwang Jan 24, 2024

gassmoeller commented Jan 26, 2024

bangerth commented Mar 9, 2024

bangerth commented Mar 9, 2024

gassmoeller commented Mar 15, 2024


		## Running on your desktop

		If you run in your local JupyetrLab environment, note the following dependencies:

	If you run in your local JupyetrLab environment, note the following dependencies:
	If you run in your local JupyterLab environment, note the following dependencies:

		@@ -0,0 +1,161 @@
		# A description of convection in a 2d box. See the manual for more information.


		The current version is verified to run within the ASPECT Jupyter Notebooks tool which can be launched from the CIG website:

		https://geodynamics.org/resources/aspectnotebook

		# A description of convection in a 2d box. See the manual for more information.


		# At the top, we define the number of space dimensions we would like to


		# Introduction to ASPECT

		This notebook is based on tutorials by J. Dannberg that provide a basic introduction to ASPECT.

Adds an updated version of the Jupyter notebook tutorial for the onse… #5533

Adds an updated version of the Jupyter notebook tutorial for the onse… #5533

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ljhwang commented Dec 19, 2023

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gassmoeller commented Jan 26, 2024

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gassmoeller commented Mar 15, 2024