cad_geometry_example

[meltawila]

This PR is to add CAD-based Geometry Workflow example for Multiphysics Fusion Problems Using OpenMC and MOOSE. Work and results taken from M. Eltawila, A. J. Novak, P.C. A. Simon, G. Giudicelli, D. Gaston, “Investigating CAD-based Geometry Workflows for Multiphysics Fusion Problems Using OpenMC and MOOSE,” Submitted to Pacific Basin Nuclear Conference (PBNC) (2024)

(Ref. #30)

[simopier]

First of all, thank you for contributing this example to FENIX! I'm thrilled to see it added!
A few things to keep in mind:

1. You are currently getting the error:

ERROR: Your patch does not contain a valid ticket reference! (i.e. #1234)
Merge branch 'cardinal_example' of github.com:meltawila/fenix into test
cad_geometry_example

This is because you need an issue number in one of your commits (and it's also best to include it in the description at the top of your PR). I just created an issue for you and here is what you want to provide: (Ref. #30). In the future, make sure to create an issue before creating the PR (or even before creating your first commit). You can find guidance for that here: https://fenix-dev.hpc.inl.gov/site/sqa/contributing.html

2. You are currently getting the error:

ERROR: The following files contain trailing whitespace after applying your patch:
	doc/content/examples/cad_geometry_model/input_files/model.py

Run the "delete_trailing_whitespace.sh" script in your $MOOSE_DIR/scripts directory.

Follow this guidance, or, in VSCode, you can go to Code->settings->settings
then type whitespace, and then you can select a couple of options, including Editor:trim auto whitespace and File:trim trailing whitespace, which should prevent you from running into this issue in the future.

3. You are currently getting the error:

ERROR: The following files contain windows line endings:
	doc/content/examples/cad_geometry_model/input_files/model.py

Make sure to remove those.

4. Just like in a paper, make sure to reference the figures in the text in the documentation.
5. The current location of the input files is not appropriate, but I'll create a PR to prepare things a little better in FENIX and will tell you where to move them. You will also need a test file to run this case and test it, as well as some gold files that will contain the test results, and then ensure that the results remain consistent as FENIX gets further developed.
6. To address these comments, you can go to 'Files Changes' at the top of this page and add suggestions to batch when you agree with them. This will create a commit with these changes.
   Then, pull this PR locally and make further edits
   To pull a PR locally, do:

git checkout <branch_name> 
git branch --set-upstream-to=origin/<branch_name> 
git fetch origin <branch_name> 
git status # to check that fetch pulled new commits and that tracking is showing the commit difference 
git pull

Let me know if you have any questions.
Thanks!

[simopier]

@meltawila: #33 is merged, so you should have everything you need to reorganize this PR.
Let me know if you have any questions and need more clarity about the instructions I provided above.

[simopier]

The tests are failing for the reasons described in my comment above. Use the guidance I provided to fix these.

[moosebuild]

Job Documentation on 09a3c46 wanted to post the following:

View the site here

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[moosebuild]

Job Coverage on 09a3c46 wanted to post the following:

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[simopier]

Thank you @meltawila!

I provided some changes to fix the tests that are currently failing.

The main changes that you still have to do are:

• Create a new folder under test/tests' titled cad_geometry_exampleand move the content of the currentinput_files` folder you created there. The input files and mesh should be in the test folder, not the documentation folder.
• Once you have created the cad_geometry_example folder and moved the input files and mesh there, then you'll need to create a tests file like you can find here that automatically run the input file as part of a test for FENIX.
• Then, you will need to create - within test/tests/cad_geometry_example - a gold folder that contains the outputs created by your tests. This file will be used in the future to ensure that this example case still reproduces the same output as FENIX evolves (if one day it doesn't, then it means something is broken, or the gold file should be updated). This is a crucial part of our Software Quality Assurance.
• I would also like to see, in the documentation, a section dedicated to listing the instructions to run the example case that you are creating there.

There are also a few comments from previous reviews that were not fully addressed (see above).

Let me know if you have any questions.

[simopier]

@meltawila
In the future, make sure to add descriptive commit messages to document what you do rather than just ..

[simopier]

Starting to look really good! Thank you @meltawila!
Make sure to add the tests file and a gold folder as described in previous reviews.

Also, tmesh_1.e is missing from the PR.

[moosebuild]

Job Precheck on 09a3c46 wanted to post the following:

Warning: This PR changes repo size by 12.59 MiB.

[simopier]

Some minor comments. I'll follow your instructions locally and let you know if there's anything else that should be added to the documentation or these input file.

[simopier]

Suggested change

	requirement = "The system shall be able to solve for the temperature distribution."
	requirement = "The system shall be able to run a coupled neutronics and heat conduction simulation and solve for the temperature distribution."

[simopier]

Suggested change

	requirement = "The system shall be able to solve for the heat source and tritium production."
	requirement = "The system shall be able to run a coupled neutronics and heat conduction simulation and solve for the heat source and tritium production."

[simopier]

Suggested change

	exodiff = solid_out_openmc0.e
	exodiff = solid_out_openmc0.e
	should_execute = False # this test relies on the output files from solid_diff, so it shouldn't be run twice
	prereq = solid_diff

[simopier]

This prevents the same test from being run twice, it simply leverages the results from the previous test.

[simopier]

The test are actually skipped with the message:

SKIP test:cad_geometry_example.openmc_diff [OpenMCCellAverageProblem not found in executable]
SKIP test:cad_geometry_example.solid_diff [OpenMCCellAverageProblem not found in executable]

You should add to the PR (or a separate one) the changes that need to happen in FENIX to be able to run Cardinal/OpenMC.

[simopier]

@meltawila you might need to follow the instructions described at the bottom of #43.