Extended PCT capabilities to low pressure for YHx

[Anthony-Bowers08]

(Ref. #261)

[moosebuild]

Job Coverage, step Generate coverage on f0140fa wanted to post the following:

Coverage

	f80c7c	#292 f0140f
	Total	Total	+/-	New
Rate	91.30%	88.08%	-3.22%	100.00%
Hits	1049	1049	-	42
Misses	100	142	+42	0

Diff coverage report

Full coverage report

This comment will be updated on new commits.

[moosebuild]

Job Coverage, step Verify coverage on f0140fa wanted to post the following:

The following coverage requirement(s) failed:

• Coverage rate 88.08% is less than the required 90.0%

[moosebuild]

Job Documentation, step Sync to remote on f0140fa wanted to post the following:

View the site here

This comment will be updated on new commits.

[moosebuild]

Job Build test summary, step Build test summary on f0140fa wanted to post the following:

Test summary

Compared against f80c7cb in job civet.inl.gov/job/3342972.

Removed tests

Added tests

Run time changes

[moosebuild]

Job Coverage, step Verify coverage on f0140fa wanted to post the following:

The following coverage requirement(s) failed:

• Coverage rate 88.08% is less than the required 90.0%

[simopier]

Thank you for this @Anthony-Bowers08!

I have several high level requests/suggestions:

1. Instead of adding a new material class, you should instead apply this in the existing ADMatInterfaceReactionYHxPCT class. There, you will see this if statement:

if (!_silence_warnings && ((neighbor_pressure < limit_pressure) || (neighbor_pressure > 1.e6)))

You should edit this if statement so that if the neighbor_pressure is above 1.e6 or lower than ~2.e2 (the lower pressure at which we have data if I remember properly), then an error is provided, if it is between 1.e6 and limit_pressure, then the current calculations for the high pressure regime is applied, and if it is between 2.e2 and limit_pressure, then it calculates the atomic fraction at the surface following the new equation you are proposing.
I think that should do it, and capture the plateau region. My concern is that we might see some oscillations around the plateau region, but we can test that and deploy a solution once we observe that.

2. I see that you have created an input file and submitted gold file, which is great. However, you need to also edit the test file related to this capability and add tests for all the configurations in the if statement above, with a particular focus on the new cases you are creating. The reason why the coverage currently fails is because despite adding a new input file, no additional test is being run.
   Note also that rather than create a brand new input file, you should instead use the cli_args option in the test file to utilize the existing file, but in the regime of interest to you. You will find example of that in the test file.

3. You will also need to update the documentation page (format in .md) to detail your new contribution to the existing capabilities.

4. Your python script should be merged with the existing one for ADMatInterfaceReactionYHxPCT. Do it all in there.

Let me know if you have any questions.

[simopier]

The prechecks are failing due to the white spaces:

##########################################################################
ERROR: The following files contain trailing whitespace after applying your patch:
	src/interfacekernels/ADMatInterfaceReactionYHxPCT.C

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

ERROR: The following files do not contain a newline character before EOF:
	doc/content/source/interfacekernels/figures/comparison_YHx_PCT.py
	test/tests/yttrium_hydrogen_system/comparison_YHx_PCT.py

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

I thought you had applied the changes I had suggested to get rid of those. Did it not work?

[moosebuild]

Job Precheck, step Format Check Clang on 5c0e95a wanted to post the following:

Your code requires style changes.

A patch was auto generated and copied here
You can directly apply the patch by running, in the top level of your repository:

curl -s https://mooseframework.inl.gov/tmap8/docs/PRs/292/clang_format/style.patch | git apply -v

Alternatively, with your repository up to date and in the top level of your repository:

git clang-format bfc1f83801ce80841f2b7da14c4bd4d80096a3a0

[simopier]

@Anthony-Bowers08, you will need to fix the conflict with the python script.
Let me know if you don't know how to do it and I can guide you.

[Anthony-Bowers08]

@simopier , think python script is an updated one from your prior .py yttrium script. I essentially added the low pressure plotting and made into a function based filed. I can revert to your prior .py file and just add the low pressure plotting there.

[simopier]

@simopier , think python script is an updated one from your prior .py yttrium script. I essentially added the low pressure plotting and made into a function based filed. I can revert to your prior .py file and just add the low pressure plotting there.

Please do.

Also, the conflicts means that the files have been updated in your branch and in a recent merge of TMAP8. So it's less about the nature of the change, and more about the fact that several changes from different origins are in conflict. We have recently deployed a formatting script for TMAP8, which affected many of the python scripts. That is probably the culprit.