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 4d11a94 wanted to post the following:

View the site here

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%

[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?

[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.

[simopier]

You need an issue number in your commit message:

#########################################################################
ERROR: Your patch does not contain a valid ticket reference! (i.e. #1234)
Merge branch 'yttrium_hydride_lowpressure' of https://github.com/Anthony-Bowers08/TMAP8 into test
Modifications, reformatting, and cleaning YHX #Ref 262
##########################################################################

[simopier]

Thank you for this extension!
I added comments for you to incorporate.
Let me know if you have any questions.

[simopier]

Why do you cut the low pressure data at an atomic fraction of 0.5? It can/should go further than that, especially for higher temperatures.

[Anthony-Bowers08]

The fit becomes severely offset to the PCT data for values above 0.5. Please schedule a meeting to discuss if interested.

[simopier]

Please use the same colors as for the following figure. You use the same type of color palette, but it would be easier for the reader if you used the same color for the same temperature in both figures.

[simopier]

Lin is making changes to these cases, and you should be ready to use his options, which will be merged soon. See #382

[simopier]

Do not completely re-write this python script.
Add what you need and want to add by expanding what is already there.

[moosebuild]

Job Precheck, step Python: black format on fdf51b4 wanted to post the following:

Python black formatting

Your code requires style changes.

A patch was generated and copied here.

You can directly apply the patch by running the following at the top level of your repository:

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

Alternatively, you can run the following at the top level of your repository:

black --config pyproject.toml --workers 1 .

[moosebuild]

Job Precheck, step Format Check Clang on 3c02387 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 7d1a0b5b28a8af593cadf654a8165c44ffd14bc6

[simopier]

This test diffs:

DIFF test:yttrium_hydrogen_system.YHx_PCT_T1273_P3e2_csv FAILED (CSVDIFF)

Things are really taking shape otherwise!

[simopier]

This comment still holds.

[simopier]

Let's set up a meeting to chat about this. My calendar is up to date.

[moosebuild]

Job Build test summary, step Build test summary on 4d11a94 wanted to post the following:

Test summary

Compared against 7d1a0b5 in job civet.inl.gov/job/3675371.

Added tests

Test	Time (s)	Memory (MB)
test:yttrium_hydrogen_system.YHx_PCT_T1273_P1e3_csv	3.72	78.09
test:yttrium_hydrogen_system.YHx_PCT_T1473_P3e3_csv	3.28	95.09
test:yttrium_hydrogen_system.YHx_PCT_T1573_P6e2_csv	3.26	131.73
test:yttrium_hydrogen_system.YHx_PCT_T1573_P5e3_csv	3.18	101.39
test:yttrium_hydrogen_system.YHx_PCT_T1273_P3e2_csv	3.12	87.78