Extended PCT capabilities to low pressure for YHx by Anthony-Bowers08 · Pull Request #292 · idaholab/tmap8

Anthony-Bowers08 · 2025-09-11T21:41:39Z

(Ref. #261)

moosebuild · 2025-10-29T16:20:27Z

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 · 2025-10-29T16:20:27Z

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 · 2025-10-29T16:20:58Z

Job Documentation, step Sync to remote on b916521 wanted to post the following:

View the site here

This comment will be updated on new commits.

moosebuild · 2025-10-29T16:35:34Z

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:

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.

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.
You will also need to update the documentation page (format in .md) to detail your new contribution to the existing capabilities.
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 · 2026-02-09T22:08:13Z

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?

…#292

simopier · 2026-02-17T01:12:01Z

@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 · 2026-02-17T01:33:58Z

@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 · 2026-02-17T04:34:51Z

@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 · 2026-03-23T00:04:48Z

+[YHx_PCT_Data] shows the data used in this interface kernel. The experimental data originates from [!cite](Lundin_1962).
+The [YHx_PCT_fit_2D] shows high and low pressure fit with the high pressure fit from [!cite](Matthews2021SWIFT) and the low-pressure is a newly fitted curve.
+
+!media comparison_YHx_PCT.py


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 · 2026-03-23T00:26:00Z

+  nl_rel_tol = 1e-4
+  nl_abs_tol = 4e-9


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

I am surprised that you have to change the tolerances so much. Did you try reducing them back down?

moosebuild · 2026-04-01T16:27:26Z

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 .

simopier

This test diffs:

DIFF test:yttrium_hydrogen_system.YHx_PCT_T1273_P3e2_csv FAILED (CSVDIFF)

Things are really taking shape otherwise!

simopier · 2026-04-02T02:08:02Z

+  if (neighbor_pressure > limit_pressure && abs(neighbor_pressure - limit_pressure) < tolerance)
+  {
+    // High pressure region, near limit
+    atomic_fraction = 0.5;


This comment still holds.

simopier · 2026-04-03T03:56:33Z

+    // If near the start of the high pressure , jump to low pressure maximum atomic ratio
+    Ar_Max_LP_fit = 1.01e-6 * Utility::pow<2>(_neighbor_temperature[_qp]) -
+                    2.55e-3 * _neighbor_temperature[_qp] + 2.156;


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

moosebuild · 2026-04-03T04:04:26Z

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

simopier · 2026-06-04T20:30:07Z

This PR needs to be properly rebased.

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

simopier

I'm adding a few suggestions, but I'll need to see the full documentation to provide the full review. The precheck are currently filing due to clang format. The solve is provided in the comment above.

simopier · 2026-08-01T15:11:37Z

Do not add the png files directly, create them with the python script.

Will remove, thanks for pointing this out

simopier · 2026-08-01T15:33:48Z

+ax.set_ylabel("Partial Pressure (Pa)")
+ax.grid(True, which="both", linestyle=":", alpha=0.6)
+
+ncols_temp = min(len(temp_handles), 5)


please replace temp with temperature everywhere.

simopier · 2026-08-01T15:38:05Z


 # diffusivity from Majer et al., Journal of Alloys and Compounds 330-332 (2002) 438-442.
-diffusivity_Do = '${units 1.e-8 m^2/s}'
+diffusivity_Do = '${units 1 m^2/s}'


Why this change?

This is changed to reduce the time needed to reach steady-state converged solution.

simopier · 2026-08-01T15:41:08Z

  [function_BC_concentration_H_enclosure_1]
    type = ParsedFunction
-    expression = 'exp(-${tau_constant_BC}/t)* ${initial_concentration_H_enclosure_1}'
+    expression = 'exp(-${dt_init}*2e-2/t)* ${initial_concentration_H_enclosure_1}'


Please put back tau_constant_BC. Why did you remove it?

simopier · 2026-08-01T15:42:09Z

+  nl_rel_tol = 1e-4
+  nl_abs_tol = 4e-9


I am surprised that you have to change the tolerances so much. Did you try reducing them back down?

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

moosebuild · 2026-08-03T15:30:35Z

Job Precheck, step Format Check Clang on 51542d0 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 e0b788f03eee4a0821496733c419b1cb7823b221

simopier

Some small comments, and also note that you have some failing tests:

[3.180s] [ 196MB]     DIFF test:yttrium_hydrogen_system.YHx_PCT_T1273_P3e3_csv FAILED (CSVDIFF)
[15.75s] [ 234MB]     DIFF test:yttrium_hydrogen_system.YHx_PCT_T1273_P3e2_csv FAILED (CSVDIFF)
[2.835s] [ 259MB]     DIFF test:yttrium_hydrogen_system.YHx_PCT_T1473_P3e3_csv FAILED (CSVDIFF)
[9.379s] [ 300MB]     DIFF test:yttrium_hydrogen_system.YHx_PCT_T1573_P5e3_csv FAILED (CSVDIFF)

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

simopier self-assigned this Sep 11, 2025

simopier requested changes Nov 6, 2025

View reviewed changes

Anthony-Bowers08 force-pushed the yttrium_hydride_lowpressure branch from f0140fa to 05b1c7c Compare February 9, 2026 16:43

Anthony-Bowers08 pushed a commit to Anthony-Bowers08/TMAP8 that referenced this pull request Feb 9, 2026

Attempt to fix trailing space idaholab#4 and correct refence idaholab…

5bb7e66

…#292

Anthony-Bowers08 requested a review from simopier February 9, 2026 23:23

Anthony-Bowers08 force-pushed the yttrium_hydride_lowpressure branch 2 times, most recently from 8dad514 to 6a315c7 Compare February 11, 2026 18:08

Anthony-Bowers08 force-pushed the yttrium_hydride_lowpressure branch from 502a728 to b70b205 Compare March 12, 2026 14:27

simopier requested changes Mar 16, 2026

View reviewed changes

simopier requested changes Mar 23, 2026

View reviewed changes

simopier requested changes Apr 2, 2026

View reviewed changes

simopier requested changes Apr 3, 2026

View reviewed changes

Bowers and others added 7 commits July 28, 2026 08:19

Modifications, reformatting, and cleaning YHX #Ref 262

57b0ec4

Ref. idaholab#261

a42e9a5

Appling patches to python and C files

2065dea

Apply suggestions from code review

469a41c

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Apply suggestions from code review

ad721af

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Improvement to low pressure fit and corrections to python file

217edc5

Formatting

d4615d6

Bowers and others added 16 commits July 28, 2026 08:19

Formatting source files

045bc8e

Update src/interfacekernels/ADMatInterfaceReactionYHxPCT.C

1c8f62a

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Update src/interfacekernels/ADMatInterfaceReactionYHxPCT.C

e7947b1

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Modfications to linkage and C. File

711e158

Including full ranges PCT modelling for YHx

2bfbf7c

Modifications, reformatting, and cleaning YHX #Ref 262

ca72ab9

Appling patches to python and C files

b118d5d

Apply suggestions from code review

57b3909

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Improvement to low pressure fit and corrections to python file

2914e39

Formatting

cbe248a

Formatting source files

b1d774d

Update src/interfacekernels/ADMatInterfaceReactionYHxPCT.C

9fe18a9

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Update src/interfacekernels/ADMatInterfaceReactionYHxPCT.C

4783f28

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Modfications to linkage and C. File

2432d3b

Including full ranges PCT modelling for YHx

209772d

Improvements to YHx full PCT modelling

576b451

Anthony-Bowers08 force-pushed the yttrium_hydride_lowpressure branch from aa036a6 to 576b451 Compare July 30, 2026 22:00

simopier requested changes Aug 1, 2026

View reviewed changes

Apply suggestions from code review

51542d0

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Modifications to formatting and variable naming for YHx

b916521

simopier reviewed Aug 5, 2026

View reviewed changes

Comment thread test/tests/yttrium_hydrogen_system/comparison_YHx_PCT.py Outdated

Comment thread test/tests/yttrium_hydrogen_system/comparison_YHx_PCT.py Outdated

Anthony-Bowers08 and others added 5 commits August 25, 2026 14:45

Merge branch 'devel' into yttrium_hydride_lowpressure

e291778

Fixing test cases, plotting formatting, and documentation formatting.

ae455ec

Appling formatting to source file

70a77a7

Update test/tests/yttrium_hydrogen_system/comparison_YHx_PCT.py

bd63433

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Update test/tests/yttrium_hydrogen_system/comparison_YHx_PCT.py

043746c

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Uh oh!

Conversation

Anthony-Bowers08 commented Sep 11, 2025

Uh oh!

moosebuild commented Oct 29, 2025

Coverage

Uh oh!

moosebuild commented Oct 29, 2025

Uh oh!

moosebuild commented Oct 29, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

moosebuild commented Oct 29, 2025

Uh oh!

simopier left a comment

Choose a reason for hiding this comment

Uh oh!

simopier commented Feb 9, 2026

Uh oh!

simopier commented Feb 17, 2026

Uh oh!

Anthony-Bowers08 commented Feb 17, 2026

Uh oh!

simopier commented Feb 17, 2026

Uh oh!

simopier left a comment

Choose a reason for hiding this comment

Uh oh!

simopier left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

moosebuild commented Apr 1, 2026

Python black formatting

Uh oh!

simopier left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

moosebuild commented Apr 3, 2026

Test summary

Added tests

Uh oh!

simopier commented Jun 4, 2026

Uh oh!

simopier left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

moosebuild commented Oct 29, 2025 •

edited

Loading