Add Ver 1jb to TMAP8's V&V suite #185

simopier · 2024-10-13T19:31:20Z

Ref. #12
Ref. #145

moosebuild · 2024-10-13T19:48:29Z

Job Documentation, step Sync to remote on 0874728 wanted to post the following:

View the site here

This comment will be updated on new commits.

simopier · 2024-10-13T23:15:01Z

EDIT:

this issue was solved. It came from the fact that both tests added in this case were writing checkpoint files with the same name. Hence, depending on the timeline in which part 1 and recover happened, one test could end up using the checkpoint results from the other test.

This PR is fully ready for review.

Somehow, the recover test for the basic ver-1jb csv diff case fails.

in the normal test, I locally get:

Time Step 54, time = 1.60944e+09, dt = 3.15576e+07
 0 Nonlinear |R| = 2.411274e-09
      0 Linear |R| = 2.411274e-09
      1 Linear |R| = 7.021067e-25
 1 Nonlinear |R| = 4.598546e-24
  Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
 Solve Converged!

Outlier Variable Residual Norms:
  tritium_trapped_concentration_scaled: 4.275653e-24

but when I run in recover mode, I get:

Time Step 54, time = 1.60944e+09, dt = 3.15576e+07
 0 Nonlinear |R| = 2.412682e-09
      0 Linear |R| = 2.412682e-09
      1 Linear |R| = 3.107300e-24
 1 Nonlinear |R| = 1.280678e-12
      0 Linear |R| = 1.280678e-12
      1 Linear |R| = 2.833365e-28
 2 Nonlinear |R| = 4.801294e-14
      0 Linear |R| = 4.801294e-14
      1 Linear |R| = 2.043024e-29
 3 Nonlinear |R| = 1.800018e-15
      0 Linear |R| = 1.800018e-15
      1 Linear |R| = 3.814858e-31
 4 Nonlinear |R| = 6.748313e-17
      0 Linear |R| = 6.748313e-17
      1 Linear |R| = 1.430223e-32
 5 Nonlinear |R| = 2.529960e-18
      0 Linear |R| = 2.529960e-18
      1 Linear |R| = 5.706847e-34
 6 Nonlinear |R| = 9.484888e-20
  Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 6
 Solve Converged!

Outlier Variable Residual Norms:
  tritium_mobile_concentration_scaled: 9.484888e-20

and the time step ends up being different.

To be even more confusing, the case with equivalent concentrations of mobile and trapped tritium runs well in recover mode, when the only difference is the initial concentration of mobile tritium and trap_per_free value.

Any ideas or suggestions @cticenhour, @chaibhave, @lin-yang-ly?

Despite this issue, this PR is ready for review.

- decay term for trapped tritium - use unit system - update comments

- add case with equivalent concentrations of mobile and trapped tritium

(Close. #145) (Ref. #12)

…erate test, increase accuracy, and fix recover failure

This should solve the recover issue

moosebuild · 2024-10-15T20:34:00Z

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test/tests/ver-1jb/ver-1jb.i

doc/content/verification_and_validation/ver-1jb.md

test/tests/ver-1jb/ver-1jb.i

chaibhave

Basically good to go except for some documentation and python code changes.

test/tests/ver-1jb/ver-1jb.i

doc/content/verification_and_validation/ver-1jb.md

test/tests/ver-1jb/comparison_ver-1jb.py

Co-authored-by: Chaitanya Bhave <65254651+chaibhave@users.noreply.github.com>

simopier

This is not a review, just responses to @chaibhave's comments.

doc/content/verification_and_validation/ver-1jb.md

test/tests/ver-1jb/ver-1jb.i

simopier · 2024-10-16T00:28:45Z

test/tests/ver-1jb/ver-1jb.i

+ nl_rel_tol = 1e-10
+ nl_abs_tol = 1e-30


I don't think 1e-10 is absolutely needed here. I'll go back to the default if that works fine.

chaibhave

@cticenhour ready for your review, I'm done with all reviews. The comments left unresolved you can resolve, I'm not on the CCB yet so I don't have permissions for it.

cticenhour

Found a few items I'd like addressed, and I resolved the remaining comments from @chaibhave that were marked as completed.

cticenhour · 2024-10-22T14:37:06Z

doc/content/verification_and_validation/ver-1jb.md

-The first ([ver-1ja](ver-1ja.md)) is simple decay of mobile species in a slab.
-The second (ver-1jb) is decay of trapped atoms in a similar slab but with a distributed trap concentration.
+The first ([ver-1ja](ver-1ja.md)) models simple decay of mobile species in a slab.
+The second (ver-1jb) models decay of trapped atoms in a similar slab but with a distributed trap concentration.
 This page presents ver-1jb.


Suggested change

This page presents ver-1jb.

This page presents ver-1jb, based on the case published in the TMAP7 verification and validation suite [!citep](ambrosek2008verification).

cticenhour · 2024-10-22T14:40:03Z

doc/content/verification_and_validation/ver-1jb.md

+This verification case is an extension of[ver-1ja](ver-1ja.md), which tests the first order radioactive decay capabilities of TMAP8.
+In ver-1jb, however, tritium decay is coupled with trapping, which was verified in several verification cases, including [ver-1d](ver-1d.md).
+As [ver-1ja](ver-1ja.md), ver-1jb is based on the case published in the TMAP7 V&V suite [!citep](ambrosek2008verification).


Suggested change

This verification case is an extension of[ver-1ja](ver-1ja.md), which tests the first order radioactive decay capabilities of TMAP8.

In ver-1jb, however, tritium decay is coupled with trapping, which was verified in several verification cases, including [ver-1d](ver-1d.md).

As [ver-1ja](ver-1ja.md), ver-1jb is based on the case published in the TMAP7 V&V suite [!citep](ambrosek2008verification).

This verification case is an extension of[ver-1ja](ver-1ja.md), which tests the first order radioactive decay capabilities of TMAP8.

In ver-1jb, tritium decay is coupled with trapping, which itself was verified in several TMAP8 verification cases including [ver-1d](ver-1d.md).

cticenhour · 2024-10-22T14:42:02Z

doc/content/verification_and_validation/ver-1jb.md

+This verification case is an extension of[ver-1ja](ver-1ja.md), which tests the first order radioactive decay capabilities of TMAP8.
+In ver-1jb, however, tritium decay is coupled with trapping, which was verified in several verification cases, including [ver-1d](ver-1d.md).
+As [ver-1ja](ver-1ja.md), ver-1jb is based on the case published in the TMAP7 V&V suite [!citep](ambrosek2008verification).
+Similarly to [ver-1ja](ver-1ja.md), the model assumes pre-charging of an $l=1.5$ m long slab with tritium (with an assumed width and thickness of 1 m). Further complexity is added to the problem by introducing traps with a normal distribution centered at the mid-plane of the slab and a standard deviation of $l/4$, and mobile tritium.


Suggested change

Similarly to [ver-1ja](ver-1ja.md), the model assumes pre-charging of an $l=1.5$ m long slab with tritium (with an assumed width and thickness of 1 m). Further complexity is added to the problem by introducing traps with a normal distribution centered at the mid-plane of the slab and a standard deviation of $l/4$, and mobile tritium.

Similarly to [ver-1ja](ver-1ja.md), the model assumes pre-charging of an $l=1.5$ m long slab (with an assumed width and thickness of 1 m) with tritium. Further complexity is added to the problem by introducing mobile tritium and trapping sites whose locations follow a normal distribution centered at the mid-plane of the slab with a standard deviation of $l/4$.

cticenhour · 2024-10-22T14:43:02Z

doc/content/verification_and_validation/ver-1jb.md

+In ver-1jb, however, tritium decay is coupled with trapping, which was verified in several verification cases, including [ver-1d](ver-1d.md).
+As [ver-1ja](ver-1ja.md), ver-1jb is based on the case published in the TMAP7 V&V suite [!citep](ambrosek2008verification).
+Similarly to [ver-1ja](ver-1ja.md), the model assumes pre-charging of an $l=1.5$ m long slab with tritium (with an assumed width and thickness of 1 m). Further complexity is added to the problem by introducing traps with a normal distribution centered at the mid-plane of the slab and a standard deviation of $l/4$, and mobile tritium.
+The peak atomic fraction of traps is $C_{trap} = 0.001$, and the trap energy is $E=4.2$ eV. The material density used to calculate the number of traps is based on tungsten, and defined as 6.34 $\times 10^{28}$ atoms/m$^3$. The traps are initially filled with trapped tritium to 50% of trap concentration.


Suggested change

The peak atomic fraction of traps is $C_{trap} = 0.001$, and the trap energy is $E=4.2$ eV. The material density used to calculate the number of traps is based on tungsten, and defined as 6.34 $\times 10^{28}$ atoms/m$^3$. The traps are initially filled with trapped tritium to 50% of trap concentration.

The peak atomic fraction of traps is $C_{trap} = 0.001$, and the trap energy is $E=4.2$ eV. The material density used to calculate the number of traps is based on tungsten, and is defined as 6.34 $\times 10^{28}$ atoms/m$^3$. The traps are initially filled with trapped tritium to 50% of trap concentration.

cticenhour · 2024-10-22T14:48:22Z

doc/content/verification_and_validation/ver-1jb.md

+\begin{equation}
+ D_T = 1.58 \times 10^{-4} \exp \left(- \frac{308 \times 10^{3}}{RT}\right),
+\end{equation}
+where $R$ is the ideal gas constant in J/K/mol from [Physical Constants](https://mooseframework.inl.gov/tmap8/source/utils/PhysicalConstants.html) and $T=300$ K is the temperature of the domain.


Suggested change

where $R$ is the ideal gas constant in J/K/mol from [Physical Constants](https://mooseframework.inl.gov/tmap8/source/utils/PhysicalConstants.html) and $T=300$ K is the temperature of the domain.

where $R$ is the ideal gas constant in J/K/mol from [Physical Constants](utils/PhysicalConstants.md) and $T=300$ K is the temperature of the domain.

cticenhour · 2024-10-22T14:53:00Z

doc/content/verification_and_validation/ver-1jb.md

+\end{equation}
+
+where $I_{tot}^0 = I_M^0 + I_T^0$ atoms/m is the initial total inventory of tritium
+($I_M^0$ and $I_T^0$ are the initial mobile and trapped tritium inventories).


Suggested change

($I_M^0$ and $I_T^0$ are the initial mobile and trapped tritium inventories).

($I_M^0$ and $I_T^0$ are the initial mobile and trapped tritium inventories, respectively).

cticenhour · 2024-10-22T14:56:26Z

doc/content/verification_and_validation/ver-1jb.md

+#### With a small concentration of mobile tritium compared to trapped tritium
+
+[ver-1jb_results_comparison_analytical_time_evolution_1] shows the TMAP8 predictions and how they compare to the analytical solution
+for the decay of tritium and associated growth of $^3$He in a distributed trap.


Here, $^3$He is used, but earlier in the document, helium-3 is used. Stylistically, we should be consistent. I leave it to you to decide which form you want.

cticenhour · 2024-10-22T14:57:24Z

doc/content/verification_and_validation/ver-1jb.md

+ caption=Comparison of TMAP8 predictions against the analytical solution for the decay of tritium and associated growth of $^3$He in a distributed trap with a small concentration of mobile tritium compared to trapped tritium.
+
+[ver-1jb_results_profile_1] shows the depth profile of the initial trapped atoms of tritium, the concentration of trapped atoms of
+tritium after 45 years, and the distribution of $^3$He at the end of that time across the distributed trap as predicted by TMAP8. The concentration of mobile tritium remains very low.


Suggested change

tritium after 45 years, and the distribution of $^3$He at the end of that time across the distributed trap as predicted by TMAP8. The concentration of mobile tritium remains very low.

tritium after 45 years, and the distribution of $^3$He at the end of that time period across the distributed trapping sites as predicted by TMAP8. The concentration of mobile tritium remains very low.

cticenhour · 2024-10-22T14:57:53Z

doc/content/verification_and_validation/ver-1jb.md

+[ver-1jb_results_profile_1] shows the depth profile of the initial trapped atoms of tritium, the concentration of trapped atoms of
+tritium after 45 years, and the distribution of $^3$He at the end of that time across the distributed trap as predicted by TMAP8. The concentration of mobile tritium remains very low.
+
+Note that because of $^3$He is given a null diffusivity in this verification problem, the shape of the $^3$He does not broaden.


Suggested change

Note that because of $^3$He is given a null diffusivity in this verification problem, the shape of the $^3$He does not broaden.

Note that because $^3$He is given a null diffusivity in this verification problem, the shape of the $^3$He concentration does not broaden.

cticenhour · 2024-10-22T14:59:04Z

doc/content/verification_and_validation/ver-1jb.md

+ caption=Comparison of TMAP8 predictions against the analytical solution for the decay of tritium and associated growth of $^3$He in a distributed trap with equivalent initial concentrations of mobile and trapped tritium.
+
+[ver-1jb_results_profile_2] shows the depth profile of the initial trapped atoms of tritium, the concentration of mobile and trapped atoms of
+tritium after 45 years, and the distribution of $^3$He at the end of that time across the distributed trap as predicted by TMAP8.


Suggested change

tritium after 45 years, and the distribution of $^3$He at the end of that time across the distributed trap as predicted by TMAP8.

tritium after 45 years, and the distribution of $^3$He at the end of that time period across the distributed trapping sites as predicted by TMAP8.

simopier added the V&V Relevant to V&V label Oct 13, 2024

simopier requested review from cticenhour, chaibhave and lin-yang-ly October 13, 2024 19:31

simopier self-assigned this Oct 13, 2024

simopier force-pushed the ver-1jb branch from dfa784c to 6b7fcb7 Compare October 13, 2024 19:34

simopier added 12 commits October 15, 2024 13:05

Update ver-1jb

ac777db

Clean up and devel of input files:

b0a3351

- decay term for trapped tritium - use unit system - update comments

Complete input file for ver-1jb

43ad9a0

Add python script for ver-1jb

b11b671

Add tests and gold files

395b292

Update documentation

3a6bb0b

- Correct input file (one of the signs were wrong)

ecea800

- add case with equivalent concentrations of mobile and trapped tritium

Update ver-1jb documentation and clean up

14a8b9b

ver-1d and ver-1ja clean up prompted by ver-1jb case development

a71df96

(Close. #145) (Ref. #12)

Fix documentation and refine solving adn convergence options to accel…

d660948

…erate test, increase accuracy, and fix recover failure

Refine convergence and clean up

b5c8516

Update file_base output names to avoid outputs being overridden.

1c1c6ff

This should solve the recover issue

simopier force-pushed the ver-1jb branch from 364a951 to 1c1c6ff Compare October 15, 2024 20:08

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Co-authored-by: Chaitanya Bhave <65254651+chaibhave@users.noreply.github.com>

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Add Ver 1jb to TMAP8's V&V suite #185

Add Ver 1jb to TMAP8's V&V suite #185

simopier commented Oct 13, 2024

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	This page presents ver-1jb.
	This page presents ver-1jb, based on the case published in the TMAP7 verification and validation suite [!citep](ambrosek2008verification).

	Similarly to [ver-1ja](ver-1ja.md), the model assumes pre-charging of an $l=1.5$ m long slab with tritium (with an assumed width and thickness of 1 m). Further complexity is added to the problem by introducing traps with a normal distribution centered at the mid-plane of the slab and a standard deviation of $l/4$, and mobile tritium.
	Similarly to [ver-1ja](ver-1ja.md), the model assumes pre-charging of an $l=1.5$ m long slab (with an assumed width and thickness of 1 m) with tritium. Further complexity is added to the problem by introducing mobile tritium and trapping sites whose locations follow a normal distribution centered at the mid-plane of the slab with a standard deviation of $l/4$.

	The peak atomic fraction of traps is $C_{trap} = 0.001$, and the trap energy is $E=4.2$ eV. The material density used to calculate the number of traps is based on tungsten, and defined as 6.34 $\times 10^{28}$ atoms/m$^3$. The traps are initially filled with trapped tritium to 50% of trap concentration.
	The peak atomic fraction of traps is $C_{trap} = 0.001$, and the trap energy is $E=4.2$ eV. The material density used to calculate the number of traps is based on tungsten, and is defined as 6.34 $\times 10^{28}$ atoms/m$^3$. The traps are initially filled with trapped tritium to 50% of trap concentration.

	where $R$ is the ideal gas constant in J/K/mol from [Physical Constants](https://mooseframework.inl.gov/tmap8/source/utils/PhysicalConstants.html) and $T=300$ K is the temperature of the domain.
	where $R$ is the ideal gas constant in J/K/mol from [Physical Constants](utils/PhysicalConstants.md) and $T=300$ K is the temperature of the domain.

	($I_M^0$ and $I_T^0$ are the initial mobile and trapped tritium inventories).
	($I_M^0$ and $I_T^0$ are the initial mobile and trapped tritium inventories, respectively).

	tritium after 45 years, and the distribution of $^3$He at the end of that time across the distributed trap as predicted by TMAP8. The concentration of mobile tritium remains very low.
	tritium after 45 years, and the distribution of $^3$He at the end of that time period across the distributed trapping sites as predicted by TMAP8. The concentration of mobile tritium remains very low.

	Note that because of $^3$He is given a null diffusivity in this verification problem, the shape of the $^3$He does not broaden.
	Note that because $^3$He is given a null diffusivity in this verification problem, the shape of the $^3$He concentration does not broaden.

Add Ver 1jb to TMAP8's V&V suite #185

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