Revamp thermodynamic state documentation

[gawng]

Purpose

For computing dynamic viscosity, liquid water does not follow Sutherland's law; it follows another equation (Andrade's eqn for the interested person). I added a fix to manually set the dynamic viscosity when setting up the AeroProblem() that when you specify mu, it will override the Sutherland law calculation. Doing so avoids viscosity dependence on temperature in the self.updateViscosity() call. I decided on this fix after @awccopp said he also had a use for specifying the dynamic viscosity.

This works for all thermodynamic specification methods EXCEPT for the 'mach' + 'altitude' method.

The example aeroproblem I put in the docstring has cavitation in the evalFuncs so maybe wait until this ADflow PR is merged.

EDIT:
The new fix for water does not require overriding anything but rather, exploiting the Sutherland's law calculation. It has been documented in the code. See conversation.

Expected time until merged

Not urgent. 1-2 weeks?

Type of change

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (non-backwards-compatible fix or feature)
• Code style update (formatting, renaming)
• Refactoring (no functional changes, no API changes)
• Documentation update
• Maintenance update
• Other (please describe)

Testing

No tests because we ended up only changing the docs.

Checklist

• I have run flake8 and black to make sure the code adheres to PEP-8 and is consistently formatted
• I have run unit and regression tests which pass locally with my changes
• I have added new tests that prove my fix is effective or that my feature works
• I have added necessary documentation

[codecov]

Codecov Report

Merging #78 (36df7ab) into main (c972540) will not change coverage.
The diff coverage is 22.41%.

@@           Coverage Diff           @@
##             main      #78   +/-   ##
=======================================
  Coverage   29.67%   29.67%           
=======================================
  Files          25       25           
  Lines        2362     2362           
=======================================
  Hits          701      701           
  Misses       1661     1661           

Impacted Files	Coverage Δ
baseclasses/problems/FluidProperties.py	10.00% <ø> (ø)
baseclasses/problems/pyFieldPerformance_problem.py	16.25% <ø> (ø)
baseclasses/utils/fileIO.py	88.23% <ø> (ø)
baseclasses/problems/pyLG_problem.py	5.60% <6.25%> (ø)
baseclasses/problems/pyWeight_problem.py	10.05% <9.09%> (ø)
baseclasses/problems/pyMission_problem.py	8.13% <11.11%> (ø)
baseclasses/problems/pyAero_problem.py	18.48% <14.28%> (ø)
baseclasses/problems/ICAOAtmosphere.py	5.88% <20.00%> (ø)
baseclasses/solvers/pyAero_solver.py	19.33% <33.33%> (ø)
baseclasses/testing/pyRegTest.py	87.95% <100.00%> (ø)

📣 Codecov can now indicate which changes are the most critical in Pull Requests. Learn more

[marcomangano]

Why are you not implementing this for the MACH + altitude option too? Is that because the specific combination should explicitly rely on the ICAOAtmosphere model?

[gawng]

@marcomangano That was my logic with regards to not implementing it for that option but if you think it makes sense to be able to override it, I can fix that. I actually need to write some regression testing to make sure this code is covered (coverage just went down) so do not merge this yet.

[joanibal]

I'm fine with this feature in principle.
I'm a little wary that people can over define their thermodynamic state by specifying 3 state variables (like P+T+mu). But as long as we document this I'm good with it.

[marcomangano]

I'm fine with this feature in principle. I'm a little wary that people can over define their thermodynamic state by specifying 3 state variables (like P+T+mu). But as long as we document this I'm good with it.

Yeah I see your concern. The point of this PR is to enable the user to override the Sutherland's law calculation so the overall thermodynamic state should still be self-consistent. Maybe we can have the code printing a message when it detects the mu input that explicitly states that Sutherland's law is ignored.

[marcomangano]

@marcomangano That was my logic with regards to not implementing it for that option but if you think it makes sense to be able to override it, I can fix that. I actually need to write some regression testing to make sure this code is covered (coverage just went down) so do not merge this yet.

@awccopp I assume your cases with "custom" mu were still using air properties? If that is the case, we should probably have the option for mach + altitude too.

[sseraj]

To dos:

• mu override in the _update to reduce code duplication (Galen)
• Add a warning when Sutherland's law is ignored (Galen)
• Document the steps and equations used for each input state combination and how the non-input variables are computed (Sabet)
• Document which variables are set as inputs to ADflow (look at src/initFlow/initializeFlow.F90)
• Clean up all mu changes (Galen)

[gawng]

@sseraj I had a look at
https://github.com/mdolab/adflow/blob/7180c03d24ed9ea1f3852861430eb4c76373d37e/src/initFlow/initializeFlow.F90#L50-L51
and it looks like viscosity is computed again via Sutherland's Law so now I'm second-guessing why we have mu being computed 2 times: once in baseclasses and then again in adflow. The dimensional viscosity in the fortran layer is used to compute the non-dimensional muInf so I think this does have an effect?

[gawng]

Codecov is failing because I changed numpy to np. The solution @sseraj and I came to was to document how to better specify mu in the AeroProblem setup. If one sets muSuthDim to the desired viscosity and sets T equal to TSuthDim, then you recover the right viscosity since Sutherland's equation will just give a unity multiplier.

With this solution, no overriding of Sutherland's law has to take place in baseclasses nor ADflow and the viscosity in the entire CFD domain can be computed properly in case there are significant temperature changes.

[joanibal]

Is this PR ready for review?

[sseraj]

Is this PR ready for review?

There is one item left for me to complete (adding docs for each input combination). I will try to complete that soon.

[joanibal]

No rush. I just wasn't sure because my review was requested but it is still marked as a draft PR.

[sseraj]

This is ready for review now @joanibal @eirikurj

[marcomangano]

The docs are much clearer now, thanks for the work! Unless @eirikurj wants to take a look I will merge it soon