Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate

[BangShiuh]

Changes proposed in this pull request
This PR change the initiation of the PlasmaPhase. The PlasmaPhase after this change takes the ElectronCollisionPlasmaRate cross-section data to calculate the plasma thermal properties (specifically the elastic collision energy loss rate). The elastic collision energy loss is the energy transfer from electron to molecule when a fast electron (higher electron temperature) collides to a slower molecule (lower gas temperature). This is useful for modelling a non-equilibrium plasma in which the electron temperature is much higher than the gas temperature. The elastic collision power loss includes the energy transfer via elastic collision and via the recoil effect of an inelastic collision. The equation can be found in the manual of bolsig, https://www.bolsig.laplace.univ-tlse.fr/download.html. I have compared the value of elastic power loss to bolsig, and it is reasonably close (around 1% different).

Data download:
The collision cross section can be downloaded from https://nl.lxcat.net/data/download.php. However, the zip file is currently broken. Fortunately, I have saved a previous version. Please email me if you want to use it.

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Checklist

• The pull request includes a clear description of this code change
• Commit messages have short titles and reference relevant issues
• Build passes (scons build & scons test) and unit tests address code coverage
• Style & formatting of contributed code follows contributing guidelines
• The pull request is ready for review

[codecov]

Codecov Report

Attention: Patch coverage is 83.12500% with 27 lines in your changes missing coverage. Please review.

Project coverage is 74.43%. Comparing base (80c0bb2) to head (411e4f8).
Report is 116 commits behind head on main.

Files with missing lines	Patch %	Lines
src/thermo/PlasmaPhase.cpp	85.03%	7 Missing and 12 partials ⚠️
include/cantera/kinetics/Kinetics.h	0.00%	4 Missing ⚠️
src/kinetics/Kinetics.cpp	66.66%	0 Missing and 2 partials ⚠️
src/kinetics/Reaction.cpp	66.66%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1731      +/-   ##
==========================================
+ Coverage   73.23%   74.43%   +1.19%     
==========================================
  Files         383      382       -1     
  Lines       54652    53492    -1160     
  Branches     9109     9055      -54     
==========================================
- Hits        40027    39816     -211     
+ Misses      11612    10609    -1003     
- Partials     3013     3067      +54     

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[speth]

Thanks for working on this, @BangShiuh. I had some suggestions that I think will lead to a simpler implementation. Please let me know if you have any questions.

[speth]

@BangShiuh, I saw that you have marked all the comments from my previous review as "resolved", but I think the corresponding changes have not been pushed to this branch. Are they all in your collision-new branch that you mentioned in Cantera/enhancements#194? Could you push them to this branch?

[BangShiuh]

Hi Ray, Yes, I am mostly done. I am working on a small issue right now for updating the interpolating the cross section. I will push it once I finished! Bang

…

On Tue, Nov 12, 2024 at 10:22 PM Ray Speth ***@***.***> wrote: @BangShiuh <https://github.com/BangShiuh>, I saw that you have marked all the comments from my previous review as "resolved", but I think the corresponding changes have not been pushed to this branch. Are they all in your collision-new branch that you mentioned in Cantera/enhancements#194 <Cantera/enhancements#194>? Could you push them to this branch? — Reply to this email directly, view it on GitHub <#1731 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEZZJBQ5JNPC2LX7E6SMOID2ALAXFAVCNFSM6AAAAABKQ3OMM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZSGI4TAMRTGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[BangShiuh]

@speth I have made updating rate or adding reaction triggers updating the interpolated cross sections. I also have tried to reduce the number of interpolating the cross-sections, but not successful. The rate object in PlasmaPhase is different to the one in m_bulk_rates, which is used by updateROP.

I will check the Linters checks failure. How do I run that on my computer?

[speth]

I will check the Linters checks failure. How do I run that on my computer?

The easiest thing to do is just look at the logs here on GitHub. The problem that it is finding is with the docstring for class PlasmaPhase, which starts with:

/*!
 * Base class for handling plasma properties, specifically focusing on the
 * electron energy distribution. This class provides functionality
 * to manage the the electron energy distribution using two primary methods
 * for defining the electron distribution and electron temperature.
 *

There is a subtle difference between starting a Doxygen comment block with /** and /*!. In the former case, the first sentence of the comment block (that is, up to the first period or blank line) will be used as the brief description. In the latter case, it will not. Since we often rely on this feature for providing the brief description, the comment block should start with /** instead. The other way to write this with the brief description more explicitly provided is:

//! Base class for handling plasma properties, specifically focusing on the
//! electron energy distribution. 
/*!
 * This class provides functionality to manage the the electron energy distribution
 * using two primary methods for defining the electron distribution and electron
 * temperature.
 *

[speth]

Commit 21bbebd erroneously reverts the state of the example_data submodule. If you undo that change, that should fix the failing CI jobs.

[BangShiuh]

I am not sure why 4e7d6e2 is [1D].... I will investigate it.

[speth]

I think you've accidentally squashed a commit of yours into one of mine. The only change that should be in the commit with that message is a 3-line change to Flow1D.cpp. You might be able to resolve it by rebasing onto the current main branch, and then just editing the commit message for that commit.

[BangShiuh]

I used reset during rebase to remove the change to example_data. But I used commit --amend, so the original commit was gone and became [1D] ... should just use commit instead.

[speth]

Thanks for the updates here, @BangShiuh. I think this is just about ready -- I just have a few comments that are mostly about the documentation and code style.

[BangShiuh]

@speth The issues are fixed. Let me know if anything needs update. Thanks for the code review!

[speth]

Thanks for these updates, @BangShiuh. This looks great!