Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate #1731

BangShiuh · 2024-07-08T13:33:05Z

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.

If applicable, fill in the issue number this pull request is fixing

Closes #

If applicable, provide an example illustrating new features this pull request is introducing

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 · 2024-07-08T13:58:37Z

Codecov Report

Attention: Patch coverage is 77.19298% with 39 lines in your changes missing coverage. Please review.

Project coverage is 73.26%. Comparing base (80c0bb2) to head (9a46ebb).

Files with missing lines	Patch %	Lines
src/thermo/PlasmaPhase.cpp	83.73%	8 Missing and 12 partials ⚠️
include/cantera/kinetics/ReactionRate.h	0.00%	12 Missing ⚠️
src/kinetics/Kinetics.cpp	40.00%	2 Missing and 1 partial ⚠️
include/cantera/kinetics/Kinetics.h	50.00%	2 Missing ⚠️
src/kinetics/Reaction.cpp	66.66%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1731      +/-   ##
==========================================
+ Coverage   73.23%   73.26%   +0.02%     
==========================================
  Files         383      383              
  Lines       54652    54799     +147     
  Branches     9109     9133      +24     
==========================================
+ Hits        40027    40150     +123     
- Misses      11612    11625      +13     
- Partials     3013     3024      +11

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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.

interfaces/cython/cantera/thermo.pyx

interfaces/cython/cantera/thermo.pxd

interfaces/cython/cantera/thermo.pyx

include/cantera/thermo/PlasmaPhase.h

test/python/test_thermo.py

src/thermo/PlasmaPhase.cpp

include/cantera/thermo/ThermoPhase.h

src/base/Solution.cpp

src/thermo/PlasmaPhase.cpp

speth · 2024-11-13T03:22:04Z

@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 · 2024-11-13T03:26:28Z

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 · 2024-11-19T12:48:55Z

@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 · 2024-11-19T15:57:38Z

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 · 2024-12-12T01:58:00Z

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

BangShiuh · 2024-12-12T02:21:44Z

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

speth · 2024-12-12T05:30:20Z

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.

…nterpolated cross section

…ratureFromEnergyDist

…ctor

…ctions

BangShiuh · 2024-12-12T13:04:12Z

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.

speth · 2025-01-20T23:35:52Z

include/cantera/thermo/PlasmaPhase.h

+ * distribution (as described by @cite gudmundsson2001 @cite khalilpour2020)
+ * is given by:


Because the @cite command only produces the numerical reference (for example [10]), write this as:

Suggested change

* distribution (as described by @cite gudmundsson2001 @cite khalilpour2020)

* is given by:

* distribution (as described by Gudmundsson @cite gudmundsson2001 and Khalilpour and Foroutan @cite khalilpour2020)

* is given by:

speth · 2025-01-20T23:36:14Z

include/cantera/thermo/PlasmaPhase.h

 *          f(\epsilon) = c_1 \frac{\sqrt{\epsilon}}{\epsilon_m^{3/2}}
- *          \exp(-c_2 (\frac{\epsilon}{\epsilon_m})^x),
+ *          \exp(-c_2 \left(\frac{\epsilon}{\epsilon_m}\right)^x),


Suggested change

* f(\epsilon) = c_1 \frac{\sqrt{\epsilon}}{\epsilon_m^{3/2}}

* \exp(-c_2 (\frac{\epsilon}{\epsilon_m})^x),

* \exp(-c_2 \left(\frac{\epsilon}{\epsilon_m}\right)^x),

* f(\epsilon) = c_1 \frac{\sqrt{\epsilon}}{\epsilon_m^{3/2}}

* \exp\left(-c_2 \left(\frac{\epsilon}{\epsilon_m}\right)^x\right),

Likewise below in the definition of $F(\epsilon)$.

speth · 2025-01-20T23:39:54Z

include/cantera/thermo/PlasmaPhase.h

+    //! @param  updateEnergyDist update electron energy distribution
+    void setElectronEnergyLevels(const double* levels, size_t length,
+                                 bool updateEnergyDist);


Can this be simplified by just adding updateEnergyDist=true as an optional argument to the existing version of setElectronEnergyLevels?

speth · 2025-01-20T23:44:00Z

include/cantera/thermo/PlasmaPhase.h

+    virtual void addSolution(std::weak_ptr<Solution> soln) override;
+
+    /**
+     * The elastic power loss(J/s/m3)


Missing a space. I've also started to prefer writing subscripts and superscripts for units using the corresponding unicode characters, though you can also stick to just m^3 for now if you prefer.

Suggested change

* The elastic power loss(J/s/m3)

* The elastic power loss (J/s/m³)

speth · 2025-01-20T23:45:02Z

include/cantera/thermo/PlasmaPhase.h

+    //! update the elastic electron energy loss coefficient of i collision
+    void updateElasticElectronEnergyLossCoefficient(size_t i);
+
+    //! update elastic electron energy loss coefficients
+    void updateElasticElectronEnergyLossCoefficients();


Can you elaborate on the conditions where these functions might need to be called?

speth · 2025-01-21T02:32:42Z

src/kinetics/Kinetics.cpp


+    for (const auto& [id, callback] : m_reactionChangedCallbacks) {
+        callback();
+    }


Based on where this is called, and how it is used in conjunction with PlasmaPhase, it might be more accurate to name this a reactionAddedCallback.

speth · 2025-01-21T02:34:03Z

src/thermo/PlasmaPhase.cpp

+        // register callback when reaction is added later
+        // The modifyReaction


Comment here seems incomplete.

speth · 2025-01-21T02:35:42Z

src/thermo/PlasmaPhase.cpp

@@ -8,9 +8,15 @@
 #include "cantera/thermo/Species.h"
 #include "cantera/base/global.h"
 #include "cantera/numerics/funcs.h"
+#include "cantera/kinetics/Kinetics.h"
+#include "cantera/kinetics/Reaction.h"
+#include "cantera/kinetics/KineticsFactory.h"


I don't think you need KineticsFactory.h here, do you?

speth · 2025-01-21T02:37:15Z

src/thermo/PlasmaPhase.cpp


 namespace Cantera {

+static const double gamma = sqrt(2 * ElectronCharge / ElectronMass);


Rather than static const double, this would be better as just const double in an unnamed namespace.

speth · 2025-01-21T02:43:35Z

src/thermo/PlasmaPhase.cpp

+
+    if (shared_ptr<Solution> soln = m_soln.lock()) {
+        shared_ptr<Kinetics> kin = soln->kinetics();
+        if (!kin) return;


Please don't use the one-line version of the if statement -- always use braces and put the body on a separate line.

BangShiuh changed the title ~~Collision~~ Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate Jul 8, 2024

BangShiuh changed the title ~~Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate~~ Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate (WIP) Jul 8, 2024

BangShiuh changed the title ~~Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate (WIP)~~ Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate Jul 8, 2024

speth requested changes Jul 22, 2024

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BangShiuh mentioned this pull request Aug 12, 2024

Non-equilibrium plasma including EEDF computation (two-term approximation) Cantera/enhancements#194

Open

ischoegl added the Thermo label Sep 1, 2024

BangShiuh force-pushed the collision branch 2 times, most recently from bde326e to 5f00629 Compare November 19, 2024 04:33

BangShiuh force-pushed the collision branch from 5f00629 to 9f4a423 Compare November 20, 2024 01:06

BangShiuh force-pushed the collision branch from 9f4a423 to 9cd1461 Compare December 9, 2024 02:31

BangShiuh force-pushed the collision branch from 9cd1461 to 29ec918 Compare December 12, 2024 02:10

BangShiuh force-pushed the collision branch from 29ec918 to 4f09ef6 Compare December 12, 2024 12:58

BangShiuh added 9 commits December 12, 2024 08:01

[phase] make PlasmaPhase using collisions and add the method to set i…

bcfb4ad

…nterpolated cross section

[plasma] fix the documentation

36addc7

[plasma] fix the isotropic electron energy distribustion

20aad0f

[test] add test_elastic_power_loss

c601dda

[plasma] fix the failed tests due to m_cs_interp

265315b

[plasma] add safe guard to prevent negative Te in updateElectronTempe…

bca959a

…ratureFromEnergyDist

[plasma] improve performance of setParamaters and PlasmaPhase constru…

879a7db

…ctor

[plasma] make changing reaction and rate update interpolated cross se…

2953cc2

…ctions

[plasma] fix setIsotropicShapeFactor

9a46ebb

BangShiuh force-pushed the collision branch from 4f09ef6 to 9a46ebb Compare December 12, 2024 13:02

speth requested changes Jan 21, 2025

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Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate #1731

Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate #1731

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		* distribution (as described by @cite gudmundsson2001 @cite khalilpour2020)
		* is given by:

	* The elastic power loss(J/s/m3)
	* The elastic power loss (J/s/m³)

		// register callback when reaction is added later
		// The modifyReaction


		namespace Cantera {

		static const double gamma = sqrt(2 * ElectronCharge / ElectronMass);

Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate #1731

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Enhance the PlasmaPhase to use the cross section data with an example of calculating the elastic collision energy loss rate #1731

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BangShiuh commented Jul 8, 2024 •

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