change A, b, Ea in memory

[Weiqi Ji]

Hi,

I am working on optimizing reaction mechanisms, in which all of three Arrhenius parameters A, b, Ea are changed. Now, I want to test it in Cantera. I can thinking of two ways to do it:

1) manually (automatically) modify the mechanism file

2) modify A, b, Ea in memory.

Is there any way to do 2) in Cantera?

Thanks

Weiqi

[Travis Sikes]

Weiqi,

You should check out Frhodo. It optimizes all three arrhenius parameters and allows you to set uncertainties on them as well as the rate. All modification of the mechanism is done in memory. It's optimization is multiprocessing enabled. The version forked onto my github has Bayesian parameter estimation-based optimization (thanks to Ashi Savara and CHeKiPEUQ) as well as residual-based optimization. It also has quite a few other cool features. If there is something that you want it to do that it doesn't, it's open source. I'd love to work with you to add features.

Travis

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[travis....@gmail.com]

Weiqi,

There are a number of choices for optimization algorithms. For global optimization schemes it has stochastic methods, similar to what you mentioned, and ones which subdivide the parameter space into increasingly small hyperrectangles. Local optimization has options for simplex type methods and model based optimization. 

It's easier to answer your question directly as my implementation is bound up with my gui. You need to use modify_reaction(rxnIdx, rxn) where you specify what reaction is being modified and then provide it with a new reaction which you define. Changes made directly to the reaction do not change the underlying solution object until that function is called.

Travis

On Wednesday, March 17, 2021 at 10:55:29 PM UTC-5 Weiqi Ji wrote:

Hi Travis,

Can you point to the code block that modifies the mechanism in memory?

best,

Weiqi

[Ray Speth]

Hi Weiqi,

I added the modify_reaction functionality back in 2015, as part of Cantera 2.2. We don’t currently have any examples showing it’s use, so I guess it’s not very easy to discover.

Regards,
Ray

​

On Thursday, March 18, 2021 at 11:07:40 AM UTC-4 Weiqi Ji wrote:

Hi Travis,

Nice! I am curious if those methods work sufficiently well for large models with hundreds of parameters? I am mostly focusing on more sophistically methods developed for deep learning models and thus is good at complex models, even with thousands of parameters. Maybe we should schedule a call sometime to discuss :)

For the reaction modification, thanks for pointing out the function https://cantera.org/documentation/docs-2.5/sphinx/html/cython/kinetics.html#cantera.Kinetics.modify_reaction. I didn't know it and it seems added recently.

Currently, I wrote a short script to regenerate the updated mechanism with YAML.

Weiqi

[Weiqi Ji]

Hi Ray,

Good to know that. It is very useful for mechanism optimization and uncertainty quantification.

Best,

Weiqi

[adityasa...@u.northwestern.edu]

Weiqi, I'm not sure if you are using surface reactions. I remember there was some complication for surface reactions the last time I checked.  Because of that, I had to re-import the cantera model each optimization step.

But if you are using only gas phase reactions it should be fine. For optimizaition and UQ, I do think that Travis's software Frhodo is a good software for the community to continue to advance.

I had started building an interface for very general optimization: https://github.com/AdityaSavara/CheKiPEUQ/blob/master/CheKiPEUQ/simulationDriver/example_runfile.py

https://github.com/AdityaSavara/CheKiPEUQ/blob/master/CheKiPEUQ/simulationDriver/canteraKineticsParametersParser.py

https://github.com/AdityaSavara/CheKiPEUQ/blob/master/CheKiPEUQ/simulationDriver/canteraSimulate.py

If you wish to build upon what I made further, that would be excellent also. I stopped working on it (for now) due to the Surface Reactions complication.

[Ray Speth]

Hi Aditya,

If there are aspects of surface reactions that can't be updated dynamically, can you please provide an example and post an issue on the GitHub Issue Tracker? In principle, there shouldn't be any problem with updating any parameters related to the rate constant. Some of the other parameters like efficiencies are more difficult to allow changes to.

Regards,

Ray

[Aditya Ashi Savara]

Will do! I thought I brought this up once but could not find evidence that I did so. I will try to put together an example in the next 5 days. I apologize for any delay as I have a couple of urgent deadlines!

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[Ingmar Schoegl]

Hi Aditya,

You did bring it up, but the issue was moved to 'enhancements', see https://github.com/Cantera/enhancements/issues/8

-ingmar-

[adityasa...@u.northwestern.edu]

Ingmar, thank you for finding my earlier enhancement request! It is nice to see I did make an example back then :)

Do I understand correctly that once MultiRateBase is merged in, you would expect the modify_reaction command to work correctly for surface reactions?

In case anybody reading this thread else wants to look, here are the relevant threads for the new code that has not yet been merged in.

https://github.com/Cantera/enhancements/issues/87

https://github.com/Cantera/cantera/pull/995

[Ingmar Schoegl]

Hi Aditya,

MultiRateBase is already merged in, but the reactions need to be ported to the new framework. This will likely take a couple of PR's - see https://github.com/Cantera/enhancements/issues/87, and I anticipate InterfaceKinetics to be the last. It should, however, get fixed once the process is complete; if things proceed as anticipated it should also be possible to change some of the parameters directly in memory without having to modify/overwrite the reaction rate definition. It is, however, very much work in progress so take things with a grain of salt.

-ingmar-

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[Aditya Ashi Savara]

Ingmar, thank you! That forward-looking information is very nice!

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