Cross species collisions

[mrhardman]

Addition of a test collision operator that consists of the self collision operator, plus cross-species collisions with two fixed Maxwellian species, representing slow ions and electrons. Example input files are added. The distributions functions shown in the attached .gif files show the relaxation of the distribution function towards cold ash. Comments on the outstanding tasks below would be especially appreciated, as these have to do with the input parameters for collision operators generally.

(@LucasMontoya4 FYI do not feel pressured to read the code in detail at this point, but ideas for whether or not you are happy to restructure the collisions input struct would be very useful).

Plots of the simulated (fast) ion distribution function:

• [x] Make consistent input options for beam initial condition to permit user control without hard-coding the beam parameters.
• [x] Make the fixed Maxwellian species density, thermal speed and parallel flow to be input parameters.
• [x] Restructure the collision operator input namelists to separate Fokker-Planck collision options from Krook options for future convenience, perhaps easing the two tasks above.
• [ ] Use this test to construct a true multi-species collision operator in the moment-kinetics framework.
• [ ] CI Regression test for a slowing-down collision operator example run.

[LucasMontoya4]

@mrhardman I can't really tell (from what I know so far) how much editing elsewhere in the code it would take to change the collisions_input struct, but it sounds like it would be a good idea in future no? Maybe we could have the collisions_input struct contain structs for each collision operator (krook::krook_struct, FP::Fokker_Planck_struct etc.)?

[mrhardman]

@mrhardman I can't really tell (from what I know so far) how much editing elsewhere in the code it would take to change the collisions_input struct, but it sounds like it would be a good idea in future no? Maybe we could have the collisions_input struct contain structs for each collision operator (krook::krook_struct, FP::Fokker_Planck_struct etc.)?

This is the kind of thing that I would like to do. It would not be too much effort, but the changes might touch several files. These changes are not directly related to my cross-species collision operator, so they could go in a separate PR focussing on changing the existing input options. @johnomotani do you agree with the idea, should I make separate PR for the refactoring the existing inputs?

[johnomotani]

The input restructuring sounds like a good idea, and I'm very in favour of doing that kind of preparatory change in a small PR that we can merge early to avoid conflicts later. :+1:

[mrhardman]

The input restructuring sounds like a good idea, and I'm very in favour of doing that kind of preparatory change in a small PR that we can merge early to avoid conflicts later. 👍

Now in progress in #202. You may object to some of the input renaming, but I hope that we can find a way where we are all happy : )

[mrhardman]

FYI, the test moment_kinetics/test/fokker_planck_time_evolution_tests.jl also fails locally on my machine, which apparently can only be due to the change of the frequency_option choice, except for the fact that this doesn't make sense at all, because these tests passed for the #202 branch @johnomotani another mystery?

EDIT: This likely has to do with a poor choice for the default Zi for collisions.

[johnomotani]

Those tests started failing at 0b03e9b, which was before the merges...

Edit: sorry, you've fixed it already!

[mrhardman]

I'm now happy for this to be merged (or to have a longer discussion about the content), as I have all the features that I need for the short term.

[johnomotani]

We can ignore the failing macOS parallel tests here - the cause is some change in the OpenMPI setup, which I've worked around in #206, so those CI tests should be fixed when we merge into master.