Introduce magnetic mirror physics/ generalised geometry into moment_kinetics

[mrhardman]

To implement magnetic geometry we need to modify several features of moment_kinetics.

• We would introduce the need for arrays to hold geometric coefficients instead of just using the simple constants bzed bzeta rhostar etc in

  moment_kinetics/src/input_structs.jl

  Line 320 in 137b9ca

  mutable struct geometry_input

  .
• We would ideally make input options that result is an array B[iz,ir] and dBdz[iz,ir], dBdr[iz,ir] etc in an expanded `geometry' struct to be passed around the code.
• We would introduce magnetic mirror terms, see, e.g., eqns 3.48, 3.49 and 3.50 in https://www-thphys.physics.ox.ac.uk/people/FelixParra/CollisionlessPlasmaPhysics/notes/lecI_magnetizedmotion.pdf
• We would introduce self-consistent magnetic drift terms, see, e.g., eqns 3.28 - 3.30 of https://www-thphys.physics.ox.ac.uk/people/FelixParra/CollisionlessPlasmaPhysics/notes/lecII_driftkinetics.pdf.
• We would introduce self-consistent finite Larmor radius terms to provide classical diffusion in the Fokker-Planck collision operator.

@johnomotani thoughts appreciated on order of developments.

[johnomotani]

pinging @slnewton - any thoughts?

[mrhardman]

A first attempt to generalise the treatment of the geometry is here

https://github.com/mabarnes/moment_kinetics/tree/geometry-upgrade

I have not addressed the issue #111 although the branch above would be the natural place to do this.

[mrhardman]

@slnewton @johnomotani @mabarnes In particular, it is important now to pick a sufficiently general coordinate system that I can structure the advection terms and geometry module such that we can later easily feed in results from a Grad-Shafranov solver. I am guessing that a sensible choice could be the coordinates (Z,rho,zeta), with rho = sqrt(psi/psi_0), Z the vertical distance and zeta the toroidal angle. What do present SOL codes use? We can map z -> Z, r -> rho.

[mrhardman]

Linking the PR just to make finding it easy - the work is still draft.