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GEARRT thermochemistry fixes

Mladen Ivkovic requested to merge GEARRT_fix_thermochemistry into master

This MR contains cleanup, refactoring, and fixes to the GEAR RT thermochemistry scheme. I know it looks like a lot of changes, but most of it is just refactoring and cleanup of the codebase.

List of changes:

  • Added 3 new optional parameters for GEAR-RT ("CFL condition" for cooling time, flag to use case A recombination, let grackle be verbose)
  • The plotting scripts introduced by TK's recent SPHM1RT thermochemistry MR also needed updating to work correctly with GEAR-RT as well.
  • Added more documentation
  • Tweaked around the cooling and heating RT tests a little (those tests have only been used by GEAR-RT so far...)
  • fixed errors in IonizationEquilibriumTest py scrips
  • tweaked radiation injection scheme to not assume free streaming radiation at the particles closest to the injecting star. Otherwise, the radiation gets advected away before the thermochemistry can interact it with the gas.
  • "outsourced" all ionizing species related variables into an individual header file. Set it up to be easily extendable for future applications.

Sorry for making this MR huge again... It kinda got out of hand in the intermediate debugging steps...

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