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RT GEAR: thermochemistry I/O and ICs

Mladen Ivkovic requested to merge rt-GEAR-thermochemistry-IO into master

New in this MR:

  • added HI, HII, HeI, HeII, HeIII mass fractions to particles for thermochemistry.
  • I/O routines for these mass fractions.
  • option to overwrite all ionization states at startup added
  • option to compute initial ionization states assuming ionization equilibrium added
  • option to skip the thermochemistry for testing/debugging purposes
  • documented new parameters, and updated documentation a bit.
  • throw an error if running with cooling and RT simultaneously.

Here's the result of swift setting up initial ionization states assuming ionization equilibrium for a particles to which I've given a very wide range initial internal energies: test_ionization_equilibrium

At least for now, I'd like to keep everything contained in the RT scheme so I may tinker with it as I please. We can look into properly merging everything with possibly overlapping cooling/hydro structs/parameters etc. later.

@matthieu, @bvandenbroucke : could you have a quick look whether you're content with the I/O routines and names etc? If you are, I'd like to immediately add the new quantities to swiftsimio to facilitate further developments. Here's a sample output file : output_0000.hdf5

@tkchan : I had to modify some function prototypes. I have added the changes to your routines as well.

Edited by Mladen Ivkovic

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