collisions: Disable ion-neutral and electron-neutral by default

[bendudson]

These may be double-counted if atomic reactions are included. Added a note to the manual.

ion-electron, electron-electron, ion-ion, and neutral-neutral collisions are still enabled by default.

Fixes #241.

[mikekryjak]

How come you disabled e-n as well? Is that double counting something too?

[bendudson]

I don't think e-n are double counted, but I thought this might be the least surprising set of defaults.
electron-neutral collisions aren't included in e.g Braginskii rates, so if someone is comparing to Braginskii then they would need to remember to disable e-n collisions. This means that all plasma-neutral interactions must be explicitly turned on, which might be a simple rule to remember.

The electron-driven reactions don't modify the electron collision frequency (https://github.com/bendudson/hermes-3/blob/master/include/amjuel_reaction.hxx#L68).

Happy to change this default, if something else would be easier for people to work with.

[mikekryjak]

Hi @bendudson okay, I agree with that. There is a related question of what we do with the Braginskii collisionality implementation - whether we set Braginskii as default or not. I think that default should be Braginskii, and documentation and possibly a warning should warn the user if they are using multiple ions. I asked the question here: #195