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First step at integrating cloud particles#65

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Kiefersv wants to merge 30 commits intonatashabatalha:devfrom
Kiefersv:mixed
Open

First step at integrating cloud particles#65
Kiefersv wants to merge 30 commits intonatashabatalha:devfrom
Kiefersv:mixed

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@Kiefersv
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Hey Natasha,

As discussed here the monster PR with the first implementation of the mixed cloud particles in addition to some other changes. A quick overview:

Main addition:

  1. Mixed cloud particle physics: This includes the bulk changes in the justdoit file. The main difference is that the gas phase species are carried along to the calc_qc function to be able to calculate the density of the mixed particles.
  2. Testing: I added extensive integration and unit testing. It is not done yet, but already roughly 60% of the code is covered. Here it would make sense to also have a more clear conversation about decrypting some parts of the code to make sure we test what is actually used.
  3. GitHub Actions: Testing is now automatically done by Github Actions. There is also a CodeCoverage implementation but this will break when you add it to your branch. We can discuss how to fix it, but it should not impact anything for now.

Smaller Changes:

  1. Fixed Issue In calc_optics need to change if ibot >= nz - 2 to -3 #62: Logan was right, this needs to be -3 in the current implementation to cover all edge cases.
  2. Slight improvements to layout: As discussed, the next PR will deal with this in more detail.
  3. Fixed free-fsed, exp issue: Turns out there is a problem with combining free-fsed with the exp fsed parametrization. This is now corrected and tested.
  4. Quick mix: This first implementation of mixed cloud particle opacity handling does result in very similar opacities as homogeneous particles. It is currently implemented for testing only, but can be used scientifically in theory.

I am looking forward to your review and apologies again for the large PR.

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