1154 energy balance for understory vegetation

[vgro]

This PR adds the energy balance for the understorey vegetation following the idea of the forest floor litter model by J. Ogee and Y. Brunet (2002).

The main step is to solve the energy balance for the understorey, similar to the canopy, and add a conductive flux towards the soil. The updated docs are here.

I also fixed the vertical mixing which caused the model to crash and added some functions to make things a bit tidies, like update_profile_from_reference.

This step revealed a whole bunch of gaps and problems which should be addressed separately to stop this PR from getting more complicated (and clarified some of the older issues, should be doable now):

• Surface precipitation should not get negative #1162
• Albedo is missing from radiation balance #1164
• Adjust flux_layers index to account for understorey vegetation #1172
• tidy dymmy climate data in conftest #1173
• abiotic simple model should populate basic microclimate variables in init #1175
• canopy evaporation is not returned properly #1181
• Plant model needs to return understorey transpiration #1182
• reactivate aerodynamic resistance calculation #967
• revisit implementation of soil temperature #919

Fixes #1154

Type of change

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that speeds up the code)
• Bug fix (non-breaking change which fixes an issue)

Key checklist

• Make sure you've run the pre-commit checks: $ pre-commit run -a
• All tests pass: $ poetry run pytest

Further checks

• Code is commented, particularly in hard-to-understand areas
• Tests added that prove fix is effective or that feature works
• Relevant documentation reviewed and updated

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.43%. Comparing base (d9a335b) to head (5353e9a).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1183      +/-   ##
===========================================
+ Coverage    94.39%   94.43%   +0.04%     
===========================================
  Files           71       71              
  Lines         7169     7229      +60     
===========================================
+ Hits          6767     6827      +60     
  Misses         402      402              

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[jacobcook1995]

I can't follow all of the science, but it looks good to me in general, only had a few minor comments

[davidorme]

All looks good to me - well documented too!