Soil GHG gas tracers (CO2, CH4, N2O)

[AlexisRenchon]

Is your feature request related to a problem? Please describe. The branch CliMAsoilCO2 adds an AbstractModel to track CO2 concentration in the soil, as a prognostic variable function of depth and time, resulting from soil diffusivity of CO2 and production of CO2 by roots and microbes, inspired by the DETECT model.

Please link to any related issues/PRs. #114 #121 #132 #143

Describe the solution you'd like

• [x] prescribed SM and Ts c3db6b63b0179f526b8d28426a62fc71d6ae3ef8
• [x] Write tests d3af86028795e58b9afc32cdd7b12ffc9e312595
• [x] State boundary condition 9467ae31cc2a735f6a92fcdc060b0c71d324f2c0
• [x] create experiment files, with realistic parameters (some of them function of z) 6c74170342220365ea99b2ba300768f1ae269ecb
• [ ] Soil CO2 efflux output
• [ ] Tutorial to generate an animation of soil CO2 in depth and time - CZI test site
• [x] prognostic soil moisture (SM) and temperature (Ts)
• [x] add functions (DETECT_parameterizations.jl) to calculate SMant and Tsant, weighted average of past SM/Ts (wont do)
• [x] convert all units to standard units
• [ ] PDE for oxygen, + add oxygen sensitivity in DETECT
• [ ] PDE for Cr, Cmic, Csom (root, microbe and organic C), currently assumed constant over time
• [ ] CO2 dissolved in water
• [ ] CO2 displaced in soil air space by water
• [ ] parameterize at a single site (maybe NEON data), using CARDAMOM or MCMC?
• [ ] parameterize for global simulation
• [ ] more tweaks of mechanistic functions with Dani Or, Ruby Fu, Adrian Moure
• [ ] Add other GHG: CH4 and N2O microbial source/sink, coupled with CO2
• [ ] Can we use optimality theory to predict microbial community? (e.g., microbe adapted to anoxic conditions in wet areas)

Describe alternatives you've considered Alternative models can be implemented thanks to the modularity of ClimaLSM, for example alternate soil diffusivity of production representations.

Additional context In the context of the canopy airspace feature to come, it will be important to properly estimate soil CO2 efflux.