Make O2 and SOC prognostic (#1545)

Co-authored-by: copilot-swe-agent[bot] <[email protected]>

Author: AlexisRenchon

NEWS.md

@@ -3,6 +3,7 @@ ClimaLand.jl Release Notes
 
 main
 -------
+- Make soil organic carbon and soil O2 prognostic; remove prescribed Soil Organic Carbon driver [#1545](https://github.com/CliMA/ClimaLand.jl/pull/1545)
 
 v1.1.1
 -------

docs/src/APIs/Drivers.md

@@ -8,7 +8,6 @@ CurrentModule = ClimaLand
 ClimaLand.PrescribedAtmosphere
 ClimaLand.PrescribedPrecipitation
 ClimaLand.PrescribedRadiativeFluxes
-ClimaLand.PrescribedSoilOrganicCarbon
 ClimaLand.CoupledAtmosphere
 ClimaLand.CoupledRadiativeFluxes
 ClimaLand.PrescribedGroundConditions

docs/src/APIs/soil/SoilBiogeochemistry.md

@@ -25,6 +25,7 @@ ClimaLand.Soil.Biogeochemistry.MicrobeProduction
 ClimaLand.Soil.Biogeochemistry.SoilCO2FluxBC
 ClimaLand.Soil.Biogeochemistry.SoilCO2StateBC
 ClimaLand.Soil.Biogeochemistry.AtmosCO2StateBC
+ClimaLand.Soil.Biogeochemistry.AtmosO2StateBC
 ClimaLand.Soil.Biogeochemistry.AbstractSoilDriver
 ClimaLand.Soil.Biogeochemistry.SoilDrivers
 ClimaLand.Soil.Biogeochemistry.PrescribedMet
@@ -36,6 +37,9 @@ ClimaLand.Soil.Biogeochemistry.PrescribedMet
 ClimaLand.Soil.Biogeochemistry.volumetric_air_content
 ClimaLand.Soil.Biogeochemistry.co2_diffusivity
 ClimaLand.Soil.Biogeochemistry.microbe_source
+ClimaLand.Soil.Biogeochemistry.o2_availability
+ClimaLand.Soil.Biogeochemistry.o2_concentration
+ClimaLand.Soil.Biogeochemistry.o2_fraction_from_concentration
 ```
 
 ## Extendible Functions

docs/src/refs.bib

@@ -331,3 +331,26 @@ @article{Clark2011
   doi       = {10.5194/gmd-4-701-2011},
   url       = {https://doi.org/10.5194/gmd-4-701-2011}
 }
+
+@article{Davidson2012,
+  author  = {Davidson, E. A. and Samanta, S. and Caramori, S. S. and Savage, K.},
+  title   = {The Dual Arrhenius and Michaelis-Menten kinetics model for decomposition of soil organic matter at hourly to seasonal time scales},
+  journal = {Global Change Biology},
+  year    = {2012},
+  volume  = {18},
+  number  = {1},
+  pages   = {371--384},
+  doi     = {10.1111/j.1365-2486.2011.02546.x}
+}
+
+@article{Ryan2018,
+  author  = {Ryan, E. M. and Ogle, K. and Peltier, D. M. P. and Walker, A. P. and De Kauwe, M. G. and Medlyn, B. E. and Williams, D. G. and Parton, W. and Asao, S. and Guenet, B. and Lauerwald, R. and Carvalhais, N. and Ciais, P. and Chertov, O. and Barton, C. and Degasperi, A. and Genet, H. and Huang, M. and Jenkinson, D. S. and Koven, C. D. and Kuzyakov, Y. and Luo, Y. and Manzoni, S. and McGuire, A. D. and Parr, J. and Pendall, E. and Sampson, R. N. and Smith, P. and Talhelm, A. F. and Tucker, C. and Wieder, W. R.},
+  title   = {Gross primary production responses to warming, elevated CO₂, and irrigation: quantifying the drivers of ecosystem physiology in a semiarid grassland},
+  journal = {Geoscientific Model Development},
+  year    = {2018},
+  volume  = {11},
+  number  = {5},
+  pages   = {1909--1928},
+  doi     = {10.5194/gmd-11-1909-2018},
+  url     = {https://doi.org/10.5194/gmd-11-1909-2018}
+}

docs/src/standalone/apps/hetero_resp.jl

@@ -8,7 +8,7 @@ function ParamViz.parameterisation(
     Ea_sx,
     kM_sx,
     kM_O₂,
-    O₂_a,
+    O₂_f,
     p_sx,
     Csom, # parameters
     θ_a100,
@@ -40,7 +40,7 @@ function Rh_app_f()
             "Activation energy, Ea_sx (J mol⁻¹)",
             "Michaelis constant for soil, kM_sx (kg C m⁻³)",
             "Michaelis constant for O₂, kM_O₂ (m³ m⁻³)",
-            "Volumetric fraction of O₂ in the soil air, O₂_a (dimensionless)",
+            "Volumetric fraction of O₂ in the soil air, O₂_f (dimensionless)",
             "Fraction of soil carbon that is considered soluble, p_sx (dimensionless)",
             "Soil organic C, Csom (kg C m⁻³)",
         ),
@@ -50,7 +50,7 @@ function Rh_app_f()
             FT.([50e3, 70e3]), # Ea_sx
             FT.([1e-10, 0.1]), # kM_sx
             FT.([1e-10, 0.1]), # kM_o2
-            FT.([0.005, 0.5]), # O2_a
+            FT.([0.005, 0.5]), # O2_f
             FT.([0.005, 0.5]), # p_sx
             FT.([1.0, 10.0]), # Csom
         ),
@@ -60,7 +60,7 @@ function Rh_app_f()
             (J * mol^-1, J * mol^-1), # Ea_sx
             (kg * m^-3, kg * m^-3), # kM_sx
             (m^3 * m^-3, m^3 * m^-3), # kM_O2
-            (m, m), # O2_a
+            (m, m), # O2_f
             (m, m), # p_sx
             (kg * m^-3, kg * m^-3), # Csom
         ),