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All CO2 fluxes in mol CO2 m-2 s-1 #731

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Aug 20, 2024
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All CO2 fluxes in mol CO2 m-2 s-1 #731

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3 changes: 1 addition & 2 deletions ext/CreateParametersExt.jl
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Expand Up @@ -96,8 +96,7 @@ function AutotrophicRespirationParameters(
:live_stem_wood_coeff => :ηsl,
:specific_leaf_density => :σl,
:root_leaf_nitrogen_ratio => :μr,
:mol_CO2_to_kg_C_factor => :f1,
:relative_contribution_factor => :f2,
:relative_contribution_factor => :Rel,
:stem_leaf_nitrogen_ratio => :μs,
)
parameters = CP.get_parameter_values(toml_dict, name_map, "Land")
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5 changes: 2 additions & 3 deletions lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Ha1/US-Ha1_parameters.jl
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Expand Up @@ -60,10 +60,9 @@ function auto_resp_harvard(;
σl = FT(0.05),
μr = FT(1.0),
μs = FT(0.1),
f1 = FT(0.012),
f2 = FT(0.25),
Rel = FT(0.25),
)
return AutotrophicRespirationParameters(ne, ηsl, σl, μr, μs, f1, f2)
return AutotrophicRespirationParameters(ne, ηsl, σl, μr, μs, Rel)
end

function soil_harvard(;
Expand Down
5 changes: 2 additions & 3 deletions lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-MOz/US-MOz_parameters.jl
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Expand Up @@ -60,10 +60,9 @@ function auto_resp_ozark(;
σl = FT(0.05),
μr = FT(1.0),
μs = FT(0.1),
f1 = FT(0.012),
f2 = FT(0.25),
Rel = FT(0.25),
)
return AutotrophicRespirationParameters(ne, ηsl, σl, μr, μs, f1, f2)
return AutotrophicRespirationParameters(ne, ηsl, σl, μr, μs, Rel)
end

function soil_ozark(; # Function that returns the src function, but with ozark default args
Expand Down
5 changes: 2 additions & 3 deletions lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-NR1/US-NR1_parameters.jl
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Expand Up @@ -60,10 +60,9 @@ function auto_resp_niwotridge(;
σl = FT(0.05),
μr = FT(1.0),
μs = FT(0.1),
f1 = FT(0.012),
f2 = FT(0.25),
Rel = FT(0.25),
)
return AutotrophicRespirationParameters(ne, ηsl, σl, μr, μs, f1, f2)
return AutotrophicRespirationParameters(ne, ηsl, σl, μr, μs, Rel)
end

function soil_niwotridge(;
Expand Down
5 changes: 2 additions & 3 deletions lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Var/US-Var_parameters.jl
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Expand Up @@ -60,10 +60,9 @@ function auto_resp_vairaranch(;
σl = FT(0.05),
μr = FT(1.0),
μs = FT(0.1),
f1 = FT(0.012),
f2 = FT(0.25),
Rel = FT(0.25),
)
return AutotrophicRespirationParameters(ne, ηsl, σl, μr, μs, f1, f2)
return AutotrophicRespirationParameters(ne, ηsl, σl, μr, μs, Rel)
end

function soil_vairaranch(;
Expand Down
3 changes: 1 addition & 2 deletions lib/ClimaLandSimulations/src/Fluxnet/run_fluxnet.jl
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Expand Up @@ -95,8 +95,7 @@ function run_fluxnet(
σl = params.auto_resp.σl,
μr = params.auto_resp.μr,
μs = params.auto_resp.μs,
f1 = params.auto_resp.f1,
f2 = params.auto_resp.f2,
Rel = params.auto_resp.Rel,
)
)
# Set up radiative transfer
Expand Down
4 changes: 2 additions & 2 deletions src/diagnostics/define_diagnostics.jl
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Expand Up @@ -167,7 +167,7 @@ function define_diagnostics!(land_model)
short_name = "ra",
long_name = "Autotrophic Respiration",
standard_name = "autotrophic_respiration",
units = "kg C m^-2 s^-1",
units = "mol CO2 m^-2 s^-1",
comments = "The canopy autotrophic respiration, the sum of leaves, stems and roots respiration.",
compute! = (out, Y, p, t) ->
compute_autotrophic_respiration!(out, Y, p, t, land_model),
Expand Down Expand Up @@ -720,7 +720,7 @@ function define_diagnostics!(land_model)
short_name = "scms",
long_name = "Soil CO2 Microbial Source",
standard_name = "soil_co2_microbial_source",
units = "kg C m^-2 s^-1",
units = "kg C m^-3 s^-1",
comments = "The production of CO2 by microbes in the soil. Vary by layers of soil depth.",
compute! = (out, Y, p, t) ->
compute_soilco2_source_microbe!(out, Y, p, t, land_model),
Expand Down
17 changes: 16 additions & 1 deletion src/diagnostics/land_compute_methods.jl
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Expand Up @@ -139,7 +139,22 @@ end
@diagnostic_compute "vapor_flux" SoilCanopyModel p.soil.turbulent_fluxes.vapor_flux

# Soil - SoilCO2
@diagnostic_compute "heterotrophic_respiration" SoilCanopyModel p.soilco2.top_bc
function compute_heterotrophic_respiration!(
out,
Y,
p,
t,
land_model::SoilCanopyModel{FT},
) where {FT}
if isnothing(out)
return p.soilco2.top_bc .* FT(83.26)
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@kmdeck kmdeck Aug 20, 2024 •
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Maybe we could note that:
"To convert from kg C to mol CO2, we need to multiply by: [3.664 kg CO2/ kg C] x [10^3 g CO2/ kg CO2] x [1 mol CO2/44.009 g CO2] = 83.26 mol CO2/kg C"

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Technically 83.26 is a parameter in ClimaParams. Would it be possible to fetch its value from land_model?

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I wonder if I should remove it from ClimaParams, as it is just a conversion?

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that I added but actually we are not using it (except if we do use it here)

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To make it makes sense that it should not be a parameter (but there are other constants of nature/conversions in there). I'd remove it.

else
out .= p.soilco2.top_bc .* FT(83.26)
end
end # Convert from kg C to mol CO2.
# To convert from kg C to mol CO2, we need to multiply by:
# [3.664 kg CO2/ kg C] x [10^3 g CO2/ kg CO2] x [1 mol CO2/44.009 g CO2] = 83.26 mol CO2/kg C

@diagnostic_compute "soilco2_diffusivity" SoilCanopyModel p.soilco2.D
@diagnostic_compute "soilco2_source_microbe" SoilCanopyModel p.soilco2.Sm

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14 changes: 6 additions & 8 deletions src/standalone/Vegetation/autotrophic_respiration.jl
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Expand Up @@ -22,10 +22,8 @@ Base.@kwdef struct AutotrophicRespirationParameters{FT <: AbstractFloat}
μr::FT
"Ratio stem nitrogen to top leaf nitrogen (-), typical value 0.1"
μs::FT
"Factor to convert from mol CO2 to kg C"
f1::FT
"Factor of relative contribution or Rgrowth (-)"
f2::FT
"Relative contribution or Rgrowth (-)"
Rel::FT
end

Base.eltype(::AutotrophicRespirationParameters{FT}) where {FT} = FT
Expand Down Expand Up @@ -73,7 +71,7 @@ ClimaLand.auxiliary_domain_names(::AutotrophicRespirationModel) = (:surface,)
h,
)

Computes the autotrophic respiration as the sum of the plant maintenance
Computes the autotrophic respiration (mol co2 m^-2 s^-1) as the sum of the plant maintenance
and growth respirations, according to the JULES model.

Clark, D. B., et al. "The Joint UK Land Environment Simulator (JULES), model description–Part 2: carbon fluxes and vegetation dynamics." Geoscientific Model Development 4.3 (2011): 701-722.
Expand All @@ -92,11 +90,11 @@ function compute_autrophic_respiration(
h,
)

(; ne, ηsl, σl, μr, μs, f1, f2) = model.parameters
(; ne, ηsl, σl, μr, μs, Rel) = model.parameters
Nl, Nr, Ns =
nitrogen_content(ne, Vcmax25, LAI, SAI, RAI, ηsl, h, σl, μr, μs)
Rpm = plant_respiration_maintenance(Rd, β, Nl, Nr, Ns, f1)
Rg = plant_respiration_growth(f2, An, Rpm)
Rpm = plant_respiration_maintenance(Rd, β, Nl, Nr, Ns)
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Rg = plant_respiration_growth(Rel, An, Rpm)
Ra = Rpm + Rg
return Ra * (1 - exp(-K * LAI * Ω)) / (K * Ω) # adjust to canopy level
end
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12 changes: 5 additions & 7 deletions src/standalone/Vegetation/canopy_parameterizations.jl
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Expand Up @@ -1007,7 +1007,6 @@ end
Nl::FT, # Nitrogen content of leafs
Nr::FT, # Nitrogen content of roots
Ns::FT, # Nitrogen content of stems
f::FT # Factor to convert from mol CO2 to kg C
) where {FT}

Computes plant maintenance respiration as a function of dark respiration (Rd),
Expand All @@ -1020,24 +1019,23 @@ function plant_respiration_maintenance(
Nl::FT, # Nitrogen content of leafs
Nr::FT, # Nitrogen content of roots
Ns::FT, # Nitrogen content of stems
f1::FT, # Factor to convert from mol CO2 to kg C
) where {FT}
# When LAI is zero, Nl = 0
Rpm = f1 * Rd * (β + (Nr + Ns) / max(Nl, eps(FT)))
Rpm = Rd * (β + (Nr + Ns) / max(Nl, eps(FT)))
return Rpm
end

"""
plant_respiration_growth(
f::FT, # Factor of relative contribution
Rel::FT, # Factor of relative contribution
An::FT, # Net photosynthesis
Rpm::FT # Plant maintenance respiration
) where {FT}

Computes plant growth respiration as a function of net photosynthesis (An),
plant maintenance respiration (Rpm), and a relative contribution factor, f.
plant maintenance respiration (Rpm), and a relative contribution factor, Rel.
"""
function plant_respiration_growth(f2::FT, An::FT, Rpm::FT) where {FT}
Rg = f2 * (An - Rpm)
function plant_respiration_growth(Rel::FT, An::FT, Rpm::FT) where {FT}
Rg = Rel * (An - Rpm)
return Rg
end
8 changes: 4 additions & 4 deletions test/standalone/Vegetation/test_bigleaf_parameterizations.jl
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Expand Up @@ -291,8 +291,8 @@ for FT in (Float32, Float64)
ARparams.μr,
ARparams.μs,
)
Rpm = plant_respiration_maintenance(Rd, β, Nl, Nr, Ns, ARparams.f1)
Rg = plant_respiration_growth.(ARparams.f2, An, Rpm)
Rpm = plant_respiration_maintenance(Rd, β, Nl, Nr, Ns)
Rg = plant_respiration_growth.(ARparams.Rel, An, Rpm)

@test Nl ==
photosynthesisparams.Vcmax25 / ARparams.ne * ARparams.σl * LAI
Expand All @@ -306,8 +306,8 @@ for FT in (Float32, Float64)
h_canopy *
LAI *
ClimaLand.heaviside(SAI)# == gives a very small error
@test Rpm == ARparams.f1 * Rd * (β + (Nr + Ns) / Nl)
@test all(@.(Rg ≈ ARparams.f2 * (An - Rpm)))
@test Rpm == Rd * (β + (Nr + Ns) / Nl)
@test all(@.(Rg ≈ ARparams.Rel * (An - Rpm)))

end
end
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