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6: Wyujie r=Yujie-W a=Yujie-W



Co-authored-by: Yujie Wang <jesiner@gmail.com>
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bors[bot] and Yujie-W committed Feb 7, 2022
2 parents 56c6123 + 1647e57 commit 4c5ea58
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4 changes: 2 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "ClimaCache"
uuid = "781d2db2-48ae-11ec-81d3-0242ac130003"
authors = ["Yujie Wang <jesiner@gmail.com>"]
version = "0.1.0"
version = "0.1.1"

[deps]
DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
Expand All @@ -16,7 +16,7 @@ WaterPhysics = "20dd5ee6-61da-454b-ac5d-c09c2977e03a"
[compat]
DocStringExtensions = "0.8.6"
MAT = "0.10.1"
PkgUtility = "0.1.13"
PkgUtility = "0.1.13, 0.2"
UnPack = "1.0.2"
WaterPhysics = "0.1.3"
julia = "1.6"
90 changes: 21 additions & 69 deletions docs/Manifest.toml
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Expand Up @@ -17,30 +17,12 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
[[deps.Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[deps.Blosc]]
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[[deps.Blosc_jll]]
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Expand All @@ -55,9 +37,9 @@ version = "0.10.2"

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Expand All @@ -69,7 +51,7 @@ version = "0.1.2"
deps = ["DocStringExtensions", "LazyArtifacts", "MAT", "PkgUtility", "Statistics", "Test", "UnPack", "WaterPhysics"]
path = ".."
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version = "0.1.1"

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Expand Down Expand Up @@ -159,16 +141,16 @@ deps = ["Random"]
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Expand All @@ -178,9 +160,9 @@ version = "0.2.2"

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[[deps.InteractiveUtils]]
deps = ["Markdown"]
Expand Down Expand Up @@ -209,9 +191,9 @@ version = "1.0.0"

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version = "1.4.1"

[[deps.JSON]]
deps = ["Dates", "Mmap", "Parsers", "Unicode"]
Expand Down Expand Up @@ -255,17 +237,11 @@ version = "0.3.6"
[[deps.Logging]]
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"

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[[deps.Markdown]]
deps = ["Base64"]
Expand All @@ -287,24 +263,6 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804"
[[deps.MozillaCACerts_jll]]
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version = "0.11.9"

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Expand All @@ -325,19 +283,19 @@ version = "1.4.1"

[[deps.Parsers]]
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[[deps.Pkg]]
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uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

[[deps.PkgUtility]]
deps = ["CLIMAParameters", "CSV", "DataFrames", "Dates", "DocStringExtensions", "LazyArtifacts", "NetcdfIO", "Pkg", "Statistics", "StatsBase", "Test"]
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deps = ["CLIMAParameters", "CSV", "DataFrames", "Dates", "DocStringExtensions", "LazyArtifacts", "Pkg", "Statistics", "StatsBase", "Test"]
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Expand Down Expand Up @@ -468,9 +426,9 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[[deps.WaterPhysics]]
deps = ["DocStringExtensions", "PkgUtility", "Test", "UnPack"]
git-tree-sha1 = "54cda0d2b76e76342430ebdb9442cc12a53e11be"
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version = "0.1.3"
version = "0.1.4"

[[deps.WeakRefStrings]]
deps = ["DataAPI", "InlineStrings", "Parsers"]
Expand All @@ -482,12 +440,6 @@ version = "1.4.1"
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"

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version = "1.5.0+0"

[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
Expand Down
6 changes: 1 addition & 5 deletions src/ClimaCache.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -24,11 +24,6 @@ using UnPack: @unpack
using WaterPhysics: saturation_vapor_pressure


# export public types and constructors
export AirLayer, Arrhenius, ArrheniusPeak, C3CytochromeModel, C3VJPModel, C4VJPModel, CytochromeFluorescenceModel, CytochromeReactionCenter, GCO₂Mode, Leaf, LeafBiophysics, MinimumColimit, PCO₂Mode,
Q10, QuadraticColimit, VJPReactionCenter, VanDerTolFluorescenceModel, WaveLengthSet


#######################################################################################################################################################################################################
#
# Changes to these constants
Expand Down Expand Up @@ -60,6 +55,7 @@ include("plant/leaf_biophysics.jl")
include("plant/leaf_fluorescence.jl")
include("plant/leaf_photosynthesis.jl")
include("plant/leaf_reaction_center.jl")
include("plant/vulnerability.jl")
include("plant/leaf.jl")

# include the soil types and structures
Expand Down
6 changes: 3 additions & 3 deletions src/plant/leaf_fluorescence.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ abstract type AbstractFluorescenceModel{FT<:AbstractFloat} end

#######################################################################################################################################################################################################
#
# Changes to the type
# Changes to the struct
# General
# 2022-Jan-14: add van der Tol model struct
# 2022-Jan-24: fix documentation
Expand Down Expand Up @@ -50,7 +50,7 @@ end

#######################################################################################################################################################################################################
#
# Changes to the constructors
# Changes to the constructor
# General
# 2022-Jan-14: migrate from Photosynthesis.jl
# Sources
Expand Down Expand Up @@ -82,7 +82,7 @@ VanDerTolFluorescenceModel{FT}(drought::Bool = false) where {FT<:AbstractFloat}

#######################################################################################################################################################################################################
#
# Changes to the structure
# Changes to the struct
# General
# 2022-Jan-24: add an empty structure for Cytochrome based fluorescence model
# 2022-Jan-24: fix documentation
Expand Down
73 changes: 72 additions & 1 deletion src/plant/leaf_photosynthesis.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ abstract type AbstractPhotosynthesisModel{FT<:AbstractFloat} end
# General
# 2022-Jan-18: add C3CytochromeModel structure for C₃ photosynthesis system
# 2022-Jan-25: fix documentation
# 2022-Feb-07: add more fields to use with Photosynthesis v0.3.1
# To do
# TODO: add TD in Photosynthesis.jl
#
Expand All @@ -49,14 +50,40 @@ mutable struct C3CytochromeModel{FT<:AbstractFloat} <: AbstractPhotosynthesisMod
EFF_1::FT
"Coefficient 8.0/10.5 for NADPH/ATP requirement stochiometry, respectively"
EFF_2::FT
"[`AbstractTemperatureDependency`](@ref) type Kc temperature dependency"
TD_KC::AbstractTemperatureDependency{FT}
"[`AbstractTemperatureDependency`](@ref) type Ko temperature dependency"
TD_KO::AbstractTemperatureDependency{FT}
"[`AbstractTemperatureDependency`](@ref) type respiration temperature dependency"
TD_R::AbstractTemperatureDependency{FT}
"[`AbstractTemperatureDependency`](@ref) type Vcmax temperature dependency"
TD_VCMAX::AbstractTemperatureDependency{FT}
"[`AbstractTemperatureDependency`](@ref) type Γ* temperature dependency"
TD_Γ::AbstractTemperatureDependency{FT}

# prognostic variables that change with time
"Total concentration of Cytochrome b₆f `[μmol m⁻²]`"
b₆f::FT
"Maximal turnover rate of Cytochrome b₆f `[e⁻ s⁻¹]`"
k_q::FT
"Respiration rate at 298.15 K `[μmol m⁻² s⁻¹]`"
r_d25::FT
"Maximal carboxylation rate at 298.15 K `[μmol m⁻² s⁻¹]`"
v_cmax25::FT

# dignostic variables that change with time
"RubisCO limited photosynthetic rate `[μmol m⁻² s⁻¹]`"
a_c::FT
"Gross photosynthetic rate `[μmol m⁻² s⁻¹]`"
a_gross::FT
"Light limited photosynthetic rate `[μmol m⁻² s⁻¹]`"
a_j::FT
"Net photosynthetic rate `[μmol m⁻² s⁻¹]`"
a_net::FT
"Product limited photosynthetic rate `[μmol m⁻² s⁻¹]`"
a_p::FT
"Electron to CO₂ coefficient"
e_to_c::FT
"PS II electron transport rate `[μmol e⁻ m⁻² s⁻¹]`"
j_p680_a::FT
"Rubisco limited PS II electron transport rate `[μmol e⁻ m⁻² s⁻¹]`"
Expand All @@ -73,6 +100,16 @@ mutable struct C3CytochromeModel{FT<:AbstractFloat} <: AbstractPhotosynthesisMod
j_p700_j::FT
"Product limited PS I electron transport rate `[μmol e⁻ m⁻² s⁻¹]`"
j_p700_p::FT
"RubisCO coefficient Kc `[Pa]`"
k_c::FT
"Michaelis-Menten's coefficient `[Pa]`"
k_m::FT
"RubisCO coefficient Ko `[Pa]`"
k_o::FT
"Respiration rate at leaf temperature `[μmol m⁻² s⁻¹]`"
r_d::FT
"Maximal carboxylation rate at leaf temperature `[μmol m⁻² s⁻¹]`"
v_cmax::FT
"Maximal Cytochrome b₆f activity `[μmol e⁻ m⁻² s⁻¹]`"
v_qmax::FT
"ratio between J_P700 and J_P680"
Expand Down Expand Up @@ -106,7 +143,41 @@ cy = C3CytochromeModel{Float64}(v_cmax25 = 30, r_d25 = 1);
```
"""
C3CytochromeModel{FT}(; v_cmax25::Number = 50, r_d25::Number = 0.75) where {FT<:AbstractFloat} = (
return C3CytochromeModel{FT}(MinimumColimit{FT}(), 4, 8, 350 / 300, 300, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
return C3CytochromeModel{FT}(
MinimumColimit{FT}(), # COLIMIT
4, # EFF_1
8, # EFF_2
KcTDCLM(FT), # TD_KC
KoTDCLM(FT), # TD_KO
RespirationTDCLM(FT), # TD_R
VcmaxTDCLM(FT), # TD_VCMAX
ΓStarTDCLM(FT), # TD_Γ
350 / 300, # b₆f
300, # k_q
r_d25, # r_d25
v_cmax25, # v_cmax25,
0, # a_c
0, # a_gross
0, # a_j
-r_d25, # a_net
0, # a_p
0, # e_to_c
0, # j_p680_a
0, # j_p680_c
0, # j_p680_j
0, # j_p680_p
0, # j_p700_a
0, # j_p700_c
0, # j_p700_j
0, # j_p700_p
0, # k_c
0, # k_m
0, # k_o
r_d25, # r_d
v_cmax25, # v_cmax
0, # v_qmax
0, # η
0) # γ_star
);


Expand Down

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