minor update

Project.toml

@@ -8,7 +8,6 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
-MutableNamedTuples = "af6c499f-54b4-48cc-bbd2-094bba7533c7"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
@@ -20,7 +19,6 @@ UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 DataFrames = "1.5, 1.6"
 DelimitedFiles = "1.9"
 LabelledArrays = "1.14"
-MutableNamedTuples = "0.1.3"
 Parameters = "0.12"
 Reexport = "1"
 UnPack = "1.0"

data/dat_气象驱动.md

@@ -12,7 +12,7 @@
 
 - `tem`: Tair, degC
 
-- `hum`: q (specific humidity), kg/kg
+- `hum`: q (specific humidity), g/kg
 
 - `pre`: prcp (precipitation), mm
 

src/BEPS/evaporation_canopy.jl

@@ -1,4 +1,4 @@
-function evaporation_canopy_jl(tempL::Leaf, Ta::Float64, rh_air::Float64,
+function evaporation_canopy_jl(T_leaf::Leaf, Ta::Float64, rh_air::Float64,
   Gwater::Leaf, lai::Leaf,
   perc_water_o::Float64, perc_water_u::Float64, perc_snow_o::Float64, perc_snow_u::Float64)
 
@@ -11,15 +11,15 @@ function evaporation_canopy_jl(tempL::Leaf, Ta::Float64, rh_air::Float64,
   latent_snow = 2.83 * 1000000
 
   # leaf level latent heat caused by evaporation or sublimation
-  LHw_o_sunlit = perc_water_o * latent_heat(Ta, tempL.o_sunlit, Gwater.o_sunlit, met)
-  LHw_o_shaded = perc_water_o * latent_heat(Ta, tempL.o_shaded, Gwater.o_shaded, met)  
-  LHw_u_sunlit = perc_water_u * latent_heat(Ta, tempL.u_sunlit, Gwater.u_sunlit, met)
-  LHw_u_shaded = perc_water_u * latent_heat(Ta, tempL.u_shaded, Gwater.u_shaded, met)
-
-  LHs_o_sunlit = perc_snow_o * latent_heat(Ta, tempL.o_sunlit, Gwater.o_sunlit, met)
-  LHs_o_shaded = perc_snow_o * latent_heat(Ta, tempL.o_shaded, Gwater.o_shaded, met)
-  LHs_u_sunlit = perc_snow_u * latent_heat(Ta, tempL.u_sunlit, Gwater.u_sunlit, met)
-  LHs_u_shaded = perc_snow_u * latent_heat(Ta, tempL.u_shaded, Gwater.u_shaded, met)
+  LHw_o_sunlit = perc_water_o * latent_heat(Ta, T_leaf.o_sunlit, Gwater.o_sunlit, met)
+  LHw_o_shaded = perc_water_o * latent_heat(Ta, T_leaf.o_shaded, Gwater.o_shaded, met)  
+  LHw_u_sunlit = perc_water_u * latent_heat(Ta, T_leaf.u_sunlit, Gwater.u_sunlit, met)
+  LHw_u_shaded = perc_water_u * latent_heat(Ta, T_leaf.u_shaded, Gwater.u_shaded, met)
+
+  LHs_o_sunlit = perc_snow_o * latent_heat(Ta, T_leaf.o_sunlit, Gwater.o_sunlit, met)
+  LHs_o_shaded = perc_snow_o * latent_heat(Ta, T_leaf.o_shaded, Gwater.o_shaded, met)
+  LHs_u_sunlit = perc_snow_u * latent_heat(Ta, T_leaf.u_sunlit, Gwater.u_sunlit, met)
+  LHs_u_shaded = perc_snow_u * latent_heat(Ta, T_leaf.u_shaded, Gwater.u_shaded, met)
 
   evapo_water_o = 1 / (latent_water) * (LHw_o_sunlit * lai.o_sunlit + LHw_o_shaded * lai.o_shaded)
   evapo_water_u = 1 / (latent_water) * (LHw_u_sunlit * lai.u_sunlit + LHw_u_shaded * lai.u_shaded)

src/BEPS/evaporation_soil.jl

@@ -1,7 +1,7 @@
 function evaporation_soil_jl(Tair::FT, Tg::FT, RH::FT, Rn_g::FT, Gheat_g::FT,
-  percent_snow_g::Ref{FT}, depth_water::Ref{FT}, depth_snow::Ref{FT}, mass_water_g::Ref{FT}, mass_snow_g::Ref{FT}, # Ref{FT}
+  percent_snow_g::Ref{FT}, depth_water::Ref{FT}, depth_snow::Ref{FT}, mass_water_g::Ref{FT}, mass_snow_g::Ref{FT},
   density_snow::FT, swc_g::FT, porosity_g::FT) where {FT<:Real}
-  # evapo_soil::Ref{FT}, evapo_water_g::Ref{FT}, evapo_snow_g::Ref{FT}
+
   met = meteo_pack_jl(Tg, RH)
   ρ_a = met.rho_a
   cp = met.cp

src/BEPS/lai2.jl

@@ -15,3 +15,14 @@ function lai2(clumping::Float64, CosZs::Float64,
   LAI.u_sunlit = CosZs > 0 ? 2 * CosZs * (1 - exp(-0.5 * clumping * (lai_o + lai_u) / CosZs)) - LAI.o_sunlit : 0
   LAI.u_shaded = max(0, lai_u - LAI.u_sunlit)  # edited by J. Leng
 end
+
+function lai2(clumping::Float64, CosZs::Float64,
+  stem_o::Float64, stem_u::Float64,
+  lai_o::Float64, lai_u::Float64)
+
+  LAI = Leaf()
+  PAI = Leaf()
+
+  lai2(clumping, CosZs, stem_o, stem_u, lai_o, lai_u, LAI, PAI)
+  LAI, PAI
+end

src/BEPS/netRadiation.jl

@@ -159,3 +159,6 @@ function netRadiation_jl(Rs_global::FT, CosZs::FT,
   # 参考Chen 2012年的聚集指数论文
   Rn_o, Rn_u, Rn_g
 end
+
+
+# TODO: 切分成两个函数，长波与短波

src/DataType/Soil.jl

@@ -1,54 +1,54 @@
 T = Vector{Float64}
 
 @with_kw mutable struct Soil
-  flag::Cint = Cint(0)
-  n_layer::Cint = Cint(5)
-  step_period::Cint = Cint(1)
+  flag        ::Cint    = Cint(0)
+  n_layer     ::Cint    = Cint(5)
+  step_period ::Cint    = Cint(1)
 
-  Zp::Cdouble = Cdouble(0)
-  Zsp::Cdouble = Cdouble(0)
-  r_rain_g::Cdouble = Cdouble(0)
-  soil_r::Cdouble = Cdouble(0)
-  r_drainage::Cdouble = Cdouble(0)
+  Zp          ::Cdouble = Cdouble(0)
+  Zsp         ::Cdouble = Cdouble(0)
+  r_rain_g    ::Cdouble = Cdouble(0)
+  soil_r      ::Cdouble = Cdouble(0)
+  r_drainage  ::Cdouble = Cdouble(0)
   r_root_decay::Cdouble = Cdouble(0)
-  psi_min::Cdouble = Cdouble(0)
-  alpha::Cdouble = Cdouble(0)
-  f_soilwater::Cdouble = Cdouble(0)
-  
-  d_soil::T = zeros(10)
-  f_root::T = zeros(10)
-  dt::T = zeros(10)
+  psi_min     ::Cdouble = Cdouble(0)
+  alpha       ::Cdouble = Cdouble(0)
+  f_soilwater ::Cdouble = Cdouble(0)
+
+  d_soil      ::T = zeros(10)
+  f_root      ::T = zeros(10)
+  dt          ::T = zeros(10)
   thermal_cond::T = zeros(10)
-  theta_vfc::T = zeros(10)
-  theta_vwp::T = zeros(10)
-  fei::T = zeros(10)
-  Ksat::T = zeros(10)
-  psi_sat::T = zeros(10)
-  b::T = zeros(10)
+  theta_vfc   ::T = zeros(10)
+  theta_vwp   ::T = zeros(10)
+  fei         ::T = zeros(10)
+  Ksat        ::T = zeros(10)
+  psi_sat     ::T = zeros(10)
+  b           ::T = zeros(10)
   density_soil::T = zeros(10)
-  f_org::T = zeros(10)
-  ice_ratio::T = zeros(10)
-  thetam::T = zeros(10)
-  thetam_prev::T = zeros(10)
-  temp_soil_p::T = zeros(10)
-  temp_soil_c::T = zeros(10)
-  f_ice::T = zeros(10)
-  psim::T = zeros(10)
-  thetab::T = zeros(10)
-  psib::T = zeros(10)
-  r_waterflow::T = zeros(10)
-  km::T = zeros(10)
-  Kb::T = zeros(10)
-  KK::T = zeros(10)
-  Cs::T = zeros(10)
-  lambda::T = zeros(10)
-  Ett::T = zeros(10)
-  G::T = zeros(10)
+  f_org       ::T = zeros(10) # organic matter
+  ice_ratio   ::T = zeros(10) # ice ratio
+  thetam      ::T = zeros(10) # soil moisture
+  thetam_prev ::T = zeros(10) # soil moisture in previous time
+  temp_soil_p ::T = zeros(10) # soil temperature in previous time
+  temp_soil_c ::T = zeros(10) # soil temperature in current time
+  f_ice       ::T = zeros(10) 
+  psim        ::T = zeros(10)
+  thetab      ::T = zeros(10)
+  psib        ::T = zeros(10)
+  r_waterflow ::T = zeros(10)
+  km          ::T = zeros(10) # hydraulic conductivity
+  Kb          ::T = zeros(10)
+  KK          ::T = zeros(10) # average conductivity of two soil layers
+  Cs          ::T = zeros(10)
+  lambda      ::T = zeros(10)
+  Ett         ::T = zeros(10)
+  G           ::T = zeros(10)
 
   # temporary variables in soil_water_factor_v2
-  ft::T = zeros(10)
-  dtt::T = zeros(10)
-  fpsisr::T = zeros(10)
+  ft          ::T = zeros(10)
+  dtt         ::T = zeros(10)
+  fpsisr      ::T = zeros(10)
 end
 
 # ft = zeros(Float64, p.n_layer)

src/Ipaper.jl

@@ -1,62 +1,4 @@
-# using BEPS
-## MutableNamedTuples
-# using MutableNamedTuples
-# using Ipaper
-import MutableNamedTuples: MutableNamedTuple
-
-const MNT = MutableNamedTuple
-
-# mnt(keys::Vector{Symbol}, values) = (; zip(keys, values)...)
-"""
-    mnt(keys::Vector{Symbol}, values)
-    mnt(keys::Vector{<:AbstractString}, values)
-    
-# Examples
-```julia
-mnt([:dw, :betaw, :swmax, :a, :c, :kh, :uh]
-```
-"""
-mnt(; kw...) = MNT(; kw...)
-
-
-mnt(keys::Vector{Symbol}, values) = MNT(; zip(keys, values)...)
-
-mnt(keys::Vector{<:AbstractString}, values) = mnt(Symbol.(keys), values)
-
-mnt(keys::Vector{Symbol}) = mnt(Symbol.(keys), zeros(length(keys)))
-
-mnt(keys::Tuple, values) = MNT(; zip(keys, values)...)
-mnt(keys::Tuple) = mnt(keys, zeros(length(keys)))
-
-mnt(keys::Vector{<:AbstractString}) = mnt(Symbol.(keys))
-
-to_list = mnt;
-
-Base.names(x::MNT) = keys(x) |> collect
-
-# function Base.values(x::MNT)
-#   @show "hello"
-#   getindex.(values(getfield(x, :nt))) |> collect
-#   # values(x) |> collect
-# end
-
-
-function add(x::MutableNamedTuple, y::MutableNamedTuple)
-  mnt([keys(x)..., keys(y)...],
-    [values(x)..., values(y)...],)
-end
-
-function Base.:(==)(x::MNT, y::MNT)
-  if length(x) != length(y)
-    return false
-  end
-  keys(x) == keys(y) && values(x) == values(y)
-end
-
-export mnt, add, MNT
-
-# a = MNT{(:o_sunlit, :o_shaded, :u_sunlit, :u_shaded), NTuple{4, Base.RefValue{Int64}}}
-
+export LVector, list
 
 ## second version
 import LabelledArrays
@@ -99,6 +41,3 @@ Base.:+(x::T1, y::AbstractVector{T2}) where {T1<:Real,T2<:Real} = x .+ y
 Base.:-(x::T1, y::AbstractVector{T2}) where {T1<:Real,T2<:Real} = x .- y
 Base.:*(x::T1, y::AbstractVector{T2}) where {T1<:Real,T2<:Real} = x .* y
 Base.:/(x::T1, y::AbstractVector{T2}) where {T1<:Real,T2<:Real} = x ./ y
-
-
-export LVector, list

src/beps_inter_prg.jl

@@ -135,7 +135,7 @@ function inter_prg_jl(
   Ks = meteo.Srad
   rh_air = meteo.rh
   wind_sp = meteo.wind
-  precip = meteo.rain / step  # precipitation in meters
+  prcp = meteo.rain / step  # precipitation in meters
   Ta = meteo.temp
 
   VPS_air = cal_es(Ta)  # to estimate saturated water vapor pressure in kpa
@@ -194,7 +194,7 @@ function inter_prg_jl(
   # for(kkk = 1;kkk <= kloop;kkk++)
   @inbounds for kkk = 2:kloop+1
     # /*****  Snow pack stage 1 by X. Luo  *****/
-    var.Xcs_o[kkk], var.Xcs_u[kkk], var.Xg_snow[kkk] = snowpack_stage1_jl(Ta, precip,
+    var.Xcs_o[kkk], var.Xcs_u[kkk], var.Xg_snow[kkk] = snowpack_stage1_jl(Ta, prcp,
       # var.Wcs_o[kkk-1], var.Wcs_u[kkk-1], var.Wg_snow[kkk-1],
       Ref(var.Wcs_o, kkk), Ref(var.Wcs_u, kkk), Ref(var.Wg_snow, kkk),
       lai_o, lai_u, clumping,
@@ -204,7 +204,7 @@ function inter_prg_jl(
 
     # /*****  Rain fall stage 1 by X. Luo  *****/
     var.Wcl_o[kkk], var.Wcl_u[kkk], var.Xcl_o[kkk], var.Xcl_u[kkk], var.r_rain_g[kkk] = 
-      rainfall_stage1_jl(Ta, precip, var.Wcl_o[kkk-1], var.Wcl_u[kkk-1], lai_o, lai_u, clumping)
+      rainfall_stage1_jl(Ta, prcp, var.Wcl_o[kkk-1], var.Wcl_u[kkk-1], lai_o, lai_u, clumping)
 
     # Old version
     # if(thetam[0][kkk-1]<soilp.theta_vwp[1]*0.5) var.alpha_g = alpha_dry;
@@ -220,12 +220,8 @@ function inter_prg_jl(
 
     # /*****  Soil water factor module by L. He  *****/
     soil_water_factor_v2(soilp)
-    f_soilwater = soilp.f_soilwater
-
-    if (f_soilwater > 1.0)
-      f_soilwater = 1.0
-    end  # to be used for module photosynthesis
-
+    f_soilwater = min(soilp.f_soilwater, 1.0) # used in `photosynthesis`
+
     GH_o = var.Qhc_o[kkk-1]# to be used as the init. for module aerodynamic_conductance
 
     init_leaf_dbl(Ci_old, 0.7 * CO2_air)