全线竣工

.github/workflows/CI.yml

@@ -15,7 +15,7 @@ jobs:
           - '1'
           # - 'nightly'
         os:
-          # - ubuntu-latest
+          - ubuntu-latest
           # - macOS-latest
           - windows-latest
         arch:

README.md

@@ -9,16 +9,30 @@ Boreal Ecosystem Productivity Simulator in Julia
 
 > Dongdong Kong
 
+BEPS.jl is alive in Julia now. All functions have been ported to Julia, and the
+performance is about 2.5 times faster than C version.
+
+> - Julia: 0.286327 seconds (822.38 k allocations: 22.998 MiB, 0.85% gc time)
+> - C    : 0.787059 seconds (629.95 k allocations: 13.915 MiB)
+
 > [!CAUTION]
 > `BEPS.clang` only works under Windows.
 
 ## Install
+
+* For developers
 ```bash
 git clone https://github.com/CUG-hydro/BEPS.jl
 cd BEPS.jl/deps
 git clone https://github.com/CUG-hydro/BEPS.c
 ```
 
+* For users
+```bash
+# In Julia
+] add https://github.com/CUG-hydro/BEPS.jl
+```
+
 ## Usage
 
 ```julia
@@ -33,16 +47,11 @@ par = (lon=120.5, lat=30.5, landcover=25, clumping=0.85,
 @time df_jl, df_ET_jl = besp_main(d, lai, par; version="julia");
 ```
 
-> Figure1: The bias of Julia version compared with C.
+> Figure1: The bias of Julia version compared with C, `bias = (Julia - C)/ C`.
 ![Figure1: bias of julia version compared with c](./images/Figure1_bias_of_julia-version.png)
 
 The bias of `SH` is the largest due to double number accuracy, about 1.48%, which is acceptable.
 
-> The Julia version is about 2X times faster than C.
-
-- Julia:   0.327014 seconds (1.09 M allocations: 47.056 MiB, 2.32% gc time)
-- C    :   0.831637 seconds (629.96 k allocations: 13.916 MiB)
-
 See [examples/example_01.qmd](examples/example_01.qmd) for details.
 
 ## TODO

examples/example_01.qmd

@@ -61,6 +61,7 @@ write_fig("images/Figure1_bias_of_julia-version.png", 15, 8; show=false)
 # @time df_jl, df_ET_jl = besp_main(d, lai, par; version="julia");
 # @profview df_jl, df_ET_jl = besp_main(d, lai, par; version="julia");
 @profview_allocs df_jl, df_ET_jl = besp_main(d, lai, par; version="julia");
+@profview df_jl, df_ET_jl = besp_main(d, lai, par; version="julia");
 ```
 
 

src/BEPS.jl

@@ -6,16 +6,16 @@ import Parameters: @with_kw, @with_kw_noshow
 using Printf
 using Reexport
 @reexport using Serialization: deserialize, serialize
+@reexport using DelimitedFiles: readdlm
 
-export clang
 export besp_main
 export init_soil!
 
 path_proj(f...) = normpath(joinpath(@__DIR__, "..", f...))
 libbeps = path_proj("deps/libbeps.dll")
 
 # import Statistics: mean, std
-include("IO.jl")
+include("DataFrames.jl")
 include("Ipaper.jl")
 # include("c2julia.jl")
 
@@ -26,7 +26,8 @@ include("BEPS_helper.jl")
 include("BEPS/BEPS.jl")
 
 include("clang/BEPS_c.jl")
-@reexport using BEPS.clang;
+@reexport import BEPS.clang;
+import BEPS.clang: inter_prg_c, photosynthesis_c
 
 include("beps_inter_prg.jl")
 include("beps_main.jl")

src/BEPS/soil_thermal_regime.jl

@@ -83,9 +83,9 @@ end
 
 # Function to compute soil water stress factor
 function soil_water_factor_v2(p::Soil)
-  ft = zeros(Float64, p.n_layer)
-  fpsisr = zeros(Float64, p.n_layer)
-  dtt = zeros(Float64, p.n_layer)
+  # ft = zeros(Float64, p.n_layer)
+  # fpsisr = zeros(Float64, p.n_layer)
+  # dtt = zeros(Float64, p.n_layer)
 
   t1 = -0.02
   t2 = 2.0
@@ -99,29 +99,29 @@ function soil_water_factor_v2(p::Soil)
 
   for i in 1:p.n_layer
     # psi_sr in m H2O! This is the old version. LHE.
-    fpsisr[i] = p.psim[i] > p.psi_min ? 1.0 / (1 + ((p.psim[i] - p.psi_min) / p.psi_min)^p.alpha) : 1.0
+    p.fpsisr[i] = p.psim[i] > p.psi_min ? 1.0 / (1 + ((p.psim[i] - p.psi_min) / p.psi_min)^p.alpha) : 1.0
 
-    ft[i] = p.temp_soil_p[i] > 0.0 ? 1.0 - exp(t1 * p.temp_soil_p[i]^t2) : 0
+    p.ft[i] = p.temp_soil_p[i] > 0.0 ? 1.0 - exp(t1 * p.temp_soil_p[i]^t2) : 0
 
-    fpsisr[i] *= ft[i]
+    p.fpsisr[i] *= p.ft[i]
   end
 
   for i in 1:p.n_layer
-    dtt[i] = FW_VERSION == 1 ? p.f_root[i] * fpsisr[i] : p.f_root[i]
+    p.dtt[i] = FW_VERSION == 1 ? p.f_root[i] * p.fpsisr[i] : p.f_root[i]
   end
-  dtt_sum = sum(dtt)
+  dtt_sum = sum(p.dtt)
 
   if dtt_sum < 0.000001
     p.f_soilwater = 0.1
   else
     fpsisr_sum = 0
     for i in 1:p.n_layer
-      p.dt[i] = dtt[i] / dtt_sum
+      p.dt[i] = p.dtt[i] / dtt_sum
 
       if isnan(p.dt[i])
         println(p.dt[1])
       end
-      fpsisr_sum += fpsisr[i] * p.dt[i]
+      fpsisr_sum += p.fpsisr[i] * p.dt[i]
     end
     p.f_soilwater = max(0.1, fpsisr_sum)
   end

src/IO.jl → src/DataFrames.jl

@@ -1,7 +1,4 @@
-
 import DataFrames: DataFrame
-using DelimitedFiles: readdlm
-
 
 function Base.sum(df::DataFrame)
   vals = [sum(df[!, c]) for c in names(df)]

src/DataType/Soil.jl

@@ -44,4 +44,13 @@ T = Vector{Float64}
   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)
 end
+
+# ft = zeros(Float64, p.n_layer)
+# fpsisr = zeros(Float64, p.n_layer)
+# dtt = zeros(Float64, p.n_layer)

src/clang/BEPS_c.jl

@@ -9,7 +9,7 @@ using BEPS
 import BEPS: libbeps
 # const libbeps = "deps/libbeps.dll"
 
-include("../DataType/Constant.jl")
+# include("../DataType/Constant.jl")
 include("SOIL_c.jl")
 include("module.jl")
 # include("beps_inter_prg.jl")
@@ -164,7 +164,7 @@ end
 # end
 
 export inter_prg_c,
-  Vcmax_Jmax, 
+  # Vcmax_Jmax, 
   # readparam, 
   # readcoef, 
   # lai2, s_coszs,

test/test-soil.jl

@@ -2,7 +2,7 @@ using Test
 import BEPS: kstep
 
 function is_soil_equal(p_jl, p_c; tol=1e-7, verbose=false)
-  names = fieldnames(typeof(p_jl))
+  names = fieldnames(typeof(p_c))
   for name in names
     x_jl = getfield(p_jl, name)
     x_c = getfield(p_c, name)