Merge #30

30: fix: write namelist and paramlist to file r=charleskawczynski a=haakon-e

Store namelist and paramlist in output folder together with the NetCDF datafile.

Co-authored-by: Haakon Ludvig Langeland Ervik <45243236+haakon-e@users.noreply.github.com>

integration_tests/utils/main.jl

@@ -14,14 +14,14 @@ mutable struct Simulation1d
     Stats
 end
 
-function Simulation1d(namelist, paramlist, inpath = pwd())
+function Simulation1d(namelist, paramlist)
     Gr = TurbulenceConvection.Grid(namelist)
     Ref = TurbulenceConvection.ReferenceState(Gr)
     GMV = TurbulenceConvection.GridMeanVariables(namelist, Gr, Ref)
     Case = Cases.CasesFactory(namelist, paramlist, Gr, Ref)
     Turb = TurbulenceConvection.ParameterizationFactory(namelist, paramlist, Gr, Ref)
     TS = TurbulenceConvection.TimeStepping(namelist)
-    Stats = TurbulenceConvection.NetCDFIO_Stats(namelist, paramlist, Gr, inpath)
+    Stats = TurbulenceConvection.NetCDFIO_Stats(namelist, paramlist, Gr)
     return Simulation1d(Gr, Ref, GMV, Case, Turb, TS, Stats)
 end
 
@@ -94,12 +94,12 @@ function force_io(self::Simulation1d)
     return
 end
 
-function main(namelist, paramlist, inpath = pwd(); kwargs...)
-    main1d(namelist, paramlist, inpath; kwargs...)
+function main(namelist, paramlist; kwargs...)
+    main1d(namelist, paramlist; kwargs...)
 end
 
-function main1d(namelist, paramlist, inpath = pwd(); time_run = false)
-    Simulation = Simulation1d(namelist, paramlist, inpath)
+function main1d(namelist, paramlist; time_run = false)
+    Simulation = Simulation1d(namelist, paramlist)
     TurbulenceConvection.initialize(Simulation, namelist)
     if time_run
         @time run(Simulation)

src/NetCDFIO.jl

@@ -1,4 +1,5 @@
 using NCDatasets
+using JSON
 
 # TODO: remove `vars` hack that avoids https://github.com/Alexander-Barth/NCDatasets.jl/issues/135
 
@@ -13,7 +14,7 @@ mutable struct NetCDFIO_Stats
     stats_path::String
     path_plus_file::String
     vars::Dict{String, Any} # Hack to avoid https://github.com/Alexander-Barth/NCDatasets.jl/issues/135
-    function NetCDFIO_Stats(namelist, paramlist, Gr::Grid, inpath = pwd())
+    function NetCDFIO_Stats(namelist, paramlist, Gr::Grid)
 
         # Initialize properties with valid type:
         tmp = tempname()
@@ -52,10 +53,13 @@ mutable struct NetCDFIO_Stats
         #     end
         # end
 
-        # Copy namefile and paramfile to output directory
-        # TODO: this was commented:
-        # cp(joinpath(inpath, "$simname.in"), joinpath(outpath, "$simname.in"))
-        # cp(joinpath(inpath, "paramlist_$casename.in"), joinpath(outpath, "paramlist_$casename.in"))
+        # Write namefile and paramfile to output directory
+        open(joinpath(outpath, "$simname.in"), "w") do io
+            JSON.print(io, namelist, 4)
+        end
+        open(joinpath(outpath, "paramlist_$casename.in"), "w") do io
+            JSON.print(io, namelist, 4)
+        end
 
         # TODO: make cell centers and cell faces different sizes
         cinterior = Gr.cinterior