### A Pluto.jl notebook ###
# v0.17.4

using Markdown
using InteractiveUtils

# ╔═╡ 3668f786-9597-11eb-01a1-87d34b49eef9
begin	
	#packages for I/O, interpolation, etc	
	using MITgcmTools, MeshArrays, Plots, PlutoUI
	PICKUP_hs94_download()
			
	🏁 = "🏁"
	"Downloads and packages : complete."
end

# ╔═╡ 19095067-33f5-495f-bc4d-ee6dacbf6ca8
begin
	imgB="https://user-images.githubusercontent.com/20276764/113531401-b1780d00-9596-11eb-8e96-990cf9533ada.png"

	md"""# Simple Atmosphere

	### 


	In this notebook we:
	
	1. run the Held and Suarez Benchmark
	1. read MITgcm output for temperature
	1. interpolate it via **`MeshArrays.jl`** 
	1. plot and animate 
	
	This should generate something like this:
	
	$(Resource(imgB, :width => 240))
	
	$(TableOfContents())

	!!! note
		If you use a live version of this notebook, selecting a different configuration from the list below will make the other notebook cells react (e.g. displayed contents). If you visualize an html version of this notebook, then cells wont react.
	"""
end

# ╔═╡ 207e4c15-7818-4dc3-a048-1dd36ba5a73e
begin
	myexp=verification_experiments("hs94.cs-32x32x5")
	pth_run=joinpath(myexp.folder,string(myexp.ID),"run")
	md""" ## Model Configuration

	This is a data structure of type `MITgcm_config` (a concrete type of `AbstractModelConfig`).
	"""
end	

# ╔═╡ 2fd1ddf0-c3ee-4076-9f7f-b066da2baf50
myexp

# ╔═╡ bd0803d8-c70d-47b8-a76e-5765f4ba01c6
md""" ## Worflow Steps

The animation just above results from the following workflow steps:

- setup & compile
- run model
- process output
"""

# ╔═╡ 9238b863-dd69-42ce-8f36-995b4757cc1a
md""" #### Contents of model run folder

The first cell below list all files found in files the run directory. The second displays the end of the standard output file (e.g. `output.txt`) generated during the model run. The third is the result of the `scan_rundir` function.
"""

# ╔═╡ 88a5819f-6f35-40e8-9a82-8fd6f97001b1
md""" #### Contents of the pickup folder"""

# ╔═╡ 37294d8a-a70e-419a-a60b-11d09930c6b0
readdir(PICKUP_hs94_path)

# ╔═╡ f0185b52-2297-4e8c-b44b-8c29b634607a
md""" ## Appendices"""

# ╔═╡ fa968801-6892-4475-9b27-56472ca611b4
begin
	#function used to modify model parameters (e.g. duration)
	function modify_params_HS94(myexp)
		par_path=joinpath(myexp.folder,string(myexp.ID),"log","tracked_parameters")

		fil=joinpath(par_path,"data")
		nml=read(fil,MITgcm_namelist())

		nml.params[1][:useSingleCpuIO]=true

		nml.params[3][:nIter0]=43200
		nml.params[3][:nTimeSteps]=720
		nml.params[3][:monitorFreq]= 21600.0

		write(fil,nml)
		#ClimateModels.git_log_fil(myexp,fil,"update parameter file : "*split(fil,"/")[end])

		fil=joinpath(par_path,"data.pkg")
		nml=read(fil,MITgcm_namelist())

		nml.params[1][:useDiagnostics]=false
		nml.params[1][:useMNC]=false

		write(fil,nml)
		#ClimateModels.git_log_fil(myexp,fil,"update parameter file : "*split(fil,"/")[end])

	end

	"helper function"
end

# ╔═╡ aad7e042-ba39-4518-8f3e-da59b77c13cb
begin	
	#set up run directory
	setup(myexp)

	#compile model if not already done
	build(myexp,"--allow-skip")

	#modify parameters to start from time step 43200, etc
	modify_params_HS94(myexp)

	#provide initial condition for time step 43200
	fil1=joinpath(PICKUP_hs94_path,"pickup.0000043200.data")
	fil2=joinpath(pth_run,"pickup.0000043200.data")
	!isfile(fil2) ? cp(fil1,fil2) : nothing
	
	fil1=joinpath(PICKUP_hs94_path,"pickup.0000043200.meta")
	fil2=joinpath(pth_run,"pickup.0000043200.meta")
	!isfile(fil2) ? cp(fil1,fil2) : nothing

	#readdir(joinpath(myexp.folder,string(myexp.ID),"log"))
	step1=🏁
end

# ╔═╡ 0aa37844-b4b9-4f58-adf7-15ae9a490993
begin
	step1==🏁
	MITgcmTools.launch(myexp)
	step2=🏁
end

# ╔═╡ b77f7ff2-da7e-41b3-b3f6-3819b09cd33c
begin
	step2==🏁
	
#	isfile(joinpath(MITgcm_path[1],"verification",myexp.configuration,"build","mitgcmuv"))
	isfile(joinpath(pth_run,"output.txt")) ? sc=scan_rundir(pth_run) : sc=(completed=false,)


	#copy files to known location for subsequent notebooks (Makie, particles, etc)
	function cp_run_dir()
		p2=joinpath(PICKUP_hs94_path,"run")
		tst = sc.completed&(!isdir(p2))
		tst ? run(`cp -pr $pth_run $p2`) : nothing
		isdir(p2)
	end
	cp_run_dir()

	## read grid variables (for interpolation)
	Γ = GridLoad_mdsio(myexp)
	
	## setup interpolation (for plotting)
	lon=[i for i=-179.5:1.0:179.5, j=-89.5:1.0:89.5]
	lat=[j for i=-179.5:1.0:179.5, j=-89.5:1.0:89.5]
	(f,i,j,w,_,_,_)=InterpolationFactors(Γ,vec(lon),vec(lat))
	IntFac=(f,i,j,w)
	
	#list of output files (1 per time record)
	ff=readdir(pth_run); fil="T.0000"
	ff=ff[findall(occursin.(fil,ff).*occursin.(".data",ff))]	
	nt=length(ff)
	γ=Γ.XC.grid
	
	step3=🏁
end

# ╔═╡ ee0e6f28-aa26-48de-8ddd-8bb2d1102ee9
begin
	#function used to plot one time record
	function myplot(fil,pth)
		T=read(joinpath(pth,fil),MeshArray(γ,Float64))
		TT=Interpolate(T,IntFac...)
		contourf(vec(lon[:,1]),vec(lat[1,:]),TT,clims=(260.,320.))
	end

	#loop over model output files
	dt=6
	anim = @animate for i ∈ 1:dt:nt
	    myplot(ff[i],pth_run)
	end
	pp=tempdir()*"/"
	
	gif(anim,pp*"hs94.cs.gif", fps = 8)
end

# ╔═╡ 0ca84f4e-f5bf-40d0-bf46-7a0e70b7aded
begin
	step3==🏁
	ls_run_dir=readdir(pth_run)
	ls_run_dir
end

# ╔═╡ ca299148-6aa8-4379-88e3-c4500ddc779f
begin
	step3==🏁
	stdout=readlines(joinpath(pth_run,"output.txt"))
	Dump(stdout)
end

# ╔═╡ b1ca8b16-7b63-470b-90d0-6ea41eeb5211
sc

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[[deps.x264_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "d713c1ce4deac133e3334ee12f4adff07f81778f"
uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a"
version = "2020.7.14+2"

[[deps.x265_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "487da2f8f2f0c8ee0e83f39d13037d6bbf0a45ab"
uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76"
version = "3.0.0+3"

[[deps.xkbcommon_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"]
git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6"
uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd"
version = "0.9.1+5"
"""

# ╔═╡ Cell order:
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# ╟─207e4c15-7818-4dc3-a048-1dd36ba5a73e
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# ╟─37294d8a-a70e-419a-a60b-11d09930c6b0
# ╟─f0185b52-2297-4e8c-b44b-8c29b634607a
# ╟─3668f786-9597-11eb-01a1-87d34b49eef9
# ╟─fa968801-6892-4475-9b27-56472ca611b4
# ╟─00000000-0000-0000-0000-000000000001
# ╟─00000000-0000-0000-0000-000000000002
