### A Pluto.jl notebook ###
# v0.20.17

using Markdown
using InteractiveUtils

# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
    #! format: off
    return quote
        local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end
        local el = $(esc(element))
        global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el)
        el
    end
    #! format: on
end

# ╔═╡ 8cf4d8ca-84eb-11eb-22d2-255ce7237090
begin
	using MITgcm, ClimateModels, PlutoUI, Printf, Plots
	using MITgcm.MeshArrays
    list_main,list_adj,list_inp,list_out=MITgcm.scan_verification()
	md"""😸"""
end

# ╔═╡ f588eaba-84ef-11eb-0755-bf1b85b2b561
begin
	md"""# Typical Modeling Workflow

	In this notebook we : 
	
	- setup, build, and run the [MIT general circulation model](https://mitgcm.readthedocs.io/en/latest/?badge=latest) interactively via [MITgcm.jl](https://gaelforget.github.io/MITgcm.jl/dev/). 
	- read model output files and plot some of the numerical model result.
	
	using the [ClimateModels.jl](https://github.com/gaelforget/ClimateModels.jl) interface_ (`setup`, `build`, `launch`, etc) via [MITgcm.jl](https://gaelforget.github.io/MITgcm.jl/dev/) for [MITgcm](https://github.com/MITgcm/MITgcm/#readme). 
		
	!!! note
		With a live version of this notebook, each selection of a different configuration from the list below will make the other notebook cells react (e.g. displayed contents). With a static html version of this notebook, then cells wont react.
	"""
end

# ╔═╡ 901d2844-83be-4767-b169-dfb7701ce15e
begin
	🏁 = "🏁"
	imgA="https://user-images.githubusercontent.com/20276764/111042787-12377e00-840d-11eb-8ddb-64cc1cfd57fd.png"
	imgB="https://user-images.githubusercontent.com/20276764/97648227-970b9780-1a2a-11eb-81c4-65ec2c87efc6.png"
	md"""$(Resource(imgB, :width => 120))"""
end



# ╔═╡ 98b6621c-85ab-11eb-29d1-af0433598c6a
md"""# Setup & Build Model

$(TableOfContents())

!!! tip
	Selecting a new model configuration typically means recompiling the model. This can take longer than a normal model run due to the one-time cost of compiling the model (see below for more on this).

## Select Model Configuration
"""

# ╔═╡ a28f7354-84eb-11eb-1830-1f401bf2db97
@bind myexp Select(list_main,default="advect_xy")

# ╔═╡ 766f87b8-f3d4-4e39-8cae-d91679d9af6f
begin
	iexp=findall(list_main.==myexp)[1]
	MC=MITgcm_config(configuration=myexp)
end

# ╔═╡ 27227e2d-350a-446b-9d70-b9a83b588ff4
md"""
!!! note 
	The folders listed will be created according to the `ClimateModels.jl` interface. This also creates a `log` subfolder to document wokflows (using `git` internally). Below, the _Modify Parameters_ section uses functionality. 
"""

# ╔═╡ 8fb0f378-2363-4f3e-ac45-440d6e87b92a
begin
	step1=true
	setup(MC)
	readdir(MC)
end

# ╔═╡ ee0ed0a0-8817-11eb-124d-a197f1d4545a
md"""## Where Is `mitgcmuv` compiled?

- The model executable `mitcmuv` is generally found in a `build/` subfolder within the selected model configuration.
- If `mitcmuv` is not found there, then it needs to be compiled, before we can then run the model. 
- Once `mitgcmuv` is found, then the executable file name should appear just below.

!!! note
    It should also be noted that compiling the model can take a lot longer than running it for a few time steps (as done in this notebook's sample model runs).
"""

# ╔═╡ eca925ba-8816-11eb-1d6d-39bf08bfe979
begin
	step1

	filexe=MC.inputs[:setup][:build][:path]
	build(MC,"allow-skip")

	rundir=joinpath(MC,"run")
	filout=joinpath(rundir,"output.txt")
	filstat=joinpath(rundir,"onestat.txt")
	filexe
end

# ╔═╡ f051e094-85ab-11eb-22d4-5bd61ac572a1
md"""## Where Is `mitgcmuv` run?

Once the model has been compliled and setup for the selected configuration, the model run directory path should appear just below this comment bloc. At this point, we are ready to call `launch` to run the model. 
"""

# ╔═╡ f7e66980-9ec5-43cf-98b1-37aa6823d64a
rundir

# ╔═╡ 5d775d7b-98d6-4d96-aee2-bae961379fd4
md"""# Run Model

You can click on the `Launch Model` button to manually trigger a model run.
This will happen automatically the first time, and then once gain after modifying parameters (see below).
"""

# ╔═╡ 6f618b2c-86bd-11eb-1607-a179a349378e
@bind do_run1 PlutoUI.Button("Launch Model")

# ╔═╡ 6404fddf-3c46-4015-9580-b9159c76b30a
md"""# Analyze Results

Let's look at the model run folder and visualize results.

!!! tip
    The MITgcm can output various results and store them in several types of files (text, binary, or netcdf). For more information about file formats and contents, please refer to the [MITgcm documentation](https://mitgcm.readthedocs.io/en/latest/getting_started/getting_started.html#output-files)

## Browse Run Folder

Below is a list of all files (by default) contained in the `run/` directory. Clicking on a list like this should expand its display.

To narrow the selection, try typing something in the text field 👉 $(@bind search_txt TextField(; default=""))	👈
"""

# ╔═╡ 0f920f90-86e9-11eb-3f6d-2d530bd2e9db
md"""## Plot Results

Here we show mean temperature in **$(myexp)** as a function of time. 

_Note: in the absence of air-sea fluxes, for example, this quantity is "conserved" but in other configurarions it can vary with time._
"""

# ╔═╡ e6c10fb5-ee95-41a0-982e-3910a8ce1d00
md"""

If a map appears below (only for some configurations), then it can be animated by clicking on `start`.

$(@bind t_slow PlutoUI.Clock(1.0, true))
"""

# ╔═╡ c7670d00-868c-11eb-1889-4d3ffe621dd2
md"""# Modify & Rerun Model

Often we want to experiment with parameters e.g. to tune models, generate more output, or generate a model ensemble. The climate model interface provides a simple way to do this interactively and document changes via `git` along the way.

## Modify Parameters

**First, select a model parameter group** (or the default): 
"""

# ╔═╡ d7f2c656-8512-11eb-2fdf-47a3e57a55e6
begin
	function list_namelist_files(pth)
		tmpA=readdir(pth)
		tmpA=tmpA[findall([length(tmpA[i])>3 for i in 1:length(tmpA)])]
		tmpA=tmpA[findall([tmpA[i][1:4]=="data" for i in 1:length(tmpA)])]
	end
	dats=list_namelist_files(rundir)
	try
		@bind mydats Select([dats[i] for i in 1:length(dats)])
	catch e
		"Error: could not find any namelist in $(rundir)"
	end
end

# ╔═╡ af176e6c-8695-11eb-3e34-91fbdb9c52fa
md"""# Appendices

###

Code cells below handle Julia packages and help set up the notebook.
"""

# ╔═╡ 348c692e-84fe-11eb-3288-dd0a1dedce90
begin	
	fil=joinpath(rundir,mydats)
	nml=read(fil,MITgcm_namelist())
	md"""😸"""
end

# ╔═╡ ca7bb004-8510-11eb-379f-632c3b40723d
try
	@bind nmlgroup Select(String.(nml.groups))
catch e
	"Error: could not find any namelist in $(rundir)"
end

# ╔═╡ 002171f5-8d6d-4197-8a3c-642f3337a01b
begin
	nmlgroup
	
	md"""
	
	**Then, enter parameter name** (without ":") **and new value:** 
	
	parameter name 👉 $(@bind p_name TextField(; default=""))	👈
	
	new value 👉 $(@bind p_value TextField(; default=""))	👈

	## Rerun Model
	
	**Once ready, click** `Update & Relaunch` **to:**

	- update parameter file
	- rerun the model
	- update the plots 

	$(@bind update_param PlutoUI.Button("Update & Relaunch"))
	
	"""
end

# ╔═╡ 52d7c7a2-8693-11eb-016f-4fc3eb516d44
begin
	inml=findall(nml.groups.==Symbol(nmlgroup))[1]
	md"""😸"""
end

# ╔═╡ e658d885-ad25-4b47-b0ee-6c97a204f731
begin
	update_param
	nml.params[inml]
end

# ╔═╡ 15746ef0-8617-11eb-1160-5f48a95d94d0
begin
	update_param
	
	if !isempty(p_value)
		tmptype=typeof(nml.params[inml][Symbol(p_name)])
		nml.params[inml][Symbol(p_name)]=parse(tmptype,p_value)
		
		tmpfil=joinpath(rundir,mydats)
		rm(tmpfil)
		write(tmpfil,nml)

		tmpfil=joinpath("tracked_parameters",mydats)
		ClimateModels.git_log_fil(MC,tmpfil,"update parameter file")
	end
	
	#@bind do_run2 PlutoUI.Button("Launch Model")
	do_run2="🐎"
	
	md"""🐎"""
end

# ╔═╡ 96492c18-86bd-11eb-35ca-dff79e6e7818
begin
	do_run1
	do_run2
	isempty(MC.channel) ? put!(MC.channel,MITgcm_launch) : nothing
	launch(MC)
	refresh_plot=true
	md"""Model run for the **$(MC.configuration)** configuration has completed!
	
	🏇 🏁 🏁 🏁 🎉 🎊 """
end

# ╔═╡ 6edcbba3-8485-44d2-940a-e4f2df019373
begin
	refresh_plot
	list1=readdir(rundir)
	search_txt!=="*" ? list1[findall(occursin.(search_txt,list1))] : list1
end

# ╔═╡ d0bbb668-86e0-11eb-1a9b-8f2b0175f7c1
begin
	refresh_plot

	run(pipeline(`grep dynstat_theta_mean $(filout)`,filstat))

	tmp0 = read(filstat,String)
	tmp0 = split(tmp0,"\n")
	Tmean=[parse(Float64,split(tmp0[i],"=")[2]) for i in 1:length(tmp0)-1]
end

# ╔═╡ 8ad9d646-4eec-45b9-938b-21df34da2d6b
begin
	refresh_plot
	
	if MC.configuration=="advect_xy"||MC.configuration=="advect_xz"
		tmp2=readdir(rundir)
		
		x=read_mdsio(rundir,"XC")
		y=read_mdsio(rundir,"YC")
		z=read_mdsio(rundir,"RC")

		tmp2=tmp2[findall(occursin.("T.0000",tmp2))]
		tmp2=tmp2[findall(occursin.("001.001.data",tmp2))]
		tmp2=[i[1:end-13] for i in tmp2]
	
		!isnothing(t_slow) ? i=mod(t_slow,length(tmp2)) : i=length(tmp2)-1
		
		tmp3=read_mdsio(rundir,tmp2[i+1])
		length(size(tmp3))==3 ? tmp3=dropdims(tmp3;dims=2) : nothing

		if MC.configuration=="advect_xz"
			contourf(1e-3*x[:,1],reverse(z[:]),reverse(tmp3,dims=2),xlabel="km",ylabel="m",
				levels=(-0.04:0.02:0.2),leg=:none,c = :terrain)
		else
			contourf(1e-3*x[:,1],1e-3*y[1,:],tmp3,xlabel="km",ylabel="km",
				levels=(-0.02:0.01:0.1),leg=:none,c = :terrain)
		end
	else
		plot(Tmean,label="mean temperature")
	end
end

# ╔═╡ 734e2b5a-8866-11eb-0025-bd9544f4c30d
begin
	#Read grid (as if rectangular domain for initial test) 
	
	try
		XC=read_mdsio(rundir,"XC"); siz=size(XC)

		mread(xx::Array,x::MeshArray) = read(xx,x)	
		function mread(fil::String,x::MeshArray)
			d=dirname(fil)
			b=basename(fil)[1:end-5]
			read(read_mdsio(d,b),x)
		end

		γ=gcmgrid(rundir,"PeriodicChannel",1,fill(siz,1), [siz[1] siz[2]], eltype(XC), mread, write)
		Γ=GridLoad(γ)
	catch e
		γ=[]
		Γ=[]
		println("no grid files")
	end
	
	md"""😸"""
end


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git-tree-sha1 = "11e1772e7f3cc987e9d3de991dd4f6b2602663a5"
uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
version = "1.3.8+0"

[[deps.mtdev_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "b4d631fd51f2e9cdd93724ae25b2efc198b059b1"
uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e"
version = "1.1.7+0"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.64.0+1"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.5.0+2"

[[deps.x264_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "14cc7083fc6dff3cc44f2bc435ee96d06ed79aa7"
uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a"
version = "10164.0.1+0"

[[deps.x265_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "e7b67590c14d487e734dcb925924c5dc43ec85f3"
uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76"
version = "4.1.0+0"

[[deps.xkbcommon_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"]
git-tree-sha1 = "a1fc6507a40bf504527d0d4067d718f8e179b2b8"
uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd"
version = "1.13.0+0"
"""

# ╔═╡ Cell order:
# ╟─f588eaba-84ef-11eb-0755-bf1b85b2b561
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# ╟─af176e6c-8695-11eb-3e34-91fbdb9c52fa
# ╟─8cf4d8ca-84eb-11eb-22d2-255ce7237090
# ╟─348c692e-84fe-11eb-3288-dd0a1dedce90
# ╟─52d7c7a2-8693-11eb-016f-4fc3eb516d44
# ╟─734e2b5a-8866-11eb-0025-bd9544f4c30d
# ╟─00000000-0000-0000-0000-000000000001
# ╟─00000000-0000-0000-0000-000000000002