### A Pluto.jl notebook ###
# v0.19.19

using Markdown
using InteractiveUtils

# ╔═╡ 1e3a3928-eccb-11eb-3acb-6f829eeca032
begin
	using ShallowWaters, IndividualDisplacements, ClimateModels
	using Plots, NetCDF, Printf, CSV, DataFrames
	md"""#### Julia Packages"""
end

# ╔═╡ 90992888-fd0f-44af-bd61-f5f3d750b34b
begin
	md"""# Particle Tracking Tutorial

	###

	Here we employ [IndividualDisplacements.jl](https://juliaclimate.github.io/IndividualDisplacements.jl/dev/) (<https://doi.org/10.21105/joss.02813>) to simulate the advection and dispersion of particles by a turbulent flow field computed using [ShallowWaters.jl](https://github.com/milankl/ShallowWaters.jl) based on an [example provided by Milan Klöwer](https://www.milank.de/turbulent-confetti#main).	
	"""
end

# ╔═╡ 650ae02b-4f7b-4afe-9f91-676e3ad2ab01
md"""!!! note "Model Documentation"

	As in the global ocean biogeochemistry tutorial, the  [ClimateModels.jl](https://github.com/gaelforget/ClimateModels.jl) interface is used to run this modeling workflow.
"""

# ╔═╡ 779730d8-557b-41fd-8b46-907ca744f46a
md"""## Model Configuration

The model configuration can be summarized like this:	
"""

# ╔═╡ 5fddbd14-b3c6-4c63-a459-b9ce8a3cab98
md"""## Model Run
"""

# ╔═╡ b9c1be88-783b-4873-a5f2-f91e415e9032
md"""## Model Output 
"""

# ╔═╡ 72371695-0b7d-4db9-adef-69f71b5a6b05
md"""## Appendices 
"""

# ╔═╡ 8f8ddaa8-49bf-4d68-a75b-121d39ce0be2
md"""#### Model (Top Level Function)"""

# ╔═╡ 42459023-cbf6-4f66-94a9-4fa0c917d658
md"""#### Ancillary Functions"""

# ╔═╡ 92f66ca9-e53b-46e0-82c8-86101c96f1bf
function SWM(m)
	# Produce some turbulent flows with ShallowWaters.jl
	nx = m.inputs["nx"]           # parameters
	ny = m.inputs["ny"]
	Lx = m.inputs["Lx"]
	L_ratio = nx/ny
	dx = Lx/nx

	# spin up, starting from rest storing u,v,eta in run0000
	run_model(;nx,Lx,L_ratio,Ndays=100,output=true)    # may take 10min depending on resolution

	# use previous run as initial condition, and advect tracer with readily turbulent flow
	run_model(;nx,Lx,L_ratio,Ndays=50,output=true,initial_cond="ncfile")

	return true
end

# ╔═╡ cb2cc51a-cf1d-4369-b00a-c14057e33a61
function SWM_replay(m)
	nx = m.inputs["nx"]           # parameters
	ny = m.inputs["ny"]
	Lx = m.inputs["Lx"]
	L_ratio = nx/ny
	dx = Lx/nx
	rundir=joinpath(m.folder,string(m.ID))

	# reload model output from file, and process for use in IndividualDisplacements.jl
	ncfile = NetCDF.open(joinpath(rundir,"run0001","u.nc"))
	u = ncfile.vars["u"][:,:,:]
	u /= dx                      # normalise m/s to 1/s by division with grid spacing dx

	ncfile = NetCDF.open(joinpath(rundir,"run0001","v.nc"))
	v = zero(u)                  # pad with zeros
	v[:,2:end,:] .= ncfile.vars["v"][:,:,:]
	v /= dx                      # normalise

	ncfile = NetCDF.open(joinpath(rundir,"run0001","sst.nc"))
	sst = ncfile.vars["sst"][:,:,:]
	t = ncfile.vars["t"][:];      # time

	return (u,v,sst,t)
end

# ╔═╡ 0521fadb-fab7-4415-82a6-76a7a68eaaf3
function update_FlowFields!(F::𝐹_Array2D{T},
                            u0::AbstractMatrix,
                            u1::AbstractMatrix,
                            v0::AbstractMatrix,
                            v1::AbstractMatrix,
                            t::AbstractVector) where {T<:Real}
    
    @boundscheck size(F.u0) == size(u0) || throw(BoundsError())
    @boundscheck size(F.u1) == size(u1) || throw(BoundsError())
    @boundscheck size(F.v0) == size(v0) || throw(BoundsError())
    @boundscheck size(F.v1) == size(v1) || throw(BoundsError())
    @boundscheck size(t) == (2,) || throw(BoundsError())
    
    # include type conversion if needed
    F.u0 .= T.(u0)
    F.u1 .= T.(u1)
    F.v0 .= T.(v0)
    F.v1 .= T.(v1)
    F.𝑇 .= T.(t)     # also reset the time
end

# ╔═╡ e9a7f9d5-a12b-4a0d-b96c-6b791054c671
function mymodel(m)
	
	pth=pwd()
    cd(joinpath(m.folder,string(m.ID)))

	#1) run ShallowWaters.jl
	SWM(m)
	
	#2) reload output from ShallowWatwers.jl
	(u,v,sst,t)=SWM_replay(m)
	nx = m.inputs["nx"]           # parameters
	ny = m.inputs["ny"]
	
	#3) set up IndividualDisplacements.jl
	nparticles = 500
	x = nx*0.1 .+ (nx*0.8)*rand(nparticles)    # seed particles a bit away from boundaries
	y = ny*0.1 .+ (ny*0.8)*rand(nparticles);   # in grid coordinates
	F = FlowFields(u[:,:,1],u[:,:,2],v[:,:,1],v[:,:,2],eltype(u).(t[1:2]))
	I = Individuals(F,x,y)

	#4) compute trajectories 
	for i in 2:length(t)
	    update_FlowFields!(F,u[:,:,i-1],u[:,:,i],v[:,:,i-1],v[:,:,i],t[i-1:i])
	    ∫!(I)
	end
	
	#5) save IndividualDisplacements.jl output 
    fil=joinpath(m.folder,string(m.ID),"IndividualPositions.csv")
    CSV.write(fil, I.🔴)
	
    cd(pth)
	
    return true
end

# ╔═╡ c8d1631a-ffe7-45ac-8223-040dcaa3039f
begin
	m=ModelConfig(model=mymodel,inputs=
		Dict("nx" => 200, "ny" => 100, "Lx" => 2000e3, "nparticles" => 500))
	setup(m)
	build(m)
	m
end

# ╔═╡ ea325591-a0cc-485d-8be6-4731f71e4a99
begin
	launch(m)
	"done"
end

# ╔═╡ cc80f696-4661-44d8-a3b2-ae3d86b7cee1
begin
	nparticles=m.inputs["nparticles"]
	fil=joinpath(m.folder,string(m.ID),"IndividualPositions.csv")
	🔴=DataFrame(CSV.File(fil))
	(u,v,sst,t)=SWM_replay(m)
	randcolours = rand(nparticles)
	
	function myplot(tstep)
		id_range = 🔴.t .== t[tstep+1]
		f=heatmap(sst[:,:,tstep+1]',c=:grays,legend = nothing)
		scatter!(🔴.x[id_range],🔴.y[id_range],zcolor=randcolours,
		leg=:none,m = (4, 0.8, :viridis, Plots.stroke(0)))
		return f
	end
	
end

# ╔═╡ 0c1165a8-34b2-4b7d-b3c6-b361865bbf02
begin
	anim = @animate for tstep in 0:length(t)-1
		myplot(tstep)
	end
	gif(anim, joinpath(m.folder,string(m.ID),"anim_fps15.gif"), fps = 15)
end


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deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"]
git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6"
uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b"
version = "1.13.0+3"

[[deps.Xorg_libxkbfile_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"]
git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2"
uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a"
version = "1.1.0+4"

[[deps.Xorg_xcb_util_image_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"]
git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97"
uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b"
version = "0.4.0+1"

[[deps.Xorg_xcb_util_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"]
git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1"
uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5"
version = "0.4.0+1"

[[deps.Xorg_xcb_util_keysyms_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"]
git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00"
uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7"
version = "0.4.0+1"

[[deps.Xorg_xcb_util_renderutil_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"]
git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e"
uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e"
version = "0.3.9+1"

[[deps.Xorg_xcb_util_wm_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"]
git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67"
uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361"
version = "0.4.1+1"

[[deps.Xorg_xkbcomp_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"]
git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b"
uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4"
version = "1.4.2+4"

[[deps.Xorg_xkeyboard_config_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"]
git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d"
uuid = "33bec58e-1273-512f-9401-5d533626f822"
version = "2.27.0+4"

[[deps.Xorg_xtrans_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845"
uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10"
version = "1.4.0+3"

[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.12+3"

[[deps.Zstd_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927"
uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
version = "1.5.2+0"

[[deps.ZygoteRules]]
deps = ["MacroTools"]
git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0"
uuid = "700de1a5-db45-46bc-99cf-38207098b444"
version = "0.2.2"

[[deps.fzf_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56"
uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09"
version = "0.29.0+0"

[[deps.libaom_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4"
uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b"
version = "3.4.0+0"

[[deps.libass_jll]]
deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47"
uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0"
version = "0.15.1+0"

[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.1.1+0"

[[deps.libfdk_aac_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55"
uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280"
version = "2.0.2+0"

[[deps.libpng_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c"
uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f"
version = "1.6.38+0"

[[deps.libvorbis_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"]
git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c"
uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
version = "1.3.7+1"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.48.0+0"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+0"

[[deps.x264_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2"
uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a"
version = "2021.5.5+0"

[[deps.x265_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9"
uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76"
version = "3.5.0+0"

[[deps.xkbcommon_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"]
git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a"
uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd"
version = "1.4.1+0"
"""

# ╔═╡ Cell order:
# ╟─90992888-fd0f-44af-bd61-f5f3d750b34b
# ╟─650ae02b-4f7b-4afe-9f91-676e3ad2ab01
# ╟─779730d8-557b-41fd-8b46-907ca744f46a
# ╟─c8d1631a-ffe7-45ac-8223-040dcaa3039f
# ╟─5fddbd14-b3c6-4c63-a459-b9ce8a3cab98
# ╟─ea325591-a0cc-485d-8be6-4731f71e4a99
# ╟─b9c1be88-783b-4873-a5f2-f91e415e9032
# ╟─0c1165a8-34b2-4b7d-b3c6-b361865bbf02
# ╟─72371695-0b7d-4db9-adef-69f71b5a6b05
# ╟─1e3a3928-eccb-11eb-3acb-6f829eeca032
# ╟─8f8ddaa8-49bf-4d68-a75b-121d39ce0be2
# ╟─e9a7f9d5-a12b-4a0d-b96c-6b791054c671
# ╟─42459023-cbf6-4f66-94a9-4fa0c917d658
# ╟─92f66ca9-e53b-46e0-82c8-86101c96f1bf
# ╟─cb2cc51a-cf1d-4369-b00a-c14057e33a61
# ╟─0521fadb-fab7-4415-82a6-76a7a68eaaf3
# ╟─cc80f696-4661-44d8-a3b2-ae3d86b7cee1
# ╟─00000000-0000-0000-0000-000000000001
# ╟─00000000-0000-0000-0000-000000000002