Merge pull request #140 from gaelforget/v0p5p3b

V0p5p3b

Project.toml

@@ -1,7 +1,7 @@
 name = "IndividualDisplacements"
 uuid = "b92f0c32-5b7e-11e9-1d7b-238b2da8b0e6"
 authors = ["gaelforget <[email protected]>"]
-version = "0.5.2"
+version = "0.5.3"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

examples/worldwide/global_ocean_circulation.jl

@@ -21,14 +21,14 @@ using Pkg; Pkg.status()
 
 # ╔═╡ 2acbfc79-3926-4c5a-9994-e3222c60c377
 begin
-	import IndividualDisplacements, Climatology, MITgcm
+	using IndividualDisplacements
+	import Climatology, MITgcm
     using Statistics, PlutoUI, CairoMakie
 
     ECCOmodule = IndividualDisplacements.ECCO
     CSV = IndividualDisplacements.CSV
     DataFrames = IndividualDisplacements.DataFrames
-    Individuals = IndividualDisplacements.Individuals
-
+
 	output_path=joinpath(tempdir(),"global_ocean_tmp")
 	!isdir(output_path) ? mkdir(output_path) : nothing
 
@@ -59,9 +59,9 @@ begin
 
 	bind_j = (@bind j Select(1:6,default=3))
 	bind_k = (@bind ktxt Select(["0","1","10","30","40"],default="0"))
-	bind_ny = (@bind nytxt Select(["1/12","1","3","10"],default="10"))
-	bind_np = (@bind nptxt Select(["10","100","10000"],default="10000"))
-	bind_replay = (@bind do_replay CheckBox(default=true))
+	bind_ny = (@bind nytxt Select(["1/12","1","3","10"],default="1"))
+	bind_np = (@bind nptxt Select(["10","100","10000"],default="100"))
+	bind_replay = (@bind do_replay CheckBox(default=false))
 	bind_zoomin = (@bind zoom_in CheckBox(default=false))
 	bind_zrng = @bind zrng Select([0:11,11:21,21:27],default=0:11)
 
@@ -71,7 +71,6 @@ begin
 	file_base = basename(file_IC)[1:end-4]
 	backward_time ? file_base=file_base*"_◀◀" : file_base=file_base*"_▶▶"
 
-#	- k  = $(bind_k) = flow field vertical level (set to 0 for 3D)
 #  - _optional :_ zrng = $(bind_zrng) = vertical coordindate range 
 #  - _(only used if k==0; if otherwise then zrng effectively is k-0.5:k-0.5)_
 
@@ -82,6 +81,7 @@ begin
 	- latitude box : $(bind_j)
 	- ny = $(bind_ny) = similated period (1/12 = 1 month)
 	- np = $(bind_np) = number of individuals (100 by default)
+	- k  = $(bind_k) = flow field vertical level (set to 0 for 3D)
 	- replay = $(bind_replay) = load results from csv instead of recomputing
 	- zoom in = $(bind_zoomin) = zoom in rather than plotting whole Earth
 	"""
@@ -114,7 +114,7 @@ begin
     #println("file_base = "*file_base)
 
 	k=parse(Int,ktxt) #vertical level or 0
-	k!==0 ? zs=[k-0.5:k-0.5] : zs=zrng
+	k!==0 ? zs=(k-0.5:k-0.5) : zs=zrng
 
 	Climatology.get_ecco_velocity_if_needed()
 
@@ -171,8 +171,8 @@ begin
 	I
 end
 
-# ╔═╡ 20ff7f0a-3b44-4580-8920-2ae6aa22c78f
-I.D
+# ╔═╡ f639ec15-a9a1-4dab-a37f-b2c96f6a80e1
+#D.Γ.RC
 
 # ╔═╡ 6158a5e4-89e0-4496-ab4a-044d1e3e8cc0
 md""" ### 3.2 Monthly Step Function
@@ -214,6 +214,7 @@ if !do_replay
 	✔1	
 	[step!(I) for y=1:ny, m=1:nm]
 	"lon" in names(I.🔴) ? nothing : add_lonlat!(I.🔴,D.XC,D.YC)
+	"d" in names(I.🔴) ? nothing : I.🔴.d.=-D.Γ.RC[k]
 	✔2="Done with Main Computation"
 else
 	✔2="Skipping Main Computation (replay instead)"
@@ -367,6 +368,7 @@ PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
+CairoMakie = "~0.12.16"
 Climatology = "~0.5.12"
 MITgcm = "~0.5.0"
 PlutoUI = "~0.7.60"
@@ -378,7 +380,7 @@ PLUTO_MANIFEST_TOML_CONTENTS = """
 
 julia_version = "1.10.5"
 manifest_format = "2.0"
-project_hash = "e5a750eb23dc50dfae9c98cecb0cd5985fd84fd0"
+project_hash = "bb5811c0e79a88f3ec92251cfbda3ab33172d8ba"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081"
@@ -1417,10 +1419,10 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe"
 version = "1.0.2"
 
 [[deps.HDF5_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"]
-git-tree-sha1 = "82a471768b513dc39e471540fdadc84ff80ff997"
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"]
+git-tree-sha1 = "38c8874692d48d5440d5752d6c74b0c6b0b60739"
 uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
-version = "1.14.3+3"
+version = "1.14.2+1"
 
 [[deps.HTTP]]
 deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
@@ -2148,10 +2150,10 @@ uuid = "30363a11-5582-574a-97bb-aa9a979735b9"
 version = "0.12.0"
 
 [[deps.NetCDF_jll]]
-deps = ["Artifacts", "Blosc_jll", "Bzip2_jll", "HDF5_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "TOML", "XML2_jll", "Zlib_jll", "Zstd_jll", "libzip_jll"]
-git-tree-sha1 = "4686378c4ae1d1948cfbe46c002a11a4265dcb07"
+deps = ["Artifacts", "Blosc_jll", "Bzip2_jll", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenMPI_jll", "XML2_jll", "Zlib_jll", "Zstd_jll", "libzip_jll"]
+git-tree-sha1 = "a8af1798e4eb9ff768ce7fdefc0e957097793f15"
 uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3"
-version = "400.902.211+1"
+version = "400.902.209+0"
 
 [[deps.Netpbm]]
 deps = ["FileIO", "ImageCore", "ImageMetadata"]
@@ -2240,10 +2242,10 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
 version = "0.8.1+2"
 
 [[deps.OpenMPI_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
-git-tree-sha1 = "e25c1778a98e34219a00455d6e4384e017ea9762"
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"]
+git-tree-sha1 = "bfce6d523861a6c562721b262c0d1aaeead2647f"
 uuid = "fe0851c0-eecd-5654-98d4-656369965a5c"
-version = "4.1.6+0"
+version = "5.0.5+0"
 
 [[deps.OpenSSL]]
 deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"]
@@ -3525,12 +3527,12 @@ version = "3.6.0+0"
 # ╟─2fb4d76d-56d5-4c3e-bc7c-ba0cac57e0e3
 # ╟─f1215951-2eb2-490b-875a-91c1205b8f63
 # ╠═f727992f-b72a-45bc-93f1-cc8daf89af0f
-# ╠═20ff7f0a-3b44-4580-8920-2ae6aa22c78f
+# ╠═f639ec15-a9a1-4dab-a37f-b2c96f6a80e1
 # ╟─6158a5e4-89e0-4496-ab4a-044d1e3e8cc0
 # ╟─a2375720-f599-43b9-a7fb-af17956309b6
 # ╟─7efadea7-4542-40cf-893a-40a75e9c52be
 # ╟─a3e45927-5d53-42be-b7b7-489d6e7a6fe5
-# ╟─1044c5aa-1a56-45b6-a4c6-63d24eea878d
+# ╠═1044c5aa-1a56-45b6-a4c6-63d24eea878d
 # ╟─42959eb9-7c14-4892-bf41-a1a434b00e27
 # ╟─fc16b761-8b1f-41de-b4fe-7fa9987d6167
 # ╟─63b68e72-76c1-4104-bf76-dd9eefc4e225

examples/worldwide/global_ocean_circulation_driver.jl

@@ -1,9 +1,10 @@
 
-using Distributed, IndividualDisplacements
+using Distributed, IndividualDisplacements, Climatology, MITgcm
 
-if !isdefined(Main,:ECCO_FlowFields) && myid()==1
-    @everywhere include("ECCO_FlowFields.jl")
-    @everywhere using Main.ECCO_FlowFields, IndividualDisplacements,  CSV
+if !isdefined(Main,:CSV) && myid()==1
+    @everywhere using IndividualDisplacements, Climatology, MITgcm
+    @everywhere CSV=IndividualDisplacements.CSV
+    @everywhere ECCOmodule=IndividualDisplacements.ECCO
 
     @everywhere path=IndividualDisplacements.datadeps.getdata("global_ocean_circulation_inputs")
     @everywhere list=readdir(path)
@@ -65,21 +66,21 @@ backward_time = false
 backward_time ? file_output=file_base*"_◀◀" : file_base=file_base*"_▶▶"
 
 k=0
-np=10000
-ny=3 #number of years
+np=1000 #number of particles
+ny=1 #number of years
 nm=12 #number of months
 
-P,D=init_FlowFields(k=k,backward_time=backward_time)
+P,D=ECCOmodule.init_FlowFields(k=k,backward_time=backward_time)
 
-df = init_positions(np,filename=file_input)
+df = IndividualDisplacements.init.init_positions(np,filename=file_input)
 #"z" in names(df) ? nothing : df.z=10.0 .+ 0.0*df.x
 
-S = init_storage(np,100,length(D.Γ.RC),50)
+S = ECCOmodule.init_storage(np,100,length(D.Γ.RC),50)
 I = Individuals(P,df.x,df.y,df.z,df.f,
-    (D=merge(D,S),∫=custom∫,🔧=custom🔧,🔴=deepcopy(custom🔴)))
+    (D=merge(D,S),∫=ECCOmodule.custom∫,🔧=ECCOmodule.custom🔧,🔴=deepcopy(ECCOmodule.custom🔴)))
 
 T=(0.0,I.P.T[2])
-custom∫!(I,T)
+ECCOmodule.custom∫!(I,T)
 
 [step!(I) for y=1:ny, m=1:nm]
 
@@ -92,5 +93,5 @@ end
 
 function step!(I::Individuals)
     I.D.🔄(I)
-    custom∫!(I)
+    ECCOmodule.custom∫!(I)
 end

examples/worldwide/three_dimensional_ocean.jl

@@ -55,30 +55,7 @@ end
 md"""## Visualize Displacements"""
 
 # ╔═╡ 8e371f54-d7f7-4f59-a2e1-9f673486f1fa
-begin
-    """
-    plot(I::Individuals)
-
-    Plot the initial and final positions as scatter plot in `lon,lat` or `x,y` plane.
-    """
-    function myplot(I::Individuals)
-    🔴_by_t = IndividualDisplacements.DataFrames.groupby(I.🔴, :t)
-    set_theme!(theme_light())
-    fig=Figure(size = (900, 600))
-    try
-        a = Axis(fig[1, 1],xlabel="longitude",ylabel="latitude")		
-        scatter!(a,🔴_by_t[1].lon,🔴_by_t[1].lat,color=:green2)
-        scatter!(a,🔴_by_t[end].lon,🔴_by_t[end].lat,color=:red)
-    catch
-        a = Axis(fig[1, 1],xlabel="longitude",ylabel="latitude")		
-        scatter!(a,🔴_by_t[1].x,🔴_by_t[1].y,color=:green2)
-        scatter!(a,🔴_by_t[end].x,🔴_by_t[end].y,color=:red)
-    end
-    return fig
-    end
-
-    myplot(I)
-end
+plot( InDiPlot( data=(I=I,), options=(plot_type=:plot_start_end,) ) )
 
 # ╔═╡ a6f4b5a0-7818-41a6-a4e5-30d80a727625
 

ext/IndividualDisplacementsMakieExt.jl

@@ -13,6 +13,8 @@ module IndividualDisplacementsMakieExt
 				simple_plot2(x.data[:I])
 			elseif string(o.plot_type)=="global_plot1"
 				global_plot1(x.data[:I],x.data[:df])
+			elseif string(o.plot_type)=="plot_start_end"
+				plot_start_end(x.data[:I])
 			else
 				println("unknown option (b)")	
 			end
@@ -132,7 +134,7 @@ function global_plot1(I::Individuals,🔴::DataFrame;
 
     np=Int(maximum(🔴.ID))
     nt=length(unique(🔴.t))
-    ii=1:10000
+    ii=1:min(10000,np)
 
     tmp1=🔴[np*0 .+ ii,:lon].!==🔴[np*(nt-1) .+ ii,:lon]
     tmp2=🔴[np*0 .+ ii,:lat].!==🔴[np*(nt-1) .+ ii,:lat]
@@ -162,4 +164,25 @@ end
 
 ##
 
+"""
+    plot_start_end(I::Individuals)
+
+Plot the initial and final positions as scatter plot in `lon,lat` or `x,y` plane.
+"""
+function plot_start_end(I::Individuals)
+🔴_by_t = IndividualDisplacements.DataFrames.groupby(I.🔴, :t)
+set_theme!(theme_light())
+fig=Figure(size = (900, 600))
+try
+	a = Axis(fig[1, 1],xlabel="longitude",ylabel="latitude")		
+	scatter!(a,🔴_by_t[1].lon,🔴_by_t[1].lat,color=:green2)
+	scatter!(a,🔴_by_t[end].lon,🔴_by_t[end].lat,color=:red)
+catch
+	a = Axis(fig[1, 1],xlabel="longitude",ylabel="latitude")		
+	scatter!(a,🔴_by_t[1].x,🔴_by_t[1].y,color=:green2)
+	scatter!(a,🔴_by_t[end].x,🔴_by_t[end].y,color=:red)
+end
+return fig
+end
+
 end

src/example_ECCO.jl

@@ -2,9 +2,10 @@ module ECCO
 
 import MeshArrays, DataDeps, CSV, JLD2
 
-import IndividualDisplacements.OrdinaryDiffEq: solve, Tsit5, ODEProblem
+import IndividualDisplacements: postprocess_MeshArray, add_lonlat!, OrdinaryDiffEq
+import OrdinaryDiffEq: solve, Tsit5, ODEProblem
 import IndividualDisplacements: update_location!, Individuals, uvMeshArrays, uvwMeshArrays
-import IndividualDisplacements: FlowFields, data_path, read_data_ECCO, order
+import IndividualDisplacements: FlowFields, ensemble_solver, data_path, read_data_ECCO, order
 import IndividualDisplacements.DataFrames: DataFrame
 import IndividualDisplacements.MeshArrays as MeshArrays
 import IndividualDisplacements.MeshArrays: gcmgrid, MeshArray, exchange

test/Project.toml

@@ -1,5 +1,6 @@
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Climatology = "9e9a4d37-2d2e-41e3-8b85-f7978328d9c7"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"

test/runtests.jl

@@ -1,6 +1,5 @@
-using Test, Documenter
-using IndividualDisplacements, Climatology, MeshArrays, NetCDF, Suppressor
-import MITgcm
+using Test, Documenter, IndividualDisplacements, Suppressor
+import Climatology, MeshArrays, NetCDF, MITgcm
 
 Climatology.get_ecco_velocity_if_needed()
 Climatology.get_occa_velocity_if_needed()
@@ -10,6 +9,50 @@ Climatology.get_ecco_variable_if_needed("SALT")
 MeshArrays.GridLoad(MeshArrays.GridSpec("LatLonCap",MeshArrays.GRID_LLC90))
 MeshArrays.GridLoad(MeshArrays.GridSpec("PeriodicChannel",MeshArrays.GRID_LL360))
 
+@testset "ECCO" begin
+    import MITgcm, CairoMakie, Climatology, MITgcm
+
+    ECCOmodule = IndividualDisplacements.ECCO
+    CSV = IndividualDisplacements.CSV
+    DataFrames = IndividualDisplacements.DataFrames
+    Individuals = IndividualDisplacements.Individuals
+
+    k=0
+    P,D=ECCOmodule.init_FlowFields(k=k); np=100
+    df = IndividualDisplacements.init.init_gulf_stream(np , D)
+    S = ECCOmodule.init_storage(np,100,length(D.Γ.RC),50)
+    I = Individuals(P,df.x,df.y,df.z,df.fid,
+        (D=merge(D,S),∫=ECCOmodule.custom∫,🔧=ECCOmodule.custom🔧,🔴=deepcopy(ECCOmodule.custom🔴)))
+    my∫! = ∫!
+    T=(0.0,I.P.T[2])
+    my∫!(I,T)
+    @test isa(I,Individuals)
+
+    tmp_🔴=I.🔴
+    nt=length(unique(tmp_🔴.t))	
+    xlims=(-85.0,5.0)
+    ylims=(20.0,67.0)
+
+    x=IndividualDisplacements.InDiPlot( data=(I=I,df=tmp_🔴,), options=(plot_type=:global_plot1,) )
+    fig,tt=CairoMakie.plot(x)
+    @test isa(fig,CairoMakie.Figure)
+end
+
+@testset "OCCA" begin
+	import CairoMakie, Climatology
+    OCCAmodule=IndividualDisplacements.OCCA
+	initial_positions=IndividualDisplacements.init.initial_positions
+	P,D=OCCAmodule.setup(nmax=5)
+	nf=100; lo=(-160.0,-150.0); la=(30.0,40.0); level=2.5;
+	df=initial_positions(D.Γ, nf, lo, la, level)
+	I=Individuals(P,df.x,df.y,df.z,df.fid,(🔴=OCCAmodule.custom🔴,🔧=OCCAmodule.custom🔧, D=D))
+	T=(0.0,10*86400.0)
+	∫!(I,T)
+
+    fig=CairoMakie.plot( InDiPlot( data=(I=I,), options=(plot_type=:plot_start_end,) ) )
+    @test isa(fig,CairoMakie.Figure)
+end
+
 @testset "downloads" begin
     p0=IndividualDisplacements.datadeps.getdata("global_ocean_circulation_inputs")
     IndividualDisplacements.datadeps.getdata("flt_example")