From 0f3065505944670aa82ca1cc26ae624dd84b9918 Mon Sep 17 00:00:00 2001 From: Boris Kaus Date: Fri, 21 Jul 2023 16:44:40 +0200 Subject: [PATCH] introduced "plot_cross_section" as a separate function, rather than overriding "heatmap" & add the required Statistics package --- Project.toml | 9 +- docs/src/man/juliasetup_LaPalma.md | 2 +- docs/src/man/juliasetup_example_sphere.md | 4 +- notebooks/FallingSphere_1.jl | 1842 ++++++++++++++++++++- src/PlotsExt.jl | 10 +- 5 files changed, 1832 insertions(+), 35 deletions(-) diff --git a/Project.toml b/Project.toml index ed036908..c039a25b 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "LaMEM" uuid = "2e889f3d-35ce-4a77-8ea2-858aecb630f7" authors = ["Boris Kaus "] -version = "0.2.0" +version = "0.2.1" [deps] DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" @@ -12,22 +12,23 @@ LaMEM_jll = "15d6fa20-f789-5486-b71b-22b4ac8eb1c1" PETSc_jll = "8fa3689e-f0b9-5420-9873-adf6ccf46f2d" ReadVTK = "dc215faf-f008-4882-a9f7-a79a826fadc3" Requires = "ae029012-a4dd-5104-9daa-d747884805df" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [compat] +DocStringExtensions = "0.9" GeoParams = "0.4" GeophysicalModelGenerator = "0.4 - 0.6" -DocStringExtensions = "0.9" Glob = "1" LaMEM_jll = "1.2.4 - 1.2.4" PETSc_jll = "3.16.8 - 3.16.8" ReadVTK = "0.1.7" Requires = "1.0, 2" +Statistics = "1.0" julia = "1.9" [extras] -Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" - +Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [targets] test = ["Test"] diff --git a/docs/src/man/juliasetup_LaPalma.md b/docs/src/man/juliasetup_LaPalma.md index fa72a4c3..7fb2b072 100644 --- a/docs/src/man/juliasetup_LaPalma.md +++ b/docs/src/man/juliasetup_LaPalma.md @@ -103,7 +103,7 @@ julia> AddEllipsoid!(model, cen=(-0,0,-23), axes=(8,8,2), StrikeAngle=0, DipAngl We can plot a cross-section through the model: ```julia - julia> heatmap(model, x=0, field=:phase) + julia> plot_cross_section(model, x=0, field=:phase) ``` ![LaPalma_CrossSection](LaPalma_CrossSection.png) diff --git a/docs/src/man/juliasetup_example_sphere.md b/docs/src/man/juliasetup_example_sphere.md index 8a9bae28..331ab861 100644 --- a/docs/src/man/juliasetup_example_sphere.md +++ b/docs/src/man/juliasetup_example_sphere.md @@ -74,7 +74,7 @@ julia> AddSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, )) It is often useful to plot the initial model setup. You can do this with the `heatmap` function from the `Plots.jl` package, for which we provide a LaMEM plugin that allows you to specify a cross-section through a 3D LaMEM setup: ```julia -julia> heatmap(model, field=:phase, y=0) +julia> plot_cross_section(model, field=:phase, y=0) ``` ![InitialSetupSphere](InitialSetupSphere.png) @@ -136,7 +136,7 @@ Time stepping parameters: Once the simulation is done, you can look at the results using the same `heatmap` function, but by specifying a timestep, which will read that timestep and plot a cross-section though it: ```julia -julia> heatmap(model, y=0, timestep=20, field=:phase) +julia> plot_cross_section(model, y=0, timestep=20, field=:phase) ``` ![FallingSphere_t20](FallingSphere_t20.png) diff --git a/notebooks/FallingSphere_1.jl b/notebooks/FallingSphere_1.jl index 6656f6de..c2803dfe 100644 --- a/notebooks/FallingSphere_1.jl +++ b/notebooks/FallingSphere_1.jl @@ -15,12 +15,7 @@ macro bind(def, element) end # ╔═╡ f744857e-20e6-11ee-1720-311279133704 -begin - import Pkg - Pkg.activate(mktempdir()) - Pkg.add(Pkg.PackageSpec(name="LaMEM", rev="bk-julia-model-setup")) - using LaMEM, GeophysicalModelGenerator, Plots, PlutoUI, GMT -end +using LaMEM,GeophysicalModelGenerator, Plots, PlutoUI, GMT # ╔═╡ 78136b07-5d33-407a-afcf-e0a656181043 md""" @@ -32,9 +27,6 @@ This is a first example that illustrates how to build a setup using the LaMEM.jl We start with loading a few packages. """ -# ╔═╡ 4cd42d73-d63d-4149-9062-037a82f54255 -Topo = ImportTopo(lon = [-18.7, -17.1], lat=[28.0, 29.2], file="@earth_relief_03s.grd"); - # ╔═╡ 03abfcd4-b3bb-44eb-ba97-c03d64126195 md""" ### Define model setup @@ -42,18 +34,17 @@ md""" Next, we define a general model setup, in which we specify the units with which we work (for most cases, you'll want to use the default `GEO` units), the size of the computational box and various timestepping parameters. In this case, we use a multigrid solver. """ -# ╔═╡ 4a533c45-2ad6-4970-963b-abbbc798275b - model = Model(Grid(nel=(32,16,16), x=[-1,1], y=[-1,1], z=[-1,1]), +# ╔═╡ 01b3370d-24b6-42a8-902b-b6b3d195d55e +model = Model(Grid(nel=(32,32,32), x=[-1,1], y=[-1,1], z=[-1,1]), Time(nstep_max=20, dt_min=1e-3, dt=1, dt_max=10, time_end=100), Solver(SolverType="multigrid", MGLevels=2), Output(out_dir="example_1")) # ╔═╡ b192e665-20f2-4f65-ace9-fe7fffd7b7c7 md""" -Note that each of the fields within `Model` has many additional and adjustable parameters. You can view that by typing `Model.Time`: -""" +Note that each of the fields within `Model` has many additional and adjustable parameters. You can view that by typing `Model.Time`""" -# ╔═╡ 965f3210-d4da-4a0b-8db5-cce85779fd58 +# ╔═╡ d2acae58-dd8e-4384-a1a2-0e61d8bedf90 model.Time # ╔═╡ e85b89ee-7452-45dc-8484-1e2497cf3f7a @@ -67,7 +58,7 @@ md""" In this simulation, we will consider two materials, the matrix and a sphere with higher density. Since pluto is reactive (implying that all cells are updated once one changes), we start with removing any previously defined phases from the setup: """ -# ╔═╡ be5335db-5535-49c6-95d2-49e53d644523 +# ╔═╡ 98542133-c507-4dab-b279-5ae3ddd7d3b7 rm_phase!(model) # ╔═╡ 6b59fe59-0d0f-4984-8464-c76c18bc8f19 @@ -104,11 +95,11 @@ AddSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, )) # ╔═╡ e0411cc1-60ae-43cf-9500-93a246e62e1b md""" -It is often useful to plot the initial model setup. You can do this with the `heatmap` function from the `Plots.jl` package, for which we provide a LaMEM plugin that allows you to specify a cross-section through a 3D LaMEM setup: +It is often useful to plot the initial model setup. You can do this with the `plot_cross_section` function that is made available once the `Plots.jl` package is loaded: """ # ╔═╡ fb23a0a3-1485-4726-8b6e-1a810e50ce7a -heatmap(model, field=:phase, y=0.1) +plot_cross_section(model, field=:phase, y=0.1) # ╔═╡ 4e5cb7d3-f6c0-4dd9-b508-643e38335297 md""" @@ -129,7 +120,7 @@ run_lamem(model,1) md""" ### Visualize results -Once the simulation is done, you can look at the results using the same `heatmap` function, but by specifying a timestep, which will read that timestep and plot a cross-section though it: +Once the simulation is done, you can look at the results using the same `plot_cross_section` function, but by specifying a timestep, which will read that timestep and plot a cross-section though it: """ # ╔═╡ eaa307f7-5655-4cf3-8638-47faa28a6a4b @@ -154,7 +145,7 @@ And use that to slice through time """ # ╔═╡ 66d66323-71a4-455a-9a7b-bd1ec3d5ae1c -heatmap(model, y=0.2, timestep=t, field=:phase, dim=3) +plot_cross_section(model, y=0.2, timestep=t, field=:phase, dim=3) # ╔═╡ 2cb9ffa5-48da-4d48-8381-51c5d8f65da5 md""" @@ -179,17 +170,1820 @@ Since we are using Pluto, changing values in one cell will update the full noteb # ╔═╡ 778d540b-5e56-463f-87a3-d14f17e452ba +# ╔═╡ 00000000-0000-0000-0000-000000000001 +PLUTO_PROJECT_TOML_CONTENTS = """ +[deps] +GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54" +GeophysicalModelGenerator = "3700c31b-fa53-48a6-808a-ef22d5a84742" +LaMEM = "2e889f3d-35ce-4a77-8ea2-858aecb630f7" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" + +[compat] +GMT = "~1.3.0" +GeophysicalModelGenerator = "~0.5.2" +LaMEM = "~0.2.0" +Plots = "~1.38.16" +PlutoUI = "~0.7.52" +""" + +# ╔═╡ 00000000-0000-0000-0000-000000000002 +PLUTO_MANIFEST_TOML_CONTENTS = """ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.9.0" +manifest_format = "2.0" +project_hash = "b622db3e4a1f456128bd46d3ea9fe2ea2784af8f" + +[[deps.AbstractFFTs]] 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"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.snappy_jll]] +deps = ["Artifacts", "JLLWrappers", "LZO_jll", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "985c1da710b0e43f7c52f037441021dfd0e3be14" +uuid = "fe1e1685-f7be-5f59-ac9f-4ca204017dfd" +version = "1.1.9+1" + +[[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: # ╟─78136b07-5d33-407a-afcf-e0a656181043 # ╠═f744857e-20e6-11ee-1720-311279133704 -# ╠═4cd42d73-d63d-4149-9062-037a82f54255 # ╟─03abfcd4-b3bb-44eb-ba97-c03d64126195 -# ╠═4a533c45-2ad6-4970-963b-abbbc798275b +# ╠═01b3370d-24b6-42a8-902b-b6b3d195d55e # ╟─b192e665-20f2-4f65-ace9-fe7fffd7b7c7 -# ╠═965f3210-d4da-4a0b-8db5-cce85779fd58 +# ╠═d2acae58-dd8e-4384-a1a2-0e61d8bedf90 # ╟─e85b89ee-7452-45dc-8484-1e2497cf3f7a # ╟─bd63ef7e-af77-44d8-8127-456f7f6d38a6 -# ╠═be5335db-5535-49c6-95d2-49e53d644523 +# ╠═98542133-c507-4dab-b279-5ae3ddd7d3b7 # ╟─6b59fe59-0d0f-4984-8464-c76c18bc8f19 # ╠═87dbe840-1d59-4608-a73b-d4dee2bd2c7a # ╠═0c1c92d8-9846-4e31-9112-6c2b57e7a069 @@ -215,3 +2009,5 @@ Since we are using Pluto, changing values in one cell will update the full noteb # ╟─e73a3f02-c1f4-46d8-a0c2-c6f6058e1ca1 # ╟─f7147dc1-17d6-47af-8d92-2f780d471e91 # ╠═778d540b-5e56-463f-87a3-d14f17e452ba +# ╟─00000000-0000-0000-0000-000000000001 +# ╟─00000000-0000-0000-0000-000000000002 diff --git a/src/PlotsExt.jl b/src/PlotsExt.jl index b46ed626..3fc21f70 100644 --- a/src/PlotsExt.jl +++ b/src/PlotsExt.jl @@ -1,18 +1,18 @@ # Plotting extensions, that are only loaded when GLMakie is available println("Adding Plots.jl plotting extensions for LaMEM") -using LaMEM, GeophysicalModelGenerator +using LaMEM, GeophysicalModelGenerator, Statistics using .Plots import .Plots: heatmap -export plot_topo +export plot_topo, plot_cross_section """ - Plots.heatmap(model::Union{Model,CartData}, args...; field::Symbol=:phase, dim=1, x=nothing, y=nothing, z=nothing, aspect_ratio::Union{Real, Symbol}=:equal) + plot_cross_section(model::Union{Model,CartData}, args...; field::Symbol=:phase, dim=1, x=nothing, y=nothing, z=nothing, aspect_ratio::Union{Real, Symbol}=:equal) -This plots a `Plots` heatmap of a cross-section through the LaMEM `model`, of the field `field`. If that is a vector or tensor field, specify `dim` to indicate which of the fields you want to see. +This plots a cross-section through the LaMEM `model`, of the field `field`. If that is a vector or tensor field, specify `dim` to indicate which of the fields you want to see. If the keyword `timestep` is specified, it will load a timestep """ -function Plots.heatmap(model::Union{Model,CartData}, args...; field::Symbol=:phase, timestep=nothing, dim=1, x=nothing, y=nothing, z=nothing, aspect_ratio::Union{Real, Symbol}=:equal) +function plot_cross_section(model::Union{Model,CartData}, args...; field::Symbol=:phase, timestep=nothing, dim=1, x=nothing, y=nothing, z=nothing, aspect_ratio::Union{Real, Symbol}=:equal) if !isnothing(timestep) # load a particular timestep