Update version to v0.19.46 in marmousi-acoustic.jl notebook

Remove unused import of ColorSchemes in GeoPhyInv.jl
Increase _fd_npml and _fd_npextend values in GeoPhyInv.jl
Add maxiter parameter to IterativeSolvers.lsmr! in fwi.jl
Update dependencies in Project.toml
Add tauii_buffer to P_x_worker_x_pw struct in fdtd.jl
Update add_velocity_source! and add_stress_source! functions in propagate.jl
Remove unused seriescolor line in plots.jl
Update compute_stressii! function in advance_elastic.jl
Update gradient_finitediff_testing.jl notebook

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.4"
 manifest_format = "2.0"
-project_hash = "b93906f24b48daeaa115e6a8eb2d9b29862f8e80"
+project_hash = "da2b1e181419a1d0edd7834abebe8c15fb72559a"
 
 [[deps.ASL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]

Project.toml

@@ -8,7 +8,6 @@ BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
-ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
 DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"

docs/make.jl

@@ -3,7 +3,6 @@ ENV["GKSwstype"] = "100"
 
 using Documenter, GeoPhyInv, SparseArrays, LinearAlgebra, Random, LinearMaps
 using Plots, Test, Luxor
-using ColorSchemes
 
 # standard setting for generating doc pages
 # @init_parallel_stencil(2, false, Float32, 2)

notebooks/gradient_finitediff_testing.jl

@@ -55,7 +55,7 @@ end
 # @time update!(m1, pa_mod, [:invK])
 
 # ╔═╡ f49439df-3db3-48ae-bf9d-1387e3c14c8f
-N = 2
+N = 100
 
 # ╔═╡ 6d47ae1d-2554-4d42-af6c-02ce952bf14e
 @bind mpara Select([:invK, :rho])
@@ -180,7 +180,7 @@ isnan.(pa_inv.dobs[1].d[1])
 begin
     g = similar(m)
     GeoPhyInv.gradient!(g, m, pa_inv)
-    heatmap(Array(pa_mod.c.gradients[1]))
+	heatmap(Array(reshape(g, N, N)), c=:seismic)
 end
 
 # ╔═╡ aa0f7f1b-65ff-4a0b-9fb0-e6660911fdc8
@@ -198,6 +198,9 @@ heatmap(Array(reshape(pa_inv.P' * m, Nz, Nx)))
 # ╔═╡ 01552458-5de7-4627-b417-21745db2ade1
 heatmap(Array(reshape(m, 176, 176)))
 
+# ╔═╡ 8ec00fb7-fe18-4741-b987-813ec97d73fe
+heatmap(Array(reshape(gm, N, N)), c=:seismic)
+
 # ╔═╡ cd5bff59-6466-43d7-bd10-795d6f55d4ef
 heatmap(Array(reshape(g, 2, 2)), c=:seismic)
 
@@ -213,6 +216,9 @@ gKI = reshape(g, N, N)
 # ╔═╡ 630faaff-f7f0-46d7-a36f-31a54e589c8e
 heatmap(Array(gKI), c=:seismic)
 
+# ╔═╡ c6007b1a-3819-4543-bab4-f0dc0c12e075
+gm1 = Array(reshape(gm, N, N))
+
 # ╔═╡ 839cf146-639c-4d13-9470-d25882837169
 # prod(step.(pa_true.c.medium.grid)) #
 pa_true.c.srcwav[1][1].grid |> step |> abs2
@@ -223,6 +229,9 @@ GeoPhyInv.Fields(pa_mod.c.attrib_mod, "v")
 # ╔═╡ b14a5a36-94c4-4a6c-8b26-730919e3e5ae
 filter(x -> x ∉ Fields(pa_mod.c.attrib_mod, "d"), Fields(pa_mod.c.attrib_mod, "v"))
 
+# ╔═╡ 60a9adc0-466d-4e54-9838-f01b0a2c50c5
+Array(gKI) ./ gm1
+
 # ╔═╡ 417388ad-8709-4d4a-9d81-d4bbb0351a92
 heatmap(Array(pa_mod.c.gradients[1]), clim=(-1e-11, 1e-11), c=:seismic)
 
@@ -238,16 +247,7 @@ end
 Js(GeoPhyInv.Data.Array(xs))
 
 # ╔═╡ c6626e0f-4bf1-4e29-a0c3-1e7f23805f61
-gm = grad(central_fdm(2, 1, factor=1e8), Js, xs)[1]
-
-# ╔═╡ 8ec00fb7-fe18-4741-b987-813ec97d73fe
-heatmap(Array(reshape(gm, N, N)), c=:seismic)
-
-# ╔═╡ c6007b1a-3819-4543-bab4-f0dc0c12e075
-gm1 = Array(reshape(gm, N, N))
-
-# ╔═╡ 60a9adc0-466d-4e54-9838-f01b0a2c50c5
-Array(gKI) ./ gm1
+# gm = grad(central_fdm(2, 1, factor=1e8), Js, xs)[1]
 
 # ╔═╡ 9371b452-4ad6-4d07-ae98-c86239b6c110
 gs = get_xs(g, xs)

notebooks/marmousi-acoustic.jl

@@ -1,5 +1,5 @@
 ### A Pluto.jl notebook ###
-# v0.19.21
+# v0.19.46
 
 #> [frontmatter]
 #> title = "Marmousi"

notebooks/reusing-seisforwexpt.jl

@@ -1,5 +1,5 @@
 ### A Pluto.jl notebook ###
-# v0.19.21
+# v0.19.46
 
 #> [frontmatter]
 #> title = "SeisForwExpt"
@@ -8,14 +8,26 @@
 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)
+    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
+end
+
 # ╔═╡ 5fc7d3bf-418d-4487-a2d6-bc07c736374b
 begin
     import Pkg
     Pkg.add("PlutoLinks")
+	Pkg.add("Revise")
     Pkg.add("PlutoUI")
     Pkg.add("PlutoTest")
     Pkg.add("Plots")
     Pkg.add("CUDA")
+	using Revise
     using PlutoLinks: @revise
     using PlutoUI, PlutoTest, Plots, CUDA
 end
@@ -52,8 +64,10 @@ various bundles of medium parameters. We will first load a predefined medium, a
 medium = ElasticMedium(Homogeneous(), 5)
 
 # ╔═╡ ded21d43-99d6-453b-a858-e32f3f82e605
-# surface seismic acquisition with 3 supersources and 100 receivers
-ageom = AGeom(medium.grid, :surf, SSrcs(1), Recs(100))
+begin
+	# surface seismic acquisition with 3 supersources and 100 receivers
+	ageom = AGeom(medium.grid, :xwell, SSrcs(1), Recs(100));
+end
 
 # ╔═╡ a47b1e5d-a08c-4750-b1f3-f8a62225a19f
 # lets choose a time grid
@@ -84,14 +98,19 @@ md"""
 Now we have all the stuff necessary to allocate an instance of `SeisForwExpt`. 
 """
 
+# ╔═╡ 14713ee7-6753-46a7-98b3-ed0b8ef48ae4
+tsnaps=tgrid
+
 # ╔═╡ c7d96dda-17f5-4dbb-98bf-4c29fd784574
 pa = SeisForwExpt(
     FdtdElastic(),
+	snaps_field=:vx,
+	tsnaps=tsnaps,
     medium=medium,
     ageom=ageom,
     srcwav=srcwav,
     tgrid=tgrid,
-    rfields=[:vz],
+    rfields=[:vz, :vx],
     verbose=true,
 );
 
@@ -103,7 +122,7 @@ Before modeling, we will now generate a perturbed medium, which is "similar" to
 # ╔═╡ df4a4072-a91a-471a-88d9-b74ed58e7823
 begin
     medium_box = deepcopy(medium)
-    update!(medium_box, [:vp, :rho, :vs], rectangle=[[-500, -500], [500, 500]], perc=5.0) # perturbed velocity box
+    update!(medium_box, [:vp, :rho, :vs], rectangle=[[-500, -500], [500, 500]], perc=20.0) # perturbed velocity box
 
 end
 
@@ -127,6 +146,12 @@ begin
     data_box = deepcopy(pa[:data]) # copy data
 end
 
+# ╔═╡ e9c4cb8b-20bf-43c3-8da5-9ecb2e0ddfd2
+@bind it Slider(1:length(tgrid), show_value=true)
+
+# ╔═╡ 3ea41115-2623-4b55-b5a0-9b3a282b6668
+heatmap(pa[:snaps,1][it], c=:seismic,aspect_ratio=:equal)
+
 # ╔═╡ fd11d02d-80cd-4373-a8d1-e0d50d93dcf8
 md"""
 Lets look at the timer objects.
@@ -139,7 +164,16 @@ t1
 t2
 
 # ╔═╡ 4612405a-530b-4eab-8b84-40dc907929e4
-plot(plot(data, 99.9), plot(data_box, 99.9), size=(800, 500))
+plot(plot(data, 10), plot(data_box, 10), size=(800, 500))
+
+# ╔═╡ c3b9e67c-ec42-422f-bb65-f12269b659d7
+plot(data, 90)
+
+# ╔═╡ 994331fc-95b7-4417-89b2-bfab6f9b912e
+data[:vz] |> maximum
+
+# ╔═╡ ca5301e3-6740-4f55-a488-121d50e72358
+data[:vx] |> maximum
 
 # ╔═╡ ec7985c6-7072-4ac4-9caa-74a815193750
 @test data ≠ data_box
@@ -160,14 +194,20 @@ plot(plot(data, 99.9), plot(data_box, 99.9), size=(800, 500))
 # ╠═10be735e-4012-4fa8-b538-9f9a08694458
 # ╠═7fa1ddc5-fe10-44e2-b764-533be1840ab6
 # ╟─cec954f6-c278-4003-99e4-6c995f74b606
+# ╠═14713ee7-6753-46a7-98b3-ed0b8ef48ae4
 # ╠═c7d96dda-17f5-4dbb-98bf-4c29fd784574
 # ╠═9a3360c0-72c7-420f-a7c0-5565a1383f07
 # ╠═df4a4072-a91a-471a-88d9-b74ed58e7823
 # ╠═07da9113-a518-4925-8978-8407dc60c605
 # ╟─7ac4f51d-73b4-4f9c-88a4-a48911742282
 # ╠═033cd313-4e87-4364-a1f8-136e0e06bb65
+# ╠═3ea41115-2623-4b55-b5a0-9b3a282b6668
+# ╠═e9c4cb8b-20bf-43c3-8da5-9ecb2e0ddfd2
 # ╠═fd11d02d-80cd-4373-a8d1-e0d50d93dcf8
 # ╠═368c2bbd-94fb-4826-96eb-8fa37a7e35a3
 # ╠═7236dc4a-fe04-492d-9532-170ac7c22fb8
 # ╠═4612405a-530b-4eab-8b84-40dc907929e4
+# ╠═c3b9e67c-ec42-422f-bb65-f12269b659d7
+# ╠═994331fc-95b7-4417-89b2-bfab6f9b912e
+# ╠═ca5301e3-6740-4f55-a488-121d50e72358
 # ╠═ec7985c6-7072-4ac4-9caa-74a815193750