index.jl

### A Pluto.jl notebook ###
# v0.19.21

using Markdown
using InteractiveUtils

# ╔═╡ 09fe08a8-610b-11ed-1f9b-2526511c166a
using Markdown, Pluto, PlutoUI;

# ╔═╡ 5b6f7d44-ac49-44e7-8c30-1fcbdcb6f1b6
md"""
# The Expt Types

The methods in this package numerically solve some
differential equations commonly faced in geophysical inverse problems.
The functionality of this package revolves around the mutable `Expt` types.
Julia's multiple dispatch is used to overload `Base` methods whenever possible. 
Which means, if one is familiar with the `Base` methods of Julia, then (almost) no additional syntax is required 
to use this package. Easy!


While performing a given experiment,
firstly, most of the memory necessary
is allocated while creating the `Expt` variables.
Then these variables are input to in-place functions 
(e.g., `update!`)  which as per Julia convention ends with an exclamation mark, to actually perform the experiment task.
For example, the
current `Expt` types within the realm of this package include:

* `SeisForwExpt` is the seismic (both acoustic and elastic) forward modeling experiment;
* `SeisInvExpt` is the type for seismic inversion experiment, including migration.

Some of the commonly used (and exported) mutable types to create the `Expt` variables are:

* `Medium` for bundling medium parameters together;
* `AGeom` stores acquisition-geometry-related parameters;
* `Srcs` allocates source signals input to an experiment;
* `Recs` allocated the output records that are fitted during inversion.
"""


# ╔═╡ 4425553d-21be-4d95-8430-1a8f7fd145bf
md"""
### Configuring the package
It is necessary to configure GeoPhyInv with a `set_preferences` before using it.
The preferences are set using [Preferences.jl](https://github.com/JuliaPackaging/Preferences.jl) package, where you can find more information.
If you need to change this configuration, julia kernel must be restarted.
```julia
using GeoPhyInv
GeoPhyInv.set_preferences(; ndims, use_gpu, datatype, order)
```
where the keyword arguments (with defaults) are 
* `ndims::Int=2`: the number of dimensions used for the stencil computations 2D or 3D 
* `use_gpu::Bool=false`: use GPU for stencil computations or not
* `datatype="Float32"`: the type of numbers used by field arrays (e.g. "Float32" or "Float64")
* `order::Int=2`: order ∈ [2,4,6,8] of the finite-difference stencil
Once changed, these preferences will apply as long as GeoPhyInv is part of your package environment.
"""

# ╔═╡ 1d12369e-3189-49df-9a1d-51be074af61f
md"""
After this, to get started with modelling or inversion, as an example, simply load a seismic inversion experiment already defined in our package gallery into REPL:
```julia
pa=SeisInvExpt(FdtdAcoustic(), LS(), :pizza); # "pizza" is the name of the experiment
```
Then, simply use `update!` to perform least-squares inversion.
```julia
update!(pa, solver=:ipopt)
```

### Fields

For a given `attrib_mod` and `ndims`, you can always print a list of scalar fields that are active. 
The idea is that these symbols will be used 
* to generate mutable types like `Srcs` or `Recs`;
* as input to keywords like `rfields` or `snaps_field`.
First, lets look at the list of all the scalar fields defined in this package.
````@example
Fields()
````
We can always filter this list depending on the type of the `SeisForwExpt` i.e., `attrib_mod` and the number of dimensions.
For example, lets check out the fields for 3-D acoustic simulation.
````@example
Fields(FdtdAcoustic(), ndims=3)
````
Similarly, for 2-D elastic simulation.
````@example
Fields(FdtdElastic(), ndims=2)
````

### Grids

It is necessary to input the evenly-spaced spatial and temporal grids while creating the `Expt` variables.
These grids can be simply created using `Base.range` in Julia, as shown below.

```julia
zgrid=range(0,stop=1000.0,length=201) # create vertical grid from 0 to 1000 m
xgrid=range(0,stop=1000.0,length=201) # similarly, create horizontal grid
```
While constructing spatial-grid bundle, watch out for order.
```julia
mgrid=[zgrid, xgrid] # 2D
mgrid=[zgrid, ygrid, xgrid] # 3D
@info string("spatial sampling intervals (dz, dy, dx)=", step.(mgrid))
```
Similarly, a temporal grid.
```julia
tgrid=range(0,stop=1.0,step=0.001) # a temporal grid from 0 to 1.0 s
```
	"""

# ╔═╡ 8abc866c-7311-4e3c-804a-106b190e4cdc
md"# Appendix"

# ╔═╡ 40f93407-05a3-4672-b314-f911a26c2072
notebook_files = mapreduce(vcat, walkdir(@__DIR__)) do (root, dirs, files)
	mapreduce(vcat, dirs, init=[]) do dir 
		filter(Pluto.is_pluto_notebook, readdir(joinpath(root, dir), join=true));
	end
end;

# ╔═╡ 88917bd4-3d7b-49da-a12c-d8d16dac84e5
html_files = broadcast(notebook_files) do f
	dir = last(split(dirname(f), basename(@__DIR__)))
	filebase = first(splitext(basename(f)))
    "https://pawbz.github.io/GeoPhyInv.jl/" * dir * "/" * filebase * ".html"
end;

# ╔═╡ 5a1b5b3d-bce0-41d7-b27c-18cf8f15b8c5
function links()
    return mapreduce(vcat, html_files, notebook_files) do ht, nb
		fm = Pluto.frontmatter(nb)
		
		if("title" ∈ keys(fm) && "description" ∈ keys(fm))
			t = fm["title"]
			d = fm["description"]
			return Markdown.parse("""#### [$(t)]($ht) 
			 $(d)""")
		else
			return md""
		end
	end
end

# ╔═╡ 823e0831-927a-4105-bff5-0eaf33956ab3
md"""
The documentation is provided by these notebooks listed below.
$(links())
"""

# ╔═╡ f47cea55-2632-4cb7-9873-99e34c1cf3af
readme = read(joinpath(@__DIR__, "README.md"), String) |> Markdown.parse;

# ╔═╡ 63c2339a-399e-4958-9230-aa0ad9981807
md"""
$readme
"""

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git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.10.0"

[[deps.Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
version = "1.10.0"

[[deps.Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[[deps.TranscodingStreams]]
deps = ["Random", "Test"]
git-tree-sha1 = "8a75929dcd3c38611db2f8d08546decb514fcadf"
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
version = "0.9.9"

[[deps.Tricks]]
git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175"
uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775"
version = "0.1.6"

[[deps.URIs]]
git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348"
uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
version = "1.4.1"

[[deps.UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

[[deps.Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.13+0"

[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.7.0+0"

[[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"
"""

# ╔═╡ Cell order:
# ╟─823e0831-927a-4105-bff5-0eaf33956ab3
# ╟─63c2339a-399e-4958-9230-aa0ad9981807
# ╟─5b6f7d44-ac49-44e7-8c30-1fcbdcb6f1b6
# ╟─4425553d-21be-4d95-8430-1a8f7fd145bf
# ╟─1d12369e-3189-49df-9a1d-51be074af61f
# ╟─8abc866c-7311-4e3c-804a-106b190e4cdc
# ╠═40f93407-05a3-4672-b314-f911a26c2072
# ╠═88917bd4-3d7b-49da-a12c-d8d16dac84e5
# ╠═5a1b5b3d-bce0-41d7-b27c-18cf8f15b8c5
# ╠═09fe08a8-610b-11ed-1f9b-2526511c166a
# ╠═f47cea55-2632-4cb7-9873-99e34c1cf3af
# ╟─00000000-0000-0000-0000-000000000001
# ╟─00000000-0000-0000-0000-000000000002