Some initial refactoring

Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.0-rc2"
+julia_version = "1.10.0"
 manifest_format = "2.0"
 project_hash = "3f47d140483a0c3112240a43a829a4e54e5b0216"
 
@@ -10,9 +10,9 @@ uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
 version = "0.0.1"
 
 [[deps.AbstractTrees]]
-git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c"
+git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
 uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
-version = "0.4.4"
+version = "0.4.5"
 
 [[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
@@ -31,10 +31,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
 version = "0.5.1"
 
 [[deps.Compat]]
-deps = ["UUIDs"]
-git-tree-sha1 = "886826d76ea9e72b35fcd000e535588f7b60f21d"
+deps = ["TOML", "UUIDs"]
+git-tree-sha1 = "d2c021fbdde94f6cdaa799639adfeeaa17fd67f5"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.10.1"
+version = "4.13.0"
 weakdeps = ["Dates", "LinearAlgebra"]
 
     [deps.Compat.extensions]
@@ -46,15 +46,15 @@ uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
 version = "1.0.5+1"
 
 [[deps.DataAPI]]
-git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c"
+git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
-version = "1.15.0"
+version = "1.16.0"
 
 [[deps.DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d"
+git-tree-sha1 = "1fb174f0d48fe7d142e1109a10636bc1d14f5ac2"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.18.15"
+version = "0.18.17"
 
 [[deps.Dates]]
 deps = ["Printf"]
@@ -91,9 +91,9 @@ version = "2.5.0+0"
 
 [[deps.FileIO]]
 deps = ["Pkg", "Requires", "UUIDs"]
-git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673"
+git-tree-sha1 = "c5c28c245101bd59154f649e19b038d15901b5dc"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.16.1"
+version = "1.16.2"
 
 [[deps.FileWatching]]
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
@@ -111,15 +111,15 @@ version = "1.3.0"
 
 [[deps.Git_jll]]
 deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"]
-git-tree-sha1 = "bb8f7cc77ec1152414b2af6db533d9471cfbb2d1"
+git-tree-sha1 = "b30c473c97fcc1e1e44fab8f3e88fd1b89c9e9d1"
 uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb"
-version = "2.42.0+0"
+version = "2.43.0+0"
 
 [[deps.IOCapture]]
 deps = ["Logging", "Random"]
-git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6"
+git-tree-sha1 = "8b72179abc660bfab5e28472e019392b97d0985c"
 uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
-version = "0.2.3"
+version = "0.2.4"
 
 [[deps.InteractiveUtils]]
 deps = ["Markdown"]
@@ -132,9 +132,9 @@ version = "0.2.2"
 
 [[deps.JLD2]]
 deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "PrecompileTools", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"]
-git-tree-sha1 = "c2d0f45afcb5f6209155670bffd100c3b4937ea3"
+git-tree-sha1 = "5ea6acdd53a51d897672edb694e3cc2912f3f8a7"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.40"
+version = "0.4.46"
 
 [[deps.JLLWrappers]]
 deps = ["Artifacts", "Preferences"]
@@ -204,9 +204,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[deps.LogExpFunctions]]
 deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa"
+git-tree-sha1 = "18144f3e9cbe9b15b070288eef858f71b291ce37"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.26"
+version = "0.3.27"
 
     [deps.LogExpFunctions.extensions]
     LogExpFunctionsChainRulesCoreExt = "ChainRulesCore"
@@ -223,9 +223,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
-git-tree-sha1 = "b211c553c199c111d998ecdaf7623d1b89b69f93"
+git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df"
 uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-version = "0.5.12"
+version = "0.5.13"
 
 [[deps.Markdown]]
 deps = ["Base64"]
@@ -291,9 +291,9 @@ version = "0.3.23+2"
 
 [[deps.OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "cc6e1927ac521b659af340e0ca45828a3ffc748f"
+git-tree-sha1 = "60e3045590bd104a16fefb12836c00c0ef8c7f8c"
 uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
-version = "3.0.12+0"
+version = "3.0.13+0"
 
 [[deps.OrderedCollections]]
 git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
@@ -307,9 +307,9 @@ version = "10.42.0+1"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "a935806434c9d4c506ba941871b327b96d41f2bf"
+git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.8.0"
+version = "2.8.1"
 
 [[deps.PartialFunctions]]
 deps = ["MacroTools"]
@@ -340,9 +340,9 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [[deps.QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
-git-tree-sha1 = "9ebcd48c498668c7fa0e97a9cae873fbee7bfee1"
+git-tree-sha1 = "9b23c31e76e333e6fb4c1595ae6afa74966a729e"
 uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
-version = "2.9.1"
+version = "2.9.4"
 
 [[deps.REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
@@ -393,9 +393,9 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
 [[deps.SortingAlgorithms]]
 deps = ["DataStructures"]
-git-tree-sha1 = "5165dfb9fd131cf0c6957a3a7605dede376e7b63"
+git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085"
 uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
-version = "1.2.0"
+version = "1.2.1"
 
 [[deps.SparseArrays]]
 deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"]
@@ -426,7 +426,7 @@ uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
 version = "1.10.0"
 
 [[deps.SuiteSparse_jll]]
-deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"]
+deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
 uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
 version = "7.2.1+1"
 
@@ -445,9 +445,9 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[deps.TranscodingStreams]]
-git-tree-sha1 = "1fbeaaca45801b4ba17c251dd8603ef24801dd84"
+git-tree-sha1 = "54194d92959d8ebaa8e26227dbe3cdefcdcd594f"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.10.2"
+version = "0.10.3"
 weakdeps = ["Random", "Test"]
 
     [deps.TranscodingStreams.extensions]

Project.toml

@@ -46,3 +46,8 @@ julia = "1.7"
 
 [extras]
 CPUSummary = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
+Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test", "Symbolics"]

docs/src/config.md

@@ -29,11 +29,9 @@ Aside from these arguments, all others have  default values provided. These are
 - `neutral_velocity`: Neutral velocity in m/s. Defaults to `300.0`
 - `neutral_temperature`: Neutral temperature in Kelvins. Defaults to `300.0`.
 - `ion_temperature`: Ion temperature in Kelvins. Defaults to 100.0
-- `electron_pressure_coupled`: Whether to use an electron-pressure-coupled method for the ions.  When using a coupled scheme, ion speed of sound is raised from the thermal speed to the ion acoustic speed, which reduces numerical oscillations around the ion stagnation point. Partial coupling is possible by supplying a value between zero and one, where zero is fully uncoupled and one is fully coupled. Described further in [K. Hara, *Non-oscillatory quasineutral fluid model of cross-field discharge plasmas*, Physics of Plasmas 25, 123508, 2018](https://aip.scitation.org/doi/pdf/10.1063/1.5055750). Defaults to `1.0`.
 - `implicit_energy`: The degree to which the energy is solved implicitly. `0.0` is a fully-explicit forward Euler, `0.5` is Crank-Nicholson, and `1.0` is backward Euler. Defaults to `1.0`.
 - `min_number_density`: Minimum allowable number density for any species. Defaults to `1e6`
 - `min_electron_temperature`: Minimum allowable electron temperature. Defaults to `1.0`.
-- `callback`: User-provided callback. This can by any standard callback from `DifferentialEquations.jl`. Defaults to `nothing`.
 - `magnetic_field_scale`: Factor by which the magnetic field is increased or decreased compared to the one in the provided `Thruster` struct. Defaults to `1.0`.
 - `source_neutrals`: Extra user-provided neutral source term. Can be an arbitrary function, but must take `(U, params, i)` as arguments. Defaults to `Returns(0.0)`. See [User-Provided Source Terms](@ref) for more information.
 - `source_ion_continuity`: Vector of extra source terms for ion continuity, one for each charge state. Defaults to `fill(Returns(0.0), ncharge)` . See [User-Provided Source Terms](@ref) for more information.
@@ -48,4 +46,4 @@ Aside from these arguments, all others have  default values provided. These are
 - `anode_boundary_condition`: Can be either `:sheath` or `:dirichlet`
 - `anom_smoothing_iters`: How many times to smooth the anomalous transport profile
 - `solve_plume`: Whether to solve for plume area variation and divergence losses
-- `electron_losses_in_plume`: Whether electron radial/wall losses are applied in the plume region
+- `electron_losses_in_plume`: Whether electron radial/wall losses are applied in the plume region

docs/src/initialization.md

@@ -39,7 +39,7 @@ u_i(z) = \begin{cases}
 
 ### Neutral density
 
-The neutral density at the anode is computed in the same way as during a simulation, namely: 
+The neutral density at the anode is computed in the same way as during a simulation, namely:
 ```math
 \rho_{n, anode} = \frac{\dot{m}}{u_n A_{ch}} - \sum_s \frac{[\rho_{is} u_{is}]_{anode}}{u_n}
 ```
@@ -101,7 +101,7 @@ We can check the behavior of our new function:
 ncells = 100
 nvars = 4
 config = (;initial_condition = MyInitialCondition())
-z_cell = LinRange(0, 0.05, ncells)
+z_cell = range(0, 0.05, length = ncells)
 U = zeros(nvars, ncells)
 params = (;config, z_cell)
 
@@ -115,4 +115,3 @@ U[1, :] == U[2, :] == U[3, :] == U[4, :] == collect(z_cell)
 
 true
 ```
-