Name change SD4SOLPS -> SOLPS2ctrl

Changed name SD4SOLPS to SOLPS2ctrl everywhere. Using new names od dependencies that are registered with Julia Registry: * IMASggd * SOLPS2imas Updating version to 2.0.0 Added test coverage Minor bug fix in using IMAS.flux_surfaces function.
ProjectTorreyPines · Oct 22, 2024 · 7e7f16d · 7e7f16d
1 parent 76b4e8c
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -20,6 +20,8 @@ jobs:
   test:
     uses: ProjectTorreyPines/GitHubActionsWorkflows/.github/workflows/test.yml@master
     secrets: inherit
+    with:
+      use_coverage: true
     # Optional inputs for artifact uploading
     # For example, uncomment the  following 4 lines to upload test result images that
     # will be generated by test/runtests.jl in test directory

diff --git a/NOTICE.md b/NOTICE.md
@@ -1,9 +1,9 @@
-GGDUtils.jl
+SOLPS2ctrl.jl
 =========
 
-The purpose of this NOTICE file is to provide legal notices and acknowledgments that must be displayed to users in any derivative works or distributions. This file does not alter the terms of the Apache 2.0 license that governs the use and distribution of the GGDUtils.jl package.
+The purpose of this NOTICE file is to provide legal notices and acknowledgments that must be displayed to users in any derivative works or distributions. This file does not alter the terms of the Apache 2.0 license that governs the use and distribution of the SOLPS2ctrl.jl package.
 
-GGDUtils.jl was originally developed under the ProjectTorreyPines by the Magnetic Fusion Energy group at General Atomics.
+SOLPS2ctrl.jl was originally developed under the ProjectTorreyPines by the Magnetic Fusion Energy group at General Atomics.
 
 If this software contributes to an academic publication, please cite it as follows:
 A. Gupta, D. Eldon, H. Anand, A. Dautt-Silva, S. De Pascuale, J. Lore, O. Meneghini, and J.S. Park, "Plasma boundary control development using a time-dependent scrape-off layer model in closed-loop simulations", Nucl. Mater. Energy, manuscript in preparation for PSI conference (2024).

diff --git a/Project.toml b/Project.toml
@@ -1,22 +1,21 @@
-name = "SD4SOLPS"
-uuid = "d8db6f1b-e564-4c04-bba3-ef399f78c070"
+name = "SOLPS2ctrl"
+uuid = "a531d12f-ac8a-43e8-b6d9-bd121431dd49"
 authors = ["David Eldon <[email protected]>"]
-version = "1.0.3"
+version = "2.0.0"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 Contour = "d38c429a-6771-53c6-b99e-75d170b6e991"
 EFIT = "cda752c5-6b03-55a3-9e33-132a441b0c17"
-Fortran90Namelists = "8fb689aa-71ff-4044-8071-0cffc910b57d"
-GGDUtils = "b7b5e640-9b39-4803-84eb-376048795def"
 IMAS = "13ead8c1-b7d1-41bb-a6d0-5b8b65ed587a"
+IMASggd = "b7b5e640-9b39-4803-84eb-376048795def"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 PhysicalConstants = "5ad8b20f-a522-5ce9-bfc9-ddf1d5bda6ab"
 PlotUtils = "995b91a9-d308-5afd-9ec6-746e21dbc043"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PolygonOps = "647866c9-e3ac-4575-94e7-e3d426903924"
-SOLPS2IMAS = "09becab6-0636-4c23-a92a-2b3723265c31"
+SOLPS2imas = "09becab6-0636-4c23-a92a-2b3723265c31"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
@@ -26,16 +25,15 @@ YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 ArgParse = "1"
 Contour = "0.6.3"
 EFIT = "1.0.0"
-Fortran90Namelists = "0.1.1"
-GGDUtils = "1.0.2"
 IMAS = "1.2.2"
+IMASggd = "2"
 Interpolations = "0.15.1"
 JSON = "0.21.4"
 PhysicalConstants = "0.2.3"
 PlotUtils = "1.4.1"
 Plots = "1.40.3"
 PolygonOps = "0.1.2"
-SOLPS2IMAS = "1.0.3"
+SOLPS2imas = "2"
 Statistics = "1.9.0"
 Unitful = "1.20.0"
 YAML = "0.4.11"

diff --git a/README.md b/README.md
@@ -1,8 +1,8 @@
-# SD4SOLPS
+# SOLPS2ctrl
 
-![Format Check](https://github.com/ProjectTorreyPines/SD4SOLPS.jl/actions/workflows/format_check.yml/badge.svg)
-![Docs](https://github.com/ProjectTorreyPines/SD4SOLPS.jl/actions/workflows/make_docs.yml/badge.svg)
-![Tests](https://github.com/ProjectTorreyPines/SD4SOLPS.jl/actions/workflows/test.yml/badge.svg)
+![Format Check](https://github.com/ProjectTorreyPines/SOLPS2ctrl.jl/actions/workflows/format_check.yml/badge.svg)
+![Docs](https://github.com/ProjectTorreyPines/SOLPS2ctrl.jl/actions/workflows/make_docs.yml/badge.svg)
+![Tests](https://github.com/ProjectTorreyPines/SOLPS2ctrl.jl/actions/workflows/test.yml/badge.svg)
 
 Synthetic diagnostic workflow manager for use with SOLPS models
 
@@ -15,19 +15,19 @@ Steps:
 3) Make assumptions to extend profiles into the core and far SOL, if needed
 4) Run synthetic diagnostic models and record output
 
-For installation and usage instructions, see the [online documentation](https://projecttorreypines.github.io/SD4SOLPS.jl/stable). For documentation on under development branch, see [dev online documentation](https://projecttorreypines.github.io/SD4SOLPS.jl/dev).
+For installation and usage instructions, see the [online documentation](https://projecttorreypines.github.io/SOLPS2ctrl.jl/stable). For documentation on under development branch, see [dev online documentation](https://projecttorreypines.github.io/SOLPS2ctrl.jl/dev).
 
 ## Installation
 
-SD4SOLPS is registered with public repository [FuseRegistry](https://github.com/ProjectTorreyPines/FuseRegistry.jl/). For installation:
+SOLPS2ctrl is registered with public repository [FuseRegistry](https://github.com/ProjectTorreyPines/FuseRegistry.jl/). For installation:
 
 ```
 using Pkg
 Pkg.Registry.add(RegistrySpec(url="https://github.com/ProjectTorreyPines/FuseRegistry.jl.git"))
 Pkg.Registry.add("General")
-Pkg.add("SD4SOLPS")
+Pkg.add("SOLPS2ctrl")
 ```
 
 ## Examples
 
-Refer to the instructions on this [wiki page](https://github.com/ProjectTorreyPines/SD4SOLPS.jl/wiki/Demo) to see how to run `examples/demo.ipynb`.
+Refer to the instructions on this [wiki page](https://github.com/ProjectTorreyPines/SOLPS2ctrl.jl/wiki/Demo) to see how to run `examples/demo.ipynb`.
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,15 +1,15 @@
 using Documenter
-using SD4SOLPS
+using SOLPS2ctrl
 
 makedocs(;
-    modules=[SD4SOLPS],
+    modules=[SOLPS2ctrl],
     format=Documenter.HTML(),
-    sitename="SD4SOLPS",
+    sitename="SOLPS2ctrl",
     checkdocs=:none,
 )
 
 deploydocs(;
-    repo="github.com/ProjectTorreyPines/SD4SOLPS.jl.git",
+    repo="github.com/ProjectTorreyPines/SOLPS2ctrl.jl.git",
     target="build",
     branch="gh-pages",
     devbranch="master",

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,5 +1,5 @@
 
-# SD4SOLPS.jl 
+# SOLPS2ctrl.jl 
 
 ```@contents
 Pages = ["index.md"]
@@ -10,21 +10,21 @@ This repository serves as the top most workflow manager with helpful utilities t
 
 ## Documentation of other repositories in this project
 
-### [GGDUtils.jl](https://projecttorreypines.github.io/GGDUtils.jl/stable)
+### [IMASggd.jl](https://projecttorreypines.github.io/IMASggd.jl/stable)
 
-### [SOLPS2IMAS.jl](https://projecttorreypines.github.io/SOLPS2IMAS.jl/stable)
+### [SOLPS2imas.jl](https://projecttorreypines.github.io/SOLPS2imas.jl/stable)
 
 ### [SynthDiag.jl](https://projecttorreypines.github.io/SynthDiag.jl/stable)
 
-SD4SOLPS is registered with public repository [FuseRegistry](https://github.com/ProjectTorreyPines/FuseRegistry.jl/). For installation:
+SOLPS2ctrl is registered with public repository [FuseRegistry](https://github.com/ProjectTorreyPines/FuseRegistry.jl/). For installation:
 
 ## Installation
 
 ```
 using Pkg
 Pkg.Registry.add(RegistrySpec(url="https://github.com/ProjectTorreyPines/FuseRegistry.jl.git"))
 Pkg.Registry.add("General")
-Pkg.add("SD4SOLPS")
+Pkg.add("SOLPS2ctrl")
 ```
 
 ## Top file handling functions

diff --git a/example/demo.ipynb b/example/demo.ipynb
@@ -10,7 +10,7 @@
     "Pkg.activate(\"./\")\n",
     "Pkg.Registry.add(RegistrySpec(url=\"https://github.com/ProjectTorreyPines/FuseRegistry.jl.git\"))\n",
     "Pkg.Registry.add(\"General\")\n",
-    "Pkg.add(\"SD4SOLPS\")\n",
+    "Pkg.add(\"SOLPS2ctrl\")\n",
     "Pkg.instantiate()"
    ]
   },
@@ -27,7 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "using SOLPS2IMAS: SOLPS2IMAS"
+    "using SOLPS2imas: SOLPS2imas"
    ]
   },
   {
@@ -52,7 +52,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ids = SOLPS2IMAS.solps2imas(b2gmtry, b2output; b2mn=b2mn, fort=fort);"
+    "ids = SOLPS2imas.solps2imas(b2gmtry, b2output; b2mn=b2mn, fort=fort);"
    ]
   },
   {
@@ -68,7 +68,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "using GGDUtils: GGDUtils\n",
+    "using IMASggd: IMASggd\n",
     "using Plots"
    ]
   },
@@ -110,21 +110,21 @@
     "\n",
     "# You can overlay any subset by giving a second argument\n",
     "# Labels\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"x_points\"), markercolor=:chocolate1, label=\"X-point\")\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"core_cut\"), linecolor=:red, linewidth=2, label=\"Core Cut\")\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"PFR_cut\"), linecolor=:darkred, linewidth=2, label=\"PFR Cut\")\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"outer_throat\"), linecolor=:limegreen, linewidth=2, label=\"Outer Throat\")\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"inner_throat\"), linecolor=:darkgreen, linewidth=2, label=\"Inner Throat\")\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"outer_midplane\"), linecolor=:cyan, linewidth=2, label=\"Outer midplane\")\n",
-    "# plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"inner_midplane\"), linecolor=:teal, linewidth=2, label=\"Inner midplane\")\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"outer_target\"), linecolor=:royalblue1, linewidth=2, label=\"Outer target\")\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"inner_target\"), linecolor=:navyblue, linewidth=2, label=\"Inner target\")\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"core_boundary\"), linecolor=:fuchsia, linewidth=2, linestyle=:dash, label=\"Core boundary\")\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, \"separatrix\"), linecolor=:purple4, linewidth=2, linestyle=:dash, label=\"Separatrix\")\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, 101), markershape=:rect, markercolor=:royalblue1)\n",
-    "# plot!(space, GGDUtils.get_grid_subset(grid_ggd, 102), markershape=:rect, markercolor=:maroon)\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, 103), markershape=:diamond, markercolor=:fuchsia)\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, 104), markershape=:diamond, markercolor=:purple4)\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, \"x_points\"), markercolor=:chocolate1, label=\"X-point\")\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, \"core_cut\"), linecolor=:red, linewidth=2, label=\"Core Cut\")\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, \"PFR_cut\"), linecolor=:darkred, linewidth=2, label=\"PFR Cut\")\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, \"outer_throat\"), linecolor=:limegreen, linewidth=2, label=\"Outer Throat\")\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, \"inner_throat\"), linecolor=:darkgreen, linewidth=2, label=\"Inner Throat\")\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, \"outer_midplane\"), linecolor=:cyan, linewidth=2, label=\"Outer midplane\")\n",
+    "# plot!(space, IMASggd.get_grid_subset(grid_ggd, \"inner_midplane\"), linecolor=:teal, linewidth=2, label=\"Inner midplane\")\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, \"outer_target\"), linecolor=:royalblue1, linewidth=2, label=\"Outer target\")\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, \"inner_target\"), linecolor=:navyblue, linewidth=2, label=\"Inner target\")\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, \"core_boundary\"), linecolor=:fuchsia, linewidth=2, linestyle=:dash, label=\"Core boundary\")\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, \"separatrix\"), linecolor=:purple4, linewidth=2, linestyle=:dash, label=\"Separatrix\")\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, 101), markershape=:rect, markercolor=:royalblue1)\n",
+    "# plot!(space, IMASggd.get_grid_subset(grid_ggd, 102), markershape=:rect, markercolor=:maroon)\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, 103), markershape=:diamond, markercolor=:fuchsia)\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, 104), markershape=:diamond, markercolor=:purple4)\n",
     "\n",
     "# Legend is supressed unless asked for specifically\n",
     "plot!(legend=true, left_margin=10Plots.pt)\n",
@@ -148,7 +148,7 @@
     "gr()           # Fast and can save pdf\n",
     "# plotlyjs()   # Use for interactive plot, can only save png\n",
     "\n",
-    "n_e = GGDUtils.get_prop_with_grid_subset_index(ids.edge_profiles.ggd[1].electrons.density, -5)\n",
+    "n_e = IMASggd.get_prop_with_grid_subset_index(ids.edge_profiles.ggd[1].electrons.density, -5)\n",
     "plot(ids.edge_profiles.grid_ggd, n_e, colorbar_title=\"Electrons density / m^(-3)\",\n",
     "     left_margin=10Plots.pt)"
    ]
@@ -172,7 +172,7 @@
     "# plotlyjs()   # Use for interactive plot, can only save png\n",
     "\n",
     "plot(ids.edge_profiles.grid_ggd, n_e) # Note default label in colorbar\n",
-    "plot!(space, GGDUtils.get_grid_subset(grid_ggd, 16), linecolor=:black, linewidth=2,\n",
+    "plot!(space, IMASggd.get_grid_subset(grid_ggd, 16), linecolor=:black, linewidth=2,\n",
     "      linestyle=:solid, label=\"Separatix\", legend=true, left_margin=10Plots.pt)"
    ]
   },
@@ -189,7 +189,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import SD4SOLPS: SD4SOLPS"
+    "import SOLPS2ctrl: SOLPS2ctrl"
    ]
   },
   {
@@ -199,7 +199,7 @@
    "outputs": [],
    "source": [
     "eqdsk = \"../sample/ITER_Lore_2296_00000/EQDSK/g002296.00200\"\n",
-    "SD4SOLPS.geqdsk_to_imas!(eqdsk, ids; set_time=0.2)"
+    "SOLPS2ctrl.geqdsk_to_imas!(eqdsk, ids; set_time=0.2)"
    ]
   },
   {
@@ -215,8 +215,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "SD4SOLPS.fill_in_extrapolated_core_profile!(ids, \"electrons.density\"; method=\"simple\", cell_subset_idx=-5)\n",
-    "SD4SOLPS.fill_in_extrapolated_core_profile!(ids, \"electrons.temperature\"; method=\"simple\", cell_subset_idx=-5)\n",
+    "SOLPS2ctrl.fill_in_extrapolated_core_profile!(ids, \"electrons.density\"; method=\"simple\", cell_subset_idx=-5)\n",
+    "SOLPS2ctrl.fill_in_extrapolated_core_profile!(ids, \"electrons.temperature\"; method=\"simple\", cell_subset_idx=-5)\n",
     "# ... more profiles here as they become available in b2time"
    ]
   },

diff --git a/example/simple_demo.jl b/example/simple_demo.jl
@@ -3,17 +3,17 @@
 # > using Revise
 # ] activate .
 # > include("example/simple_demo.jl")
-using SOLPS2IMAS: SOLPS2IMAS
-using GGDUtils: GGDUtils
+using SOLPS2imas: SOLPS2imas
+using IMASggd: IMASggd
 using Plots
-using SD4SOLPS
+using SOLPS2ctrl
 
 sample_path = "$(@__DIR__)/../sample/ITER_Lore_2296_00000/"
-solps2imas_samples = splitdir(pathof(SOLPS2IMAS))[1] * "/../samples"
+SOLPS2imas_samples = splitdir(pathof(SOLPS2imas))[1] * "/../samples"
 
-dd = SD4SOLPS.preparation(
+dd = SOLPS2ctrl.preparation(
     "Baseline2008-li0.70.x4.mod2.eqdsk",
-    [sample_path, solps2imas_samples]...;
+    [sample_path, SOLPS2imas_samples]...;
     eqdsk_set_time=0.0,
 )
 
@@ -23,14 +23,14 @@ space = grid_ggd.space[1] # First space in this grid_ggd
 # Choose backend
 gr()           # Fast and can save pdf
 # plotlyjs()   # Use for interactive plot, can only save png
-n_e = GGDUtils.get_prop_with_grid_subset_index(
+n_e = IMASggd.get_prop_with_grid_subset_index(
     dd.edge_profiles.ggd[1].electrons.density,
     5,
 )
 plot(dd.edge_profiles.grid_ggd, n_e; colorbar_title="Electrons density / m^(-3)")
 plot!(
     space,
-    GGDUtils.get_grid_subset(grid_ggd, 16);
+    IMASggd.get_grid_subset(grid_ggd, 16);
     linecolor=:black,
     linewidth=2,
     linestyle=:solid,

diff --git a/src/SD4SOLPS.jl → src/SOLPS2ctrl.jl b/src/SD4SOLPS.jl → src/SOLPS2ctrl.jl
@@ -1,7 +1,7 @@
-module SD4SOLPS
+module SOLPS2ctrl
 
 using IMAS: IMAS
-using SOLPS2IMAS: SOLPS2IMAS
+using SOLPS2imas: SOLPS2imas
 using EFIT: EFIT
 using Interpolations: Interpolations
 
@@ -24,7 +24,7 @@ about the SOLPS case. Returns a list of filenames with complete paths.
 Example:
 
 ```julia
-SD4SOLPS.find_files_in_allowed_folders(
+SOLPS2ctrl.find_files_in_allowed_folders(
     "<your samples folder>/D3D_Ma_184833_03600";
     eqdsk_file="g184833.03600",
 )
@@ -97,7 +97,7 @@ function geqdsk_to_imas!(
     eqt = eq.time_slice[time_index]
     eqt.time = g.time
 
-    source_for_summary = "gEQDSK file $gfilename loaded during SD4SOLPS workflow."
+    source_for_summary = "gEQDSK file $gfilename loaded during SOLPS2ctrl workflow."
 
     # 0D
     gq = eqt.global_quantities
@@ -284,10 +284,10 @@ function preparation(
     add_rho_to_equilibrium!(dd)  # Doesn't do anything if rho is valid
     dd.global_time = dd.equilibrium.time_slice[1].time
     for eqt ∈ dd.equilibrium.time_slice
-        IMAS.flux_surfaces(eqt)
+        IMAS.flux_surfaces(eqt, dd.wall)
     end
     # Add SOLPS data
-    dd = SOLPS2IMAS.solps2imas(b2fgmtry, b2time; b2mn=b2mn, ids=dd)
+    dd = SOLPS2imas.solps2imas(b2fgmtry, b2time; b2mn=b2mn, ids=dd)
     println("Loaded input data into IMAS DD")
 
     # Core profiles
@@ -345,4 +345,4 @@ function preparation(
     return dd
 end
 
-end # module SD4SOLPS
+end # module SOLPS2ctrl
diff --git a/src/supersize_profile.jl b/src/supersize_profile.jl
@@ -2,10 +2,9 @@
 Utilities for extrapolating profiles
 """
 
-using IMAS: IMAS
 using Interpolations: Interpolations
-using GGDUtils:
-    GGDUtils, get_grid_subset, add_subset_element!, get_subset_boundary,
+using IMASggd:
+    IMASggd, get_grid_subset, add_subset_element!, get_subset_boundary,
     project_prop_on_subset!, get_subset_centers, get_TPS_mats
 using PolygonOps: PolygonOps
 using JSON: JSON