Merge pull request #10 from ProjectTorreyPines/dev

Releasing 0.1.0

.JuliaFormatter.toml

@@ -0,0 +1,27 @@
+align_assignment = true
+align_conditional = true
+align_matrix = true
+align_pair_arrow = true
+align_struct_field = true
+always_for_in = true
+always_use_return = true
+annotate_untyped_fields_with_any = false
+conditional_to_if = true
+for_in_replacement = "∈"
+format_docstrings = true
+import_to_using = true
+indent = 4
+indent_submodule = true
+join_lines_based_on_source = true
+long_to_short_function_def = true
+margin = 88
+normalize_line_endings = "unix"
+pipe_to_function_call = true
+remove_extra_newlines = true
+separate_kwargs_with_semicolon = true
+surround_whereop_typeparameters = true
+trailing_comma = true
+whitespace_in_kwargs = false
+whitespace_ops_in_indices = false
+whitespace_typedefs = true
+yas_style_nesting = true

.dvc/.gitignore

@@ -0,0 +1,3 @@
+/config.local
+/tmp
+/cache

.dvcignore

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+# Add patterns of files dvc should ignore, which could improve
+# the performance. Learn more at
+# https://dvc.org/doc/user-guide/dvcignore

.github/workflows/format_check.yml

@@ -0,0 +1,36 @@
+name: Format Check
+
+on:
+  push:
+    branches: ["master", "dev", "format"]
+  pull_request:
+    branches: ["master", "dev"]
+jobs:
+  check:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1.9.3]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v1
+      - name: Install JuliaFormatter and format
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.gitignore

@@ -0,0 +1,5 @@
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+Manifest.toml

Project.toml

@@ -0,0 +1,13 @@
+name = "SynthDiag"
+uuid = "c6e34158-aa22-49e4-bb12-15cbcb518ce6"
+authors = ["Anchal Gupta <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+EFIT = "cda752c5-6b03-55a3-9e33-132a441b0c17"
+GGDUtils = "b7b5e640-9b39-4803-84eb-376048795def"
+OMAS = "91cfaa06-6526-4804-8666-b540b3feef2f"
+PhysicalConstants = "5ad8b20f-a522-5ce9-bfc9-ddf1d5bda6ab"
+QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
+SD4SOLPS = "d8db6f1b-e564-4c04-bba3-ef399f78c070"
+SOLPS2IMAS = "09becab6-0636-4c23-a92a-2b3723265c31"

README.md

@@ -1,2 +1,7 @@
 # SynthDiag.jl
-Package that defined synthetic diagnostics to generate sensor data based on plasma profile.
+
+![Format Check](https://github.com/ProjectTorreyPines/GGDUtils.jl/actions/workflows/format_check.yml/badge.svg)
+
+
+Package that defined synthetic diagnostics to generate sensor data based on plasma
+profile.

sample/.gitignore

@@ -0,0 +1,4 @@
+/b2fgmtry
+/b2time.nc
+/b2mn.dat
+/g002296.00200

sample/b2fgmtry.dvc

@@ -0,0 +1,12 @@
+md5: bcf05d7d7b6d91ef1025c0dc018c4bbf
+frozen: true
+deps:
+- path: ITER_Lore_2296_00000/baserun/b2fgmtry
+  repo:
+    url: [email protected]:ProjectTorreyPines/SOLPSTestSamples.git
+    rev_lock: df499f1275428ec06175c48dc4af6ecbd5ec6117
+outs:
+- md5: 6589953daeef49b21744d159af970cbb
+  size: 2908856
+  hash: md5
+  path: b2fgmtry

sample/b2mn.dat.dvc

@@ -0,0 +1,12 @@
+md5: c0c920771883f03bc0abe98425b38d5e
+frozen: true
+deps:
+- path: ITER_Lore_2296_00000/run_time_dep_EIRENE_jdl_to_ss_cont_sine2_2d_output/b2mn.dat
+  repo:
+    url: [email protected]:ProjectTorreyPines/SOLPSTestSamples.git
+    rev_lock: df499f1275428ec06175c48dc4af6ecbd5ec6117
+outs:
+- md5: 1af9d167996ea1a420f49e0d89c98e6d
+  size: 13925
+  hash: md5
+  path: b2mn.dat

sample/b2time.nc.dvc

@@ -0,0 +1,13 @@
+md5: b94876ee58c5d62734d4ee32c28bb0da
+frozen: true
+deps:
+- path: 
+    ITER_Lore_2296_00000/run_time_dep_EIRENE_jdl_to_ss_cont_sine2_2d_output/b2time.nc
+  repo:
+    url: [email protected]:ProjectTorreyPines/SOLPSTestSamples.git
+    rev_lock: df499f1275428ec06175c48dc4af6ecbd5ec6117
+outs:
+- md5: 778b3bb62b82f493c785373d872f6a1f
+  size: 13630424
+  hash: md5
+  path: b2time.nc

sample/g002296.00200.dvc

@@ -0,0 +1,12 @@
+md5: 1d967bf4b5e9d024a87a249859dd10a1
+frozen: true
+deps:
+- path: ITER_Lore_2296_00000/EQDSK/g002296.00200
+  repo:
+    url: [email protected]:ProjectTorreyPines/SOLPSTestSamples.git
+    rev_lock: df499f1275428ec06175c48dc4af6ecbd5ec6117
+outs:
+- md5: 5ab3f75addd8f1191a49e5243c96d23d
+  size: 2167720
+  hash: md5
+  path: g002296.00200

sample/gridspacedesc.yml

@@ -0,0 +1,196 @@
+identifier:                                                       # grid_ggd[#].Identifier properties
+  name: Sven                                                        
+  index: 1
+  description: This is a grid
+space:
+  1:                                                              # space_number
+    identifier:                                                   # grid_ggd[it].space[#].identifier properties
+      name: linear
+      index: 1
+      description: Linear
+    geometry_type:                                                # grid_dd[#].space[#].geometry_type properties
+      name:  "standard"                                           
+      index:  0                                                   # 0: standard, 1:Fourier, >1: Fourier with periodicity
+      description:  "trying to hold a b2/solps mesh here"         # Verbose descripition of space
+    coordinates_type:  [4, 3]                                     # r, z
+grid_subset:
+  1:
+    dimension: 0
+    identifier:
+      name: nodes
+      index: 1
+      description: All nodes (0D) belonging to the associated spaces, implicit declaration (no need to replicate the grid elements in the grid_subset structure). 
+  2:
+    dimension: 1
+    identifier:
+      name: faces
+      index: 2
+      description: All faces (1D) belonging to the associated spaces, implicit declaration (no need to replicate the grid elements in the grid_subset structure)
+  3:
+    dimension: 1
+    identifier:
+      name: x_aligned_faces
+      index: 3
+      description: All x-aligned (polidally aligned) faces
+  4:
+    dimension: 1
+    identifier:
+      name: y_aligned_faces
+      index: 4
+      description: All y-aligned (radially aligned) faces
+  5:
+    dimension: 2
+    identifier:
+      name: cells
+      index: 5
+      description: All cells (2D) belonging to the associated spaces, implicit declaration (no need to replicate the grid elements in the grid_subset structure) 
+  6:
+    dimension: 0
+    identifier:
+      name: x_points
+      index: 6
+      description: Nodes defining magnetic X-points (poloidal field nulls)
+  7:
+    dimension: 1
+    identifier:
+      name: core_cut
+      index: 7
+      description: Y-aligned faces (edges) inside the separatrix connecting to the active X-point
+  8:
+    dimension: 1
+    identifier:
+      name: PFR_cut
+      index: 8
+      description: Y-aligned faces (edges) inside the private flux region connecting to the active X-point
+  9:
+    dimension: 1
+    identifier:
+      name: outer_throat
+      index: 9
+      description: Y-aligned faces in the outer SOL connecting to the active X-point
+  10:
+    dimension: 1
+    identifier:
+      name: inner_throat
+      index: 10
+      description: Y-aligned faces in the inner SOL connecting to the active X-point
+  11:
+    dimension: 1
+    identifier:
+      name: outer_midplane
+      index: 11
+      description: Y-aligned faces connecting to the node closest to the outer midplane on the separatrix
+  12:
+    dimension: 1
+    identifier:
+      name: inner_midplane
+      index: 12
+      description: Y-aligned faces connecting to the node closest to the inner midplane on the separatrix
+  13:
+    dimension: 1
+    identifier:
+      name: outer_target
+      index: 13
+      description: Y-aligned faces defining the outer divertor target
+  14:
+    dimension: 1
+    identifier:
+      name: inner_target
+      index: 14
+      description: Y-aligned faces defining the inner divertor target
+  15:
+    dimension: 1
+    identifier:
+      name: core_boundary
+      index: 15
+      description: Innermost X-aligned faces
+  16:
+    dimension: 1
+    identifier:
+      name: separatrix
+      index: 16
+      description: X-aligned faces defining the active separatrix
+  17:
+    dimension: 1
+    identifier:
+      name: main_chamber_wall
+      index: 17
+      description: X-aligned faces defining the main chamber wall outside of the divertor regions
+  18:
+    dimension: 1
+    identifier:
+      name: outer_baffle
+      index: 18
+      description: X-aligned faces defining the chamber wall of the outer active divertor region
+  19:
+    dimension: 1
+    identifier:
+      name: inner_baffle
+      index: 19
+      description: X-aligned faces defining the chamber wall of the inner active divertor region
+  20:
+    dimension: 1
+    identifier:
+      name: outer_PFR_wall
+      index: 20
+      description: X-aligned faces defining the private flux region wall of the outer active divertor region
+  21:
+    dimension: 1
+    identifier:
+      name: inner_PFR_wall
+      index: 21
+      description: X-aligned faces defining the private flux region wall of the inner active divertor region
+  22:
+    dimension: 2
+    identifier:
+      name: core
+      index: 22
+      description: Cells (2D) inside the active separatrix in the same lobe as the magnetic axis
+  23:
+    dimension: 2
+    identifier:
+      name: sol
+      index: 23
+      description: Cells (2D) outside the active separatrix and outside the divertor regions
+  24:
+    dimension: 2
+    identifier:
+      name: outer_divertor
+      index: 24
+      description: Cells (2D) defining the (primary, if there are 2 X-points) outer divertor region
+  25:
+    dimension: 2
+    identifier:
+      name: inner_divertor
+      index: 25
+      description: Cells (2D) defining the (primary, if there are 2 X-points) inner divertor region
+  26:
+    dimension: 1
+    identifier:
+      name: core_sol
+      index: 26
+      description: X-aligned faces defining the part of the active separatrix separating core and SOL
+  27:
+    dimension: 0
+    identifier:
+      name: outer_mid_plane_separatrix
+      index: 101
+      description: Point on the active separatrix at the outer mid-plane
+  28:
+    dimension: 0
+    identifier:
+      name: inner_mid_plane_separatrix
+      index: 102
+      description: Point on the active separatrix at the inner mid-plane
+  29:
+    dimension: 0
+    identifier:
+      name: outer_target_separatrix
+      index: 103
+      description: Point on the active separatrix at the outer active divertor target plate
+  30:
+    dimension: 0
+    identifier:
+      name: inner_target_separatrix
+      index: 104
+      description: Point on the active separatrix at the inner active divertor target plate

src/SynthDiag.jl

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+module SynthDiag
+
+using OMAS: OMAS
+
+include("$(@__DIR__)/interferometer.jl")
+
+end # module SynthDiag