OpenFUSIONToolkit · logan-nc · Mar 11, 2026 · Mar 6, 2026 · Mar 6, 2026 · Mar 9, 2026
diff --git a/.claude/agents/clean-code-reviewer.md b/.claude/agents/clean-code-reviewer.md
@@ -93,6 +93,6 @@ For each issue, provide:
 - Follow the commit message format: `MODULE - TAG - Detailed message`
 - Be aware of 0-based to 1-based indexing conversions from Fortran
 - Ensure compatibility with the existing test structure in `test/`
-- Consider whether changes affect diagnostic outputs (jpec.h5, and legacy files gsec.h5, gse.h5, gsei.h5)
+- Consider whether changes affect diagnostic outputs or user-facing APIs
 
 Your goal is to help create code that a fusion physicist with moderate Julia experience can read, understand, and maintain confidently.
diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
@@ -5,7 +5,7 @@
 - Data flow: equilibrium setup → vacuum response → stability analysis (documented in [CLAUDE.md](CLAUDE.md)).
 
 ## Architecture and entry points
-- Main entry point: `JPEC.main()` in [src/JPEC.jl](src/JPEC.jl).
+- Main entry point: `GeneralizedPerturbedEquilibrium.main()` in [src/GeneralizedPerturbedEquilibrium.jl](src/GeneralizedPerturbedEquilibrium.jl).
 - Equilibrium: `setup_equilibrium(path|config)`; types in [src/Equilibrium](src/Equilibrium).
 - Vacuum: `compute_vacuum_response()`; code in [src/Vacuum](src/Vacuum).
 - ForceFreeStates (ideal MHD stability): types and functions in [src/ForceFreeStates](src/ForceFreeStates).
@@ -39,7 +39,7 @@
 - Many routines use 0-based indexing for historical consistency with the original GPEC Fortran code before converting to 1-based Julia indexing (see [CLAUDE.md](CLAUDE.md)).
 
 ## Configuration examples
-- Unified configuration: `jpec.toml` uses `[Equilibrium]`, `[Wall]`, `[ForceFreeStates]`, `[PerturbedEquilibrium]`, and `[ForcingTerms]` sections.
+- Unified configuration: `gpec.toml` uses `[Equilibrium]`, `[Wall]`, `[ForceFreeStates]`, `[PerturbedEquilibrium]`, and `[ForcingTerms]` sections.
 - Legacy configs (`equil.toml`, `dcon.toml`, `vac.in`) are deprecated.
 - Example configs in [examples/DIIID-like_ideal_example](examples/DIIID-like_ideal_example) and [examples/Solovev_ideal_example](examples/Solovev_ideal_example).
 

diff --git a/Project.toml b/Project.toml
@@ -17,6 +17,7 @@ JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+PlotlyJS = "f0f68f2c-4968-5e81-91da-67840de0976a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -41,6 +42,7 @@ JLD2 = "0.6.3"
 LinearAlgebra = "1"
 OrdinaryDiffEq = "6.102.0"
 Pkg = "1"
+PlotlyJS = "0.18.17"
 Plots = "1.40.15"
 Printf = "1"
 SparseArrays = "1"

diff --git a/docs/make.jl b/docs/make.jl
@@ -29,7 +29,8 @@ makedocs(;
             "Equilibrium" => "equilibrium.md",
             "Utilities" => "utilities.md",
             "Forcing Terms" => "forcing_terms.md",
-            "Perturbed Equilibrium" => "perturbed_equilibrium.md"
+            "Perturbed Equilibrium" => "perturbed_equilibrium.md",
+            "Analysis" => "analysis.md"
         ],
         "Citations" => "citations.md",
     ],

diff --git a/docs/src/analysis.md b/docs/src/analysis.md
@@ -0,0 +1,24 @@
+# Analysis Module
+
+The Analysis module provides post-processing and visualization utilities for GPEC simulation outputs.
+
+## Submodules
+
+- `ForceFreeStates`: Plotting functions for DCON-style ideal MHD stability results
+- `Equilibrium`: Plotting functions for equilibrium objects
+
+```@docs
+GeneralizedPerturbedEquilibrium.Analysis
+```
+
+## ForceFreeStates
+
+```@autodocs
+Modules = [GeneralizedPerturbedEquilibrium.Analysis.ForceFreeStates]
+```
+
+## Equilibrium
+
+```@autodocs
+Modules = [GeneralizedPerturbedEquilibrium.Analysis.Equilibrium]
+```
diff --git a/examples/DIIID-like_ideal_example/analyze_example.jl b/examples/DIIID-like_ideal_example/analyze_example.jl
@@ -0,0 +1,10 @@
+using Pkg;
+Pkg.activate(joinpath(@__DIR__, "../.."))
+using GeneralizedPerturbedEquilibrium, Plots, PlotlyJS
+using GeneralizedPerturbedEquilibrium: Analysis
+plotlyjs()
+
+h5path = joinpath(@__DIR__, "gpec.h5")
+p_modes = Analysis.ForceFreeStates.plot_mode_displacement(h5path; modes=1:5)
+p_eigen = Analysis.ForceFreeStates.plot_eigenmode_summary(h5path)
+p_stab = Analysis.ForceFreeStates.plot_stability_criterion(h5path)
diff --git a/examples/DIIID-like_ideal_example/run_and_analyze.ipynb b/examples/DIIID-like_ideal_example/run_and_analyze.ipynb
diff --git a/examples/DIIID-like_ideal_example/run_example.jl b/examples/DIIID-like_ideal_example/run_example.jl
@@ -0,0 +1,4 @@
+using Pkg;
+Pkg.activate(joinpath(@__DIR__, "../.."))
+using GeneralizedPerturbedEquilibrium
+GeneralizedPerturbedEquilibrium.main([dirname(@__FILE__)])
diff --git a/examples/Solovev_ideal_example/analyze_example.jl b/examples/Solovev_ideal_example/analyze_example.jl
@@ -0,0 +1,10 @@
+using Pkg;
+Pkg.activate(joinpath(@__DIR__, "../.."))
+using GeneralizedPerturbedEquilibrium, Plots, PlotlyJS
+using GeneralizedPerturbedEquilibrium: Analysis
+plotlyjs()
+
+h5path = joinpath(@__DIR__, "gpec.h5")
+p_modes = Analysis.ForceFreeStates.plot_mode_displacement(h5path; modes=1:5)
+p_eigen = Analysis.ForceFreeStates.plot_eigenmode_summary(h5path)
+p_stab = Analysis.ForceFreeStates.plot_stability_criterion(h5path)