Calin/imas integration

.github/copilot-instructions.md

@@ -1,19 +1,21 @@
-# Copilot instructions for JPEC
+# Copilot instructions for GPEC
 
 ## Project overview
-- JPEC is a Julia port of GPEC-style MHD equilibrium and stability analysis. Core modules live in [src](src): Utilities, Equilibrium, Vacuum, ForceFreeStates, ForcingTerms, PerturbedEquilibrium (see [CLAUDE.md](CLAUDE.md)).
+- GPEC is a Julia port of GPEC-style MHD equilibrium and stability analysis. Core modules live in [src](src): Utilities, Equilibrium, Vacuum, ForceFreeStates, ForcingTerms, PerturbedEquilibrium (see [CLAUDE.md](CLAUDE.md)).
 - Data flow: equilibrium setup → vacuum response → stability analysis (documented in [CLAUDE.md](CLAUDE.md)).
 
 ## Architecture and entry points
+- 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).
-- DCON stability: entry points in [src/DCON/Main.jl](src/DCON/Main.jl).
+- ForceFreeStates (ideal MHD stability): types and functions in [src/ForceFreeStates](src/ForceFreeStates).
+- PerturbedEquilibrium (plasma response): entry point in [src/PerturbedEquilibrium](src/PerturbedEquilibrium).
 
 ## Data flow and key structures
 - Equilibrium: TOML config → read equilibrium → solve → diagnostics (gse*.h5) when relevant.
 - Vacuum: initialize plasma/wall surfaces → compute response matrix → return wv, grri, xzpts.
 - Stability: equilibrium + vacuum response → integrate ODEs → compute energies.
-- Core types: `PlasmaEquilibrium` and `EquilibriumConfig` in [src/Equilibrium/EquilibriumTypes.jl](src/Equilibrium/EquilibriumTypes.jl); `DconControl` in [src/DCON/DconStructs.jl](src/DCON/DconStructs.jl).
+- Core types: `PlasmaEquilibrium` and `EquilibriumConfig` in [src/Equilibrium/EquilibriumTypes.jl](src/Equilibrium/EquilibriumTypes.jl); `ForceFreeStatesControl` and `ForceFreeStatesInternal` in [src/ForceFreeStates/ForceFreeStatesStructs.jl](src/ForceFreeStates/ForceFreeStatesStructs.jl).
 
 ## Tests and docs
 - Run all tests:
@@ -37,7 +39,8 @@
 - 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
-- TOML configs: `equil.toml` uses `[EQUIL_CONTROL]` and `[EQUIL_OUTPUT]`; `dcon.toml` uses `[DCON_CONTROL]` and `[WALL]`.
+- 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).
 
 ## Development tips

.github/workflows/test.yaml

@@ -11,8 +11,18 @@ on:
       - develop
 
 jobs:
-  runtests:
-    runs-on: ubuntu-latest
+  test:
+    name: runtests ${{ matrix.version }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - 'lts' # long-term support (currently 1.10)
+          - '1.11'
+          - '1.x'  # latest (currently 1.12)
+        os:
+          - ubuntu-latest
 
     steps:
       - name: Checkout repository
@@ -21,7 +31,7 @@ jobs:
       - name: Set up Julia
         uses: julia-actions/setup-julia@v2
         with:
-          version: '1.11'
+          version: ${{ matrix.version }}
 
       - name: Cache Julia packages
         uses: julia-actions/cache@v2

CLAUDE.md

@@ -4,19 +4,19 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 ## Overview
 
-JPEC (Julia Perturbed Equilibrium Code) is a comprehensive Julia implementation of GPEC-style (Generalized Perturbed Equilibrium Code) MHD analysis for fusion plasmas. The code performs equilibrium reconstruction, ideal MHD stability analysis, and perturbed equilibrium calculations including plasma response and singular surface coupling diagnostics.
+GPEC (Generalized Perturbed Equilibrium Code, Julia implementation) is a comprehensive Julia reimplementation of the GPEC suite for MHD analysis of fusion plasmas. The code performs equilibrium reconstruction, ideal MHD stability analysis, and perturbed equilibrium calculations including plasma response and singular surface coupling diagnostics.
 
-**Relationship to Fortran GPEC**: JPEC is an evolution of the Fortran GPEC code suite, available at https://github.com/PrincetonUniversity/GPEC. When users reference "GPEC", "the Fortran code", or "the original GPEC", they are referring to this Fortran codebase. JPEC reimplements and extends GPEC's functionality in Julia with improved performance and maintainability.
+**Relationship to Fortran GPEC**: This Julia GPEC is an evolution of the Fortran GPEC code suite, available at https://github.com/PrincetonUniversity/GPEC. When users reference "the Fortran code", "the original GPEC", or "Fortran GPEC", they are referring to that Fortran codebase. This Julia implementation reimplements and extends GPEC's functionality with improved performance and maintainability.
 
 **Local GPEC Repository**: For code conversion or comparison with the original Fortran implementation, check for a local GPEC repository at `~/Code/gpec`. If not found at this location, ask the user for the correct path.
 
-JPEC is implemented in Julia. References to “Fortran GPEC” or “legacy VACUUM” refer to the original upstream codebase, not a runtime dependency of JPEC.
+This codebase is implemented in Julia. References to “Fortran GPEC” or “legacy VACUUM” refer to the original upstream Fortran codebase, not a runtime dependency of this Julia implementation.
 
 **Current Development Focus**: The `perturbed_equilibrium` branch is implementing full GPEC-style perturbed equilibrium functionality, including singular coupling analysis, island formation diagnostics, and mode-space field reconstruction.
 
 ## Key References
 
-**IMPORTANT**: The papers in `docs/resources/` provide the theoretical foundation for JPEC's algorithms and should be referenced to understand what the code is doing. **Citing equations from these papers in code comments and annotations is strongly encouraged** to maintain traceability between theory and implementation.
+**IMPORTANT**: The papers in `docs/resources/` provide the theoretical foundation for GPEC's algorithms and should be referenced to understand what the code is doing. **Citing equations from these papers in code comments and annotations is strongly encouraged** to maintain traceability between theory and implementation.
 
 ### Vacuum Module
 
@@ -76,9 +76,9 @@ The PerturbedEquilibrium module implements GPEC-style perturbed equilibrium calc
   - Published: Physics of Plasmas **24**, 032505 (2017)
   - Describes: Self-consistent coupling with neoclassical effects
 
-### Resistive DCON Module (Future Work)
+### Resistive MHD Stability Analysis (Future Work)
 
-JPEC will eventually implement resistive MHD stability analysis based on:
+GPEC will eventually implement resistive MHD stability analysis based on:
 
 - **Glasser (2016)**: "Computation of resistive instabilities by matched asymptotic expansions"
   - Location: `docs/resources/2016-Glasser-Computation_of_resistive_instabilities_by_matched_asymptotic_expansions-compressed.pdf`
@@ -97,7 +97,7 @@ JPEC will eventually implement resistive MHD stability analysis based on:
 
 ### PENTRC Module (Future Work)
 
-JPEC will eventually port the PENTRC (Perturbed Equilibrium Neoclassical Toroidal viscosity in Realistic geometry Code) functionality from the Fortran GPEC suite. This is described in:
+GPEC will eventually port the PENTRC (Perturbed Equilibrium Neoclassical Toroidal viscosity in Realistic geometry Code) functionality from the Fortran GPEC suite. This is described in:
 
 - **Logan & Park (2013)**: "Neoclassical toroidal viscosity in perturbed equilibria with general tokamak geometry"
   - Location: `docs/resources/2013-Logan-Neoclassical_toroidal_viscosity_in_perturbed_equilibria_with_general_tokamak_geometry.pdf`
@@ -141,7 +141,7 @@ julia --project=. test/runtests.jl test/runtests_solovev.jl
 # Build documentation locally
 julia --project=. build_docs_local.jl
 
-# Documentation hosted at: https://openfusiontoolkit.github.io/JPEC/dev/
+# Documentation hosted at: https://openfusiontoolkit.github.io/GPEC/dev/
 ```
 
 ### Development with Revise
@@ -150,7 +150,7 @@ For faster recompilation during development, use Revise.jl (installed in global
 
 ```julia
 using Revise
-using JPEC
+using GeneralizedPerturbedEquilibrium
 ```
 
 ### Benchmarking
@@ -205,7 +205,7 @@ julia benchmarks/benchmark_git_branches.jl \
 
 ### Computational Workflow
 
-JPEC follows a three-stage analysis pipeline:
+GPEC follows a three-stage analysis pipeline:
 
 1. **Equilibrium** → Solve Grad-Shafranov equation, compute flux surfaces, safety factor q-profile
 2. **Stability Analysis** → Solve ideal MHD eigenvalue problem (DCON-style), identify singular surfaces
@@ -215,7 +215,7 @@ This workflow is reflected in the modular structure and data flow.
 
 ### Module Structure
 
-JPEC consists of **seven main modules** organized in `src/`:
+GPEC consists of **seven main modules** organized in `src/`:
 
 #### Foundation Modules
 
@@ -299,9 +299,9 @@ JPEC consists of **seven main modules** organized in `src/`:
 
 ### Configuration
 
-**Unified Configuration File**: `jpec.toml`
+**Unified Configuration File**: `gpec.toml`
 
-All JPEC modules are configured via a single TOML file with the following sections:
+All GPEC modules are configured via a single TOML file with the following sections:
 
 - `[Equilibrium]` - Equilibrium solver settings
 - `[Wall]` - Wall geometry and vacuum region
@@ -311,20 +311,20 @@ All JPEC modules are configured via a single TOML file with the following sectio
 
 Key parameters:
 - `force_termination` - Set to `true` to exit after equilibrium/stability (skip perturbed equilibrium)
-- `output_file` - Output filename (default: `jpec.h5`)
+- `output_file` - Output filename (default: `gpec.h5`)
 
 Example configuration files are provided in:
-- `examples/Solovev_ideal_example/jpec.toml`
-- `examples/DIIID-like_ideal_example/jpec.toml`
+- `examples/Solovev_ideal_example/gpec.toml`
+- `examples/DIIID-like_ideal_example/gpec.toml`
 
 **Note**: Legacy configuration files (`equil.toml`, `vac.in`) are deprecated.
 
 ### Data Flow
 
-The complete JPEC analysis pipeline:
+The complete GPEC analysis pipeline:
 
 1. **Equilibrium Setup**:
-   - `setup_equilibrium(config)` reads configuration from `jpec.toml`
+   - `setup_equilibrium(config)` reads configuration from `gpec.toml`
    - Parses equilibrium data (EFIT, CHEASE, or analytical)
    - Runs Grad-Shafranov solver (direct or inverse)
    - Computes global parameters: q-profile, pressure, current density, β
@@ -357,7 +357,7 @@ The complete JPEC analysis pipeline:
    - Outputs: `PerturbedEquilibriumState` with response fields and diagnostics
 
 5. **Output**:
-   - All results saved to single HDF5 file (default: `jpec.h5`)
+   - All results saved to single HDF5 file (default: `gpec.h5`)
    - HDF5 groups: `input/`, `info/`, `equil/`, `splines/`, `locstab/`, `integration/`, `singular/`, `vacuum/`, and perturbed equilibrium data
 
 ### Key Data Structures
@@ -390,7 +390,7 @@ The complete JPEC analysis pipeline:
 ### Module Dependencies
 
 ```
-JPEC
+GeneralizedPerturbedEquilibrium
 ├── Splines (foundation)
 ├── Utilities (shared tools)
 │   └── FourierTransforms
@@ -440,12 +440,12 @@ This format is used for compiling release notes, so tags should be human-readabl
 - **No step numbering in code comments** - Avoid annotations like "Step 1: do this" followed by "Step 2: do that". These get out of sync as code changes. Just describe the action without numbering.
 
 ### Output Files
-- **Default output**: `jpec.h5` (previously `euler.h5` in older versions)
-- **Legacy diagnostic files**: When modifying equilibrium code, remember that older versions output `gsec.h5`, `gse.h5`, `gsei.h5` - these are now consolidated into `jpec.h5`
+- **Default output**: `gpec.h5` (previously `euler.h5` in older versions)
+- **Legacy diagnostic files**: When modifying equilibrium code, remember that older versions output `gsec.h5`, `gse.h5`, `gsei.h5` - these are now consolidated into `gpec.h5`
 
 ### Current Development Priorities
 - **Perturbed equilibrium module**: Active development of GPEC-style singular coupling analysis
-- **Configuration**: All settings now in unified `jpec.toml` file
+- **Configuration**: All settings now in unified `gpec.toml` file
 
 ### Performance
 - Pure Julia implementations are available for all major components and offer comparable or better performance than Fortran

Project.toml

@@ -1,24 +1,36 @@
 name = "JPEC"
 uuid = "462872dd-e066-4d2e-b993-6468b5239634"
 license = "MIT"
-authors = ["Matthew Pharr <matthewcpharr@gmail.com>", "Rithik Banerjee <rb3736@columbia.edu>", "Jaebeom Cho <aspire1019@snu.ac.kr>", "Jacob Halpern <jmh2363@columbia.edu>"]
 version = "0.1.0"
+authors = ["Matthew Pharr <matthewcpharr@gmail.com>", "Rithik Banerjee <rb3736@columbia.edu>", "Jaebeom Cho <aspire1019@snu.ac.kr>", "Jacob Halpern <jmh2363@columbia.edu>"]
 
 [deps]
+AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 AdaptiveArrayPools = "4f381ef7-9af0-4cbe-99d4-cf36d7b0f233"
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
+EFIT = "cda752c5-6b03-55a3-9e33-132a441b0c17"
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
 FastInterpolations = "9ea80cae-fc13-4c00-8066-6eaedb12f34b"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
+IMASdd = "c5a45a97-b3f9-491c-b9a7-aa88c3bc0067"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -27,23 +39,41 @@ TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
-AdaptiveArrayPools = "0.2.0"
+AbstractTrees = "0.4.5"
+AdaptiveArrayPools = "0.1.2"
+BenchmarkTools = "1.6.3"
+DataFrames = "1.8.1"
 DelimitedFiles = "1.9.1"
 DiffEqCallbacks = "4.9.0"
+Distributions = "0.25.123"
 Documenter = "1.14.1"
+DynamicalSystems = "3.6.7"
+EFIT = "1.2.5"
 FFTW = "1.9.0"
 FastGaussQuadrature = "1.1.0"
 FastInterpolations = ">=0.2.13"
+FileIO = "1.18.0"
 HDF5 = "0.17.2"
+IJulia = "1.34.2"
+IMASdd = ">=8"
 JLD2 = "0.6.3"
+LaTeXStrings = "1.4.0"
 LinearAlgebra = "1.11.0"
+Measurements = "2.14.1"
 OrdinaryDiffEq = "6.102.0"
 Pkg = "1.11.0"
 Plots = "1.40.15"
 Printf = "1.11.0"
+PyPlot = "2.11.6"
 Roots = "2.2.13"
 SpecialFunctions = "2.5.1"
 StaticArrays = "1.9.15"
-Statistics = "1.11.0"
+Statistics = "1.11.1"
 TOML = "1.0.3"
 Test = "1.11.0"
+
+[extras]
+EFIT = "cda752c5-6b03-55a3-9e33-132a441b0c17"
+
+[targets]
+test = ["EFIT"]