Merge branch 'develop' into claude/julia-tests-github-workflows-9axlpa

Author: matt-pharr

.claude/agents/README.md

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+# Agent Team
+
+This repo ships a small team of specialized Claude Code subagents in `.claude/agents/`. They are **stateless reviewers**: each runs in its own context, is handed a specific deliverable, and returns its findings to the main session — they do not talk to each other. **The main session is the integrator.** You drive them; you do not delegate the whole task and walk away.
+
+**Invoke an agent by name** for the matching job — e.g. *"review this with the fortran-physics-reviewer"* or *"run the regression-guardian against develop"*. Do **not** "consult all the agents" reflexively: that burns the token budget and produces noise. Pick the agent whose job matches the change.
+
+## Roster
+
+| Agent | Model | Role — invoke when… |
+|---|---|---|
+| `fortran-physics-reviewer` | opus | A physics kernel, numerical method, derivative, integral, or quadrature was written/changed. Audits fidelity to the reference papers and the Fortran GPEC source. Carries project memory (correspondence map + per-domain audit checklists for KineticForces and InnerLayer), so its reviews compound — let it record findings. |
+| `clean-code-reviewer` | opus | A logical chunk of code is ready and you want readability/maintainability review for a fusion physicist audience (naming, magic numbers, docstrings, structure). |
+| `julia-performance-optimizer` | opus | A specific function/hotspot is slow or perf-sensitive (type stability, allocations, hot-loop work in ODE/kinetic/resistive-layer paths). |
+| `fast-interpolations-optimizer` | opus | Code uses FastInterpolations.jl and you want allocation-free / optimal-search-type review. |
+| `regression-guardian` | sonnet | **Before merging any substantive change** (mandatory per the Regression Harness policy — see `docs/development/regression-harness.md`), or when you need to know whether a tracked numerical quantity moved. Runs the harness, reports the table, flags non-OK rows, proposes new cases. |
+
+## Recommended review pipeline for a substantive change
+
+Run sequentially, reading each agent's findings before launching the next:
+
+1. **`fortran-physics-reviewer`** — physics fidelity first; a fast-but-wrong result is worthless.
+2. **`clean-code-reviewer`** — readability and maintainability.
+3. **`julia-performance-optimizer`** and/or **`fast-interpolations-optimizer`** — only if the change is performance-relevant.
+4. **`regression-guardian`** — always, last, before merge. Confirms the numbers didn't silently move.
+
+Not every change needs all four. A docs-only change needs none; a pure perf refactor still needs the physics reviewer (to confirm no numerical change) and the regression-guardian.
+
+## Budget
+
+Every consultation is bounded — see **Subagent Consultations** in `/CLAUDE.md` (≤30 tool uses, ≤10 min, one concrete deliverable, never re-launch a runaway). The agent bodies now self-enforce this, but state the budget in your prompt anyway and always hand the agent the specific file paths to act on.

CLAUDE.md

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+# Architecture
+
+## Computational Workflow
+
+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
+3. **Perturbed Equilibrium** → Compute plasma response to external fields, analyze singular coupling and island formation
+
+This workflow is reflected in the modular structure and data flow.
+
+## Module Structure
+
+GPEC consists of **seven main modules** organized in `src/`:
+
+### Foundation Modules
+
+1. **Splines** (`src/Splines/`) - Numerical interpolation library
+   - `CubicSpline.jl` - 1D cubic spline interpolation
+   - `BicubicSpline.jl` - 2D bicubic spline interpolation
+   - `FourierSpline.jl` - Fourier-based spline interpolation
+   - Status: Mature, pure Julia implementation
+
+2. **Utilities** (`src/Utilities/`) - Shared computational tools
+   - `FourierTransforms.jl` - Efficient Fourier transform utilities with pre-computed basis functions
+   - Provides type-stable functor pattern for repeated transforms
+   - Used by Vacuum and PerturbedEquilibrium modules
+
+### Core Physics Modules
+
+3. **Equilibrium** (`src/Equilibrium/`) - MHD equilibrium solvers
+   - Main entry point: `setup_equilibrium(path)` or `setup_equilibrium(config)`
+   - Supports multiple equilibrium types:
+     - `efit` - EFIT g-file format
+     - `chease`, `chease2` - CHEASE equilibrium code formats
+     - `lar` - Large Aspect Ratio analytical model
+     - `sol` - Solovev analytical equilibrium
+   - Key files:
+     - `EquilibriumTypes.jl` - Core data structures
+     - `ReadEquilibrium.jl` - Parsing equilibrium files
+     - `DirectEquilibrium.jl` - Direct Grad-Shafranov solver
+     - `InverseEquilibrium.jl` - Inverse equilibrium solver
+     - `AnalyticEquilibrium.jl` - Analytical solutions
+   - Status: Stable and feature-complete
+
+4. **Vacuum** (`src/Vacuum/`) - Vacuum field calculations and Green's functions
+   - Computes vacuum response matrices for ideal MHD analysis
+   - Calculates both **interior** (grri) and **exterior** (grre) Green's functions
+   - Main functions:
+     - `compute_vacuum_response()` - Pure Julia implementation
+   - Key files:
+     - `VacuumStructs.jl` - Data structures
+     - `VacuumInternals.jl` - Core algorithms
+     - `VacuumFromEquilibrium.jl` - Integration with equilibrium data
+   - Status: **Pure Julia implementation complete and available**
+
+5. **ForceFreeStates** (`src/ForceFreeStates/`) - Ideal MHD stability analysis (DCON-style)
+   - Solves ideal MHD eigenvalue problem with force-free boundary conditions
+   - Identifies singular surfaces where ξ·∇ψ = 0
+   - Key files:
+     - `ForceFreeStatesStructs.jl` - Core data structures
+     - `Ode.jl` - ODE solver for Euler-Lagrange equations
+     - `Sing.jl` - Singular point handling and layer analysis
+     - `Fourfit.jl` - Fourier fitting routines
+     - `FixedBoundaryStability.jl` - Fixed boundary analysis
+     - `Free.jl` - Free boundary stability
+     - `Ballooning.jl` - Local stability scan: Mercier D_I, resistive interchange D_R, and high-n ballooning Δ' (s–α). Replaces the former standalone `Mercier.jl`.
+   - Status: Stable, core DCON functionality implemented
+
+### Perturbed Equilibrium Modules
+
+6. **ForcingTerms** (`src/ForcingTerms/`) - External field specification
+   - Handles external magnetic field perturbations (coils, RMP, etc.)
+   - Supports ASCII and HDF5 forcing data formats
+   - `ForcingMode` data structure specifies amplitude and phase for each (m,n) component
+   - Status: Complete and functional
+
+7. **PerturbedEquilibrium** (`src/PerturbedEquilibrium/`) - **GPEC-style plasma response**
+   - Computes plasma response to external forcing
+   - Calculates singular coupling metrics at rational surfaces
+   - Key files:
+     - `PerturbedEquilibrium.jl` - Main entry point
+     - `PerturbedEquilibriumStructs.jl` - Data structures
+     - `ResponseMatrices.jl` - Permeability matrix calculation
+     - `FieldReconstruction.jl` - Mode-space field reconstruction
+     - `Response.jl` - Plasma response computation
+     - `SingularCoupling.jl` - **Singular surface analysis** including:
+       - Delta prime (Δ') tearing stability parameter
+       - Resonant flux and currents at rational surfaces
+       - Island half-widths and Chirikov parameters
+       - Green's functions at interior flux surfaces
+       - Surface inductance for singular surfaces
+     - `Utils.jl` - Helper functions
+   - Status: Core plasma response and singular coupling calculations implemented; active area of development
+
+## Configuration
+
+**Unified Configuration File**: `gpec.toml`
+
+All GPEC modules are configured via a single TOML file with the following sections:
+
+- `[Equilibrium]` - Equilibrium solver settings
+- `[Wall]` - Wall geometry and vacuum region
+- `[ForceFreeStates]` - Stability analysis parameters
+- `[PerturbedEquilibrium]` - Perturbed equilibrium settings
+- `[ForcingTerms]` - External field specification
+
+Key parameters:
+- `force_termination` - Set to `true` to exit after equilibrium/stability (skip perturbed equilibrium)
+- `output_file` - Output filename (default: `gpec.h5`)
+
+Example configuration files are provided in:
+- `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 GPEC analysis pipeline:
+
+1. **Equilibrium Setup**:
+   - `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
+   - Creates bicubic splines for (ψ, θ, φ) → (R, Z, Φ) mapping
+   - Outputs: `PlasmaEquilibrium` object
+
+2. **Vacuum Response**:
+   - Initialize plasma and wall surfaces from equilibrium
+   - Compute vacuum response matrices (wv, grri, grre)
+   - Calculate both interior and exterior Green's functions
+   - Pure Julia implementation
+
+3. **Stability Analysis** (ForceFreeStates):
+   - Solve ideal MHD Euler-Lagrange equations via ODE integration
+   - Identify singular surfaces where q = m/n
+   - Compute Δ' at each singular surface
+   - Calculate potential and kinetic energies
+   - Check Mercier and ballooning stability criteria
+   - Outputs: Eigenmode structure ξ(ψ,θ)
+
+4. **Perturbed Equilibrium** (GPEC-style):
+   - Load external forcing data (coil fields, RMP configuration)
+   - Compute plasma response using permeability matrices
+   - Reconstruct mode-space fields (ξ_modes, b_modes)
+   - Calculate singular coupling metrics at rational surfaces:
+     - Δ' (tearing stability parameter)
+     - Island half-widths
+     - Chirikov overlap parameter
+     - Resonant flux and currents
+   - Outputs: `PerturbedEquilibriumState` with response fields and diagnostics
+
+5. **Output**:
+   - 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
+
+### Equilibrium
+- `PlasmaEquilibrium` - Main equilibrium container with bicubic splines (rzphi), 1D profiles (sq), and global parameters
+- `EquilibriumConfig` - Configuration loaded from TOML files
+
+### Vacuum
+- `VacuumInput` - Input parameters for vacuum calculations
+- `WallShapeSettings` - Wall geometry configuration
+
+### Stability
+- `SingType` - Singular surface data including:
+  - Rational surface location (ψ, q = m/n)
+  - Δ' (tearing stability parameter)
+  - Eigenmode structure at singular surface
+  - Green's functions (grri, grre) at interior singular surfaces
+  - Surface inductance
+
+### Perturbed Equilibrium
+- `PerturbedEquilibriumControl` - User-facing TOML configuration parameters
+- `PerturbedEquilibriumInternal` - Internal state with mode arrays
+- `PerturbedEquilibriumState` - Results including:
+  - Response fields (ξ_modes, b_modes) in mode space
+  - Singular coupling matrices [msing × numpert_total]
+  - Island diagnostics (half-widths, Chirikov parameters)
+- `ForcingMode` - External forcing specification (m, n, amplitude, phase)
+
+## Module Dependencies
+
+```
+GeneralizedPerturbedEquilibrium
+├── Splines (foundation)
+├── Utilities (shared tools)
+│   └── FourierTransforms
+├── Equilibrium (uses Splines)
+├── Vacuum (uses Splines, Equilibrium, Utilities)
+├── ForcingTerms (data I/O)
+├── ForceFreeStates (uses Equilibrium, Vacuum, Splines)
+└── PerturbedEquilibrium (uses ForceFreeStates, Vacuum, ForcingTerms, Utilities)
+```

docs/development/architecture.md

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+# Benchmarking
+
+Use the generic benchmarking tool at `benchmarks/benchmark_git_branches.jl` to compare performance between branches or commits.
+
+**Tool usage:**
+
+```bash
+# Compare feature branch against develop
+julia benchmarks/benchmark_git_branches.jl \
+  --example examples/DIIID-like_ideal_example \
+  --branch1 develop \
+  --branch2 feature-branch
+
+# Compare specific commits
+julia benchmarks/benchmark_git_branches.jl \
+  --example examples/DIIID-like_ideal_example \
+  --commit1 abc123 \
+  --commit2 def456
+
+# Compare current develop vs develop from 1 month ago
+julia benchmarks/benchmark_git_branches.jl \
+  --example examples/DIIID-like_ideal_example \
+  --branch1 develop \
+  --commit1 HEAD~10 \
+  --branch2 develop
+```
+
+**Default benchmark case:** `examples/DIIID-like_ideal_example`
+
+**Reported metrics:**
+1. **Eigenmode energy (`et[1]`)** - First eigenvalue; verifies calculation correctness
+2. **Integration steps** - Total ODE solver steps
+3. **Runtime (warmed)** - Wall-clock time averaged over multiple warm runs (JIT warmup handled automatically)
+4. **Commit hash** - Git commit of code tested
+
+**The tool automatically:**
+- Handles JIT warmup (runs example 3 times, averages last 2)
+- Switches between branches/commits
+- Stashes uncommitted changes if necessary
+- Restores original branch when done
+- Reports comparison with percentage differences
+
+**Important notes:**
+- Working directory should be clean or changes will be stashed during branch switching
+- Tool requires HDF5.jl for reading `gpec.h5` output
+- Each benchmark run takes several minutes per branch (includes compilation + warm runs)
+
+**Benchmark script conventions:**
+- Benchmark scripts must reference input data from `examples/` (e.g., `joinpath(@__DIR__, "..", "examples", "DIIID-like_ideal_example")`). Never duplicate example inputs into `benchmarks/`.
+- If a benchmark needs modified TOML settings or a parameter scan, copy inputs to a temporary local directory at runtime — do not commit these copies.
+- All outputs (figures, CSVs, HDF5 files) must be saved into `benchmarks/` itself (or a self-described subdirectory within it, e.g., `benchmarks/coil_scan_results/`). Output files are not committed.

docs/development/benchmarking.md

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+# Git Workflow
+
+This project uses GitFlow (http://nvie.com/posts/a-successful-git-branching-model):
+
+- Two permanent branches: `main` and `develop`
+- `main` is updated only at release-ready stages via pull request from `develop`
+- `develop` is the integration branch — all feature branches merge here
+
+**IMPORTANT**: All development must be done on feature branches. No commits should be made directly to `develop` or `main`. Always create a branch from `develop`, do all work there, and open a pull request back into `develop`.
+
+## Branch Naming
+
+Branches use a typed prefix and a lowercase hyphen-separated description:
+
+| Prefix | Purpose | Branches from | Merges into |
+|---|---|---|---|
+| `feature/` | New functionality | `develop` | `develop` |
+| `bugfix/` | Non-critical bug fixes | `develop` | `develop` |
+| `hotfix/` | Critical production fix | `main` | `main` + `develop` |
+| `performance/` | Performance improvements | `develop` | `develop` |
+| `refactor/` | Refactoring without behavior change | `develop` | `develop` |
+| `docs/` | Documentation only | `develop` | `develop` |
+| `test/` | Test additions/improvements | `develop` | `develop` |
+| `experiment/` | Exploratory work, may not merge | `develop` | — |
+
+Examples: `bugfix/sing-lim-bounds-error`, `feature/kinetic-damping`, `performance/green-function-prefactor`
+
+Author-named branches (e.g. `jmh/`, `nlogan/`) are not used — git history already records authorship on every commit.
+
+## Hotfix Workflow
+
+Hotfixes address critical bugs in production (`main`) that cannot wait for the next release cycle:
+
+1. Branch `hotfix/description` from the current tagged `main` commit
+2. Fix the bug with one or more commits
+3. Merge into `main` via pull request; tag the merge commit with a new patch version (e.g. `v0.1.1`)
+4. Merge the same branch into `develop` so the fix is not lost in the next release
+
+## Versioning
+
+This project uses semantic versioning: `v{major}.{minor}.{patch}`
+
+- **major**: breaking API or file-format changes
+- **minor**: new features, backward-compatible
+- **patch**: bug fixes (typically via hotfix branches)
+
+Tags are applied to merge commits on `main`.
+
+## Commit Message Format
+
+```
+CODE - TAG - Detailed message
+```
+
+Where:
+- **CODE**: Module name (EQUIL, VAC, VACUUM, ForceFreeStates, PERTURBED EQUILIBRIUM, etc.)
+- **TAG**: Type descriptor (WIP, MINOR, IMPROVEMENT, BUG FIX, NEW FEATURE, REFACTOR, CLEANUP, etc.)
+
+Examples:
+- `PERTURBED EQUILIBRIUM - NEW FEATURE - Implement singular coupling diagnostics`
+- `VAC - IMPROVEMENT - Add dual Green's function computation`
+- `EQUIL - BUG FIX - Fixed separatrix finding for high kappa`
+- `ForceFreeStates - REFACTOR - Unified singular surface data structure`
+
+This format is used for compiling release notes, so tags should be human-readable and descriptive.
+
+## Merge Conflict Resolution Policy
+
+- When resolving git conflicts, do not simply accept one side.
+- Analyze what each side changed and WHY before producing a resolution.
+- Produce a merged version incorporating both sets of changes.
+- If both sides renamed the same symbol differently, prefer the current (ours) branch convention.
+- When a rename on one side conflicts with a logic change on the other, apply the logic change using the renamed symbol.
+- If a conflict involves changes to numerical parameters (tolerances, boundary conditions, grid sizes), flag for human review rather than guessing.
+- Flag any conflicts where the combination is ambiguous for human review.

docs/development/git-workflow.md

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+# Plotting Conventions
+
+## Spectrum plots
+
+Any plot with discrete mode numbers m or n on the x-axis must use `seriestype=:steppre` with a `step_series` helper that pads zeros on both ends. Pattern from `benchmarks/benchmark_coil_ForcingTerms_against_fortran.jl`:
+
+```julia
+function step_series(m_vals, amps)
+    m_ext   = [m_vals[1] - 1; m_vals; m_vals[end] + 1]
+    amp_ext = [0.0; amps; 0.0]
+    return m_ext, amp_ext
+end
+# Usage:
+m_ext, a_ext = step_series(m_vals, amplitudes)
+plot!(p, m_ext, a_ext; seriestype=:steppre, lw=2, label="...")
+```
+
+## Figures and plots
+
+- Always print the full absolute path of any figure or plot file you save, so the user can open it directly without searching the filesystem.
+- Always check that axis labels are not clipped. In Plots.jl there is no `tight_layout()` equivalent; use explicit margins instead: `left_margin=12Plots.mm`, `bottom_margin=4Plots.mm`, etc. When in doubt, add a generous `left_margin` to prevent y-axis label cutoff.