matt-pharr · Oct 27, 2026 · Oct 23, 2026 · Oct 24, 2026 · Oct 24, 2026 · Oct 26, 2026
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -77,5 +77,5 @@ repos:
       - id: toml-no-deprecated-keys
         name: 'TOML conventions: no deprecated config keys'
         language: pygrep
-        entry: '^(mer_flag|force_wv_symmetry|ode_flag|cyl_flag|mat_flag|reform_eq_with_psilim|use_riccati|use_parallel|parallel_threads|populate_dense_xi|gal_flag|nstep|diagnose_ca|diagnose|ksing|power_bp|power_b|power_r|power_rc|use_galgrid|local_stability_flag)\s*='
+        entry: '^(mer_flag|force_wv_symmetry|ode_flag|cyl_flag|mat_flag|reform_eq_with_psilim|use_riccati|use_parallel|parallel_threads|populate_dense_xi|gal_flag|nstep|diagnose_ca|diagnose|ksing|power_bp|power_b|power_r|power_rc|use_galgrid|moment|eq_out|theta_out|xlmda_out|eqpsi_out|save_records|gpec_file|fnml_flag|ellip_flag|diag_flag|force_xialpha|fixed_boundary|output_eigenmodes|filter_modes|singular_point_method|local_stability_flag)\s*='
         files: ^(examples/.*\.toml|test/test_data/.*\.toml)$
diff --git a/benchmarks/benchmark_against_fortran_run.jl b/benchmarks/benchmark_against_fortran_run.jl
@@ -440,7 +440,6 @@ function write_gpec_toml_coil(
         end
         println(io)
         println(io, "[PerturbedEquilibrium]")
-        println(io, "fixed_boundary            = false")
         println(io, "compute_response          = true")
         println(io, "compute_singular_coupling = true")
         println(io, "verbose                   = true")
@@ -493,7 +492,6 @@ function write_gpec_toml_file(
         println(io, "forcing_data_format = \"ascii\"")
         println(io)
         println(io, "[PerturbedEquilibrium]")
-        println(io, "fixed_boundary            = false")
         println(io, "compute_response          = true")
         println(io, "compute_singular_coupling = true")
         println(io, "verbose                   = true")

diff --git a/docs/development/hdf5-conventions.md b/docs/development/hdf5-conventions.md
@@ -7,7 +7,7 @@ Conventions for the structure and naming of the `gpec.h5` output file. Every wri
 **The schema must be intuitive to a plasma physicist who is not a developer of this code.** The top level largely mirrors the TOML sections / major `src/` modules — which are themselves organized along physics lines — but **physics intuition wins whenever the two diverge**. Worked examples of that rule:
 
 - All per-rational-surface stability results consolidate under `SingularSurfaces/`, regardless of which algorithm produced them: the GGJ coefficients sit beside the Δ′/PEST-3 matching results, and the Riccati BVP and the Galerkin outer-region solve write the *same* `Delta_prime_matrix`/`Delta_prime_raw`/`Delta_coil`/`pest3_*` paths rather than each owning a producer-named subgroup.
-- `EulerLagrangeMatrices` over a bare `Matrices` — group names must say what the data *is*, not which array it came from. Same reasoning renamed `records/` → `EnergyIntegrals/` and `matrices_<method>/` → `KineticMatrices/`.
+- `EulerLagrangeMatrices` over a bare `Matrices` — group names must say what the data *is*, not which array it came from. Same reasoning renamed `matrices_<method>/` → `KineticMatrices/`.
 
 Physics-topic groups elevated to top level (rather than nested under their producer): `Info/`, `Input/`, `SingularSurfaces/`, `LocalStability/`, `SurfaceGeometries/`.
 
@@ -44,7 +44,7 @@ Top level (11 groups):
 | `LocalStability/` | Mercier `D_I`, resistive interchange `D_R`, `ballooning_Delta_prime` on `psi`; the ballooning α boundary on `ballooning_psi` |
 | `SingularSurfaces/` | Per-rational-surface data: `rational_psi`/`rational_q`/`rational_m`/`rational_n`, GGJ coefficients, `Delta_prime_matrix`/`Delta_prime_raw`/`Delta_coil`/`pest3_A`/`pest3_B`/`pest3_Gamma` (Riccati or Galerkin alike), the inner-layer `Match/` results, `Kinetic/` |
 | `PerturbedEquilibrium/` | `ForcingModes/`, `Response/`, `ResponseMatrices/`, `SingularCoupling/`, `Energies/`, `TorqueResponse/` (kinetic forward solves: ψ-resolved `T_xe`, `T_source`), control-surface spectra |
-| `KineticForces/` | `<method>/` (torque/energy profiles, `dTdpsi_ell` resolved by bounce harmonic on the `ell` scale, `EnergyIntegrals/`, `KineticMatrices/`); multi-ion runs add `PerSpecies/<species>/<method>/` with the same per-method layout, summing to the top-level total |
+| `KineticForces/` | `<method>/` (torque/energy profiles, `dTdpsi_ell` resolved by bounce harmonic on the `ell` scale, `KineticMatrices/`); multi-ion runs add `PerSpecies/<species>/<method>/` with the same per-method layout, summing to the top-level total |
 | `ErrorFields/` | `CoilSensitivities/` (per-coil-set control-surface spectra and their rigid shift/tilt derivatives, `DominantMode/` full-window projection); `MonteCarlo/` (intrinsic and corrected `\|δ\|` histograms over the sampled tolerances, per batch and averaged); `Risk/` (threshold density, `P(lock\|δ)`, locking probabilities, `ToleranceScan/`); `NTV/` (correction-coil overlap and NTV torque couplings per kAt) |
 | `Tearing/` | `PerSurface/` (+ `DpMatrix/`), `Roots/`, `LayerWidths/`, `Diagnostics/{ValidRoots,Poles,FilteredRoots}`, `Scan/Surface_<k>/` |
 | `SurfaceGeometries/` | `{Plasma,Wall}/{x,y,z}` point clouds |
@@ -69,7 +69,7 @@ Mechanism: writers stay table-driven — each writer keeps a `path => (; long_na
 - Complex quantities are stored as the native HDF5.jl compound type (readable by h5py as a compound dtype) — **never split into `*_real`/`*_imag` dataset pairs**. Sole sanctioned exception: `Input/RawInputs/ForcingTerms/amplitude_{real,imag}`, which mirrors the external forcing ingest-file format and keeps pre-existing snapshots replayable.
 - `NaN` is the not-computed sentinel in numeric datasets (e.g. auto-derived settings, rootless growth-rate entries).
 - A **zero-extent array** is the not-computed sentinel for whole datasets that a given run never produces (e.g. `SingularSurfaces/ca_left`/`ca_right` on kinetic or galerkin-matched runs, the free-boundary energies when `vac_flag=false`, the on-demand derivative stores). Never write unpopulated (`undef`) memory.
-- Ragged (variable-length) data uses the flat-plus-`offsets` companion pattern (`offsets[k+1] - offsets[k]` = length of row `k`) rather than HDF5 VLEN types, e.g. `KineticForces/<method>/EnergyIntegrals/` and `Tearing/Diagnostics/*`.
+- Ragged (variable-length) data uses the flat-plus-`offsets` companion pattern (`offsets[k+1] - offsets[k]` = length of row `k`) rather than HDF5 VLEN types, e.g. `Tearing/Diagnostics/*`.
 
 ## Back-compatibility policy
 

diff --git a/docs/development/toml-conventions.md b/docs/development/toml-conventions.md
@@ -47,9 +47,9 @@ fails when its pattern matches a violation) lint-check the covered TOMLs on comm
 - `toml-no-decorative-dividers` — no `# ----`-style divider lines (all covered files).
 - `toml-inline-annotations` — every `key = value` line carries a trailing `# description`
   (`examples/*` and `test/test_data/*` only, per the rule-2 exception above).
-- `toml-no-deprecated-keys` — no deprecated config keys; its key list mirrors
-  `_DEPRECATED_FFS_KEYS`/`_DEPRECATED_EQUIL_KEYS` in `src/GeneralizedPerturbedEquilibrium.jl`,
-  so extend the hook's pattern whenever a key is deprecated there.
+- `toml-no-deprecated-keys` — no deprecated config keys; its key list mirrors the
+  `_DEPRECATED_*_KEYS` lists in `src/GeneralizedPerturbedEquilibrium.jl`, which stop any run that
+  sets one, so extend the hook's pattern whenever a key is added there.
 
 Run them manually with:
 

diff --git a/docs/src/kinetic_forces.md b/docs/src/kinetic_forces.md
@@ -70,8 +70,7 @@ The summed total is written to `KineticForces/<method>/` exactly as in a single-
 run, and each species' own contribution to `KineticForces/PerSpecies/<label>/<method>/`
 — labels are `ion_z<z>_m<m>`, `impurity_z<z>_m<m>`, and `electron` (a numeric suffix
 is appended only if a run repeats a `(z, m)` pair). Every per-species group carries the
-same datasets and metadata as the total, so `dTdpsi`, `T`, and `EnergyIntegrals/` are
-available per species. The summed cumulative torque profile is a diagnostic (linear
+same datasets and metadata as the total, so `dTdpsi` and `T` are available per species. The summed cumulative torque profile is a diagnostic (linear
 interpolation onto the union grid); the summed `total_torque` scalar is the exact
 Gauss-Kronrod value.
 
@@ -183,35 +182,13 @@ dissipation ``-2n\,\mathrm{Im}\langle \xi, u_2\rangle/4\mu_0`` — two independe
 of the same quantity — agree to a fraction of a percent with the regularization off, and disagree
 by tens of percent with it on.
 
-## HDF5 outputs: complex torque convention and the EnergyIntegrals layout
+## HDF5 outputs: complex torque convention
 
 The method level of `KineticForces/<method>/` reports the two physical scalars a user
 wants first: `total_torque` = ``T_\phi`` (N·m) and `total_energy` = ``\delta W_k`` (J).
 Internally both are halves of one complex quantity ``T = T_\phi + 2in\,\delta W_k``
 (Logan 2013), and the ψ-profiles `dTdpsi` and `T` store that complex ``T`` directly —
-so `imag(T)` carries the ``2n`` factor while `total_energy` has it divided out. The
-per-record `EnergyIntegrals/torque` and `EnergyIntegrals/kinetic_energy` are separate
-complex diagnostics of the two integrand halves at each ``(\psi, \lambda, \ell)``
-evaluation, which is why they are not packed into one number there.
-
-`EnergyIntegrals/` stores the variable-length integration trajectories in the
-flat-plus-offsets ragged layout (chosen over HDF5 VLEN types for cross-language
-support; `Tearing/Diagnostics/*` uses the same pattern). Record `k` spans
-`offsets[k]+1 : offsets[k+1]` (Julia, 1-based) of each `*_all` array:
-
-```julia
-h5open("gpec.h5", "r") do f
-    g = f["KineticForces/fgar/EnergyIntegrals"]
-    off = read(g["trajectory_offsets"])
-    x_k = read(g["x_all"])[off[k]+1:off[k+1]]          # record k's abscissae
-    I_k = read(g["integrand_all"])[off[k]+1:off[k+1]]  # its complex integrand
-end
-```
-
-```python
-g = f["KineticForces/fgar/EnergyIntegrals"]            # h5py, 0-based
-x_k = g["x_all"][g["trajectory_offsets"][k]:g["trajectory_offsets"][k + 1]]
-```
+so `imag(T)` carries the ``2n`` factor while `total_energy` has it divided out.
 
 ```@autodocs
 Modules = [GeneralizedPerturbedEquilibrium.KineticForces]

diff --git a/examples/DIIID-like_error_field_example/gpec.toml b/examples/DIIID-like_error_field_example/gpec.toml
@@ -206,8 +206,6 @@ height = -1.5780                        # Hoop height: centroid Z of the pack cr
 currents = [55000.0]                    # 1 kA per turn × 55 turns; sensitivities scale linearly with current [A]
 
 [PerturbedEquilibrium]
-fixed_boundary = false                  # Use fixed boundary conditions
-output_eigenmodes = true                # Output eigenmode fields as b-fields
 compute_response = true                 # Compute plasma response to forcing
 compute_singular_coupling = true        # Compute singular layer coupling metrics
 verbose = false                         # Enable verbose logging
@@ -260,7 +258,6 @@ impurity_mass = 12                      # Impurity mass [proton masses]
 electron = false                        # Ion-only NTV
 nutype = "harmonic"                     # Collision operator
 f0type = "maxwellian"                   # Equilibrium distribution
-moment = "pressure"                     # Pressure-moment NTV torque
 atol_pitch = 1e-9                       # Absolute tolerance for the pitch integration (median-normalized kernel)
 write_outputs_to_HDF5 = true            # Write outputs to the HDF5 file
 verbose = false                         # Enable verbose logging
diff --git a/examples/DIIID-like_gal_resistive_pe_example/gpec.toml b/examples/DIIID-like_gal_resistive_pe_example/gpec.toml
@@ -103,8 +103,6 @@ name = "c"                              # DIII-D C-coil (6 coils); resolves to c
 currents = [1000.0, 500.0, -500.0, -1000.0, -500.0, 500.0]  # n=1 cosine phasing, 1 kA peak [A]
 
 [PerturbedEquilibrium]
-fixed_boundary = false                  # Use fixed boundary conditions
-output_eigenmodes = true                # Output eigenmode fields as b-fields
 compute_response = false                # Compute plasma response to forcing
 compute_singular_coupling = false       # Compute singular layer coupling metrics
 verbose = true                          # Enable verbose logging

diff --git a/examples/DIIID-like_ideal_example/gpec.toml b/examples/DIIID-like_ideal_example/gpec.toml
@@ -75,8 +75,6 @@ name = "c"                              # Coil set; resolves to coil_geometries/
 currents = [1000.0, 500.0, -500.0, -1000.0, -500.0, 500.0]  # n=1 cosine phasing, 1 kA peak [A]
 
 [PerturbedEquilibrium]
-fixed_boundary = false                  # Use fixed boundary conditions
-output_eigenmodes = true                # Output eigenmode fields as b-fields
 compute_response = true                 # Compute plasma response to forcing
 compute_singular_coupling = true        # Compute singular layer coupling metrics
 verbose = true                          # Enable verbose logging
@@ -101,7 +99,6 @@ impurity_mass = 12                      # Impurity mass [proton masses]
 electron = false                        # Ion-only NTV
 nutype = "harmonic"                     # Collision operator
 f0type = "maxwellian"                   # Equilibrium distribution
-moment = "pressure"                     # Pressure-moment NTV torque
 atol_pitch = 1e-9                       # Absolute tolerance for the pitch integration (median-normalized kernel)
 axis_validity_suppression = true        # Suppress kinetic terms inside the near-axis orbit-width validity limit
 write_outputs_to_HDF5 = true            # Write outputs to the HDF5 file

diff --git a/examples/DIIID-like_ideal_multi_n_example/gpec.toml b/examples/DIIID-like_ideal_multi_n_example/gpec.toml
@@ -77,8 +77,6 @@ name = "c"                              # Coil set; resolves to coil_geometries/
 currents = [1800.0, -50.0, -450.0, -800.0, -450.0, -50.0]  # Sum of n=1, 2, 3 cosine phasings with 1000, 500, 300 A peaks; n=3 lies outside nn_high [A]
 
 [PerturbedEquilibrium]
-fixed_boundary = false                  # Use fixed boundary conditions
-output_eigenmodes = true                # Output eigenmode fields as b-fields
 compute_response = true                 # Compute plasma response to forcing
 compute_singular_coupling = true        # Compute singular layer coupling metrics
 verbose = false                         # Enable verbose logging

diff --git a/examples/Solovev_ideal_example/gpec.toml b/examples/Solovev_ideal_example/gpec.toml
@@ -36,8 +36,6 @@ forcing_data_file = "forcing.dat"       # Manual mode table (n, m, amplitude_rea
 forcing_data_format = "ascii"           # Format: "ascii", "hdf5", or "coil" (Biot-Savart from 3D wires)
 
 [PerturbedEquilibrium]
-fixed_boundary = false                  # Use fixed boundary conditions
-output_eigenmodes = true                # Output eigenmode fields as b-fields
 compute_response = true                 # Compute plasma response to forcing
 compute_singular_coupling = true        # Compute singular layer coupling metrics
 verbose = true                          # Enable verbose logging

diff --git a/examples/Solovev_ideal_example_3D/gpec.toml b/examples/Solovev_ideal_example_3D/gpec.toml
@@ -67,8 +67,6 @@ equal_arc_wall = false                  # Equal arc length distribution of nodes
 # [PerturbedEquilibrium]
 # forcing_data_file = "forcing.dat"      # Manual mode table (n, m, amplitude_real, amplitude_imag)
 # forcing_data_format = "ascii"          # Format: "ascii", "hdf5", or "coil" (Biot-Savart from 3D wires)
-# fixed_boundary = false                 # Use fixed boundary conditions
-# output_eigenmodes = true               # Output eigenmode fields as b-fields
 # compute_response = true                # Compute plasma response to forcing
 # compute_singular_coupling = true       # Compute singular layer coupling metrics
 # verbose = true                         # Enable verbose logging

diff --git a/examples/Solovev_kinetic_NTV_example/gpec.toml b/examples/Solovev_kinetic_NTV_example/gpec.toml
@@ -38,8 +38,6 @@ forcing_data_file = "forcing.dat"       # Manual mode table (n, m, amplitude_rea
 forcing_data_format = "ascii"           # Format: "ascii", "hdf5", or "coil" (Biot-Savart from 3D wires)
 
 [PerturbedEquilibrium]
-fixed_boundary = false                  # Use fixed boundary conditions
-output_eigenmodes = true                # Output eigenmode fields as b-fields
 compute_response = true                 # Compute plasma response to forcing
 compute_singular_coupling = true        # Compute singular layer coupling metrics
 verbose = true                          # Enable verbose logging

diff --git a/examples/Solovev_kinetic_calculated_example/gpec.toml b/examples/Solovev_kinetic_calculated_example/gpec.toml
@@ -34,8 +34,6 @@ forcing_data_file = "forcing.dat"       # Manual mode table (n, m, amplitude_rea
 forcing_data_format = "ascii"           # Format: "ascii", "hdf5", or "coil" (Biot-Savart from 3D wires)
 
 [PerturbedEquilibrium]
-fixed_boundary = false                  # Use fixed boundary conditions
-output_eigenmodes = true                # Output eigenmode fields as b-fields
 compute_response = true                 # Compute plasma response to forcing
 compute_singular_coupling = true        # Compute singular layer coupling metrics
 compute_torque_response = true          # Build the ψ-resolved torque response matrices T_xe and T_source

diff --git a/examples/Solovev_kinetic_multiion_example/gpec.toml b/examples/Solovev_kinetic_multiion_example/gpec.toml
@@ -38,8 +38,6 @@ forcing_data_file = "forcing.dat"       # Manual mode table (n, m, amplitude_rea
 forcing_data_format = "ascii"           # Format: "ascii", "hdf5", or "coil" (Biot-Savart from 3D wires)
 
 [PerturbedEquilibrium]
-fixed_boundary = false                  # Use fixed boundary conditions
-output_eigenmodes = true                # Output eigenmode fields as b-fields
 compute_response = true                 # Compute plasma response to forcing
 compute_singular_coupling = true        # Compute singular layer coupling metrics
 verbose = true                          # Enable verbose logging

diff --git a/src/Equilibrium/EquilibriumTypes.jl b/src/Equilibrium/EquilibriumTypes.jl
@@ -13,10 +13,10 @@ specified in the input.
   - `eq_type::String` - Type of equilibrium file ("efit", "solovev", "lar", etc.)
   - `eq_filename::String` - Path to equilibrium input file
   - `jac_type::String` - Jacobian coordinate type ("hamada", "pest", "equal_arc", "boozer", "park", "custom")
-  - `power_bp::Int` - Poloidal field power exponent for Jacobian (internal, derived from `jac_type`; deprecated as a TOML input key)
-  - `power_b::Int` - Total field power exponent for Jacobian (internal, derived from `jac_type`; deprecated as a TOML input key)
-  - `power_r::Int` - Major radius power exponent for Jacobian (internal, derived from `jac_type`; deprecated as a TOML input key)
-  - `power_rc::Int` - Minor radius (rfac = √((R-R₀)²+(Z-Z₀)²)) power exponent for Jacobian (internal, derived from `jac_type`; deprecated as a TOML input key)
+  - `power_bp::Int` - Poloidal field power exponent for Jacobian (internal, derived from `jac_type`; not a deck key)
+  - `power_b::Int` - Total field power exponent for Jacobian (internal, derived from `jac_type`; not a deck key)
+  - `power_r::Int` - Major radius power exponent for Jacobian (internal, derived from `jac_type`; not a deck key)
+  - `power_rc::Int` - Minor radius (rfac = √((R-R₀)²+(Z-Z₀)²)) power exponent for Jacobian (internal, derived from `jac_type`; not a deck key)
   - `jac_custom_power_bp::Int` - Poloidal-field exponent for a custom Jacobian `J = Bp^bp · B^b / (R^r · rfac^rc)`; read only when `jac_type = "custom"`, ignored for named types
   - `jac_custom_power_b::Int` - Total-field exponent for a custom Jacobian; read only when `jac_type = "custom"`, ignored for named types
   - `jac_custom_power_r::Int` - Major-radius exponent for a custom Jacobian; read only when `jac_type = "custom"`, ignored for named types