InnerLayer.SLAYER - BUGFIX - Restore the toroidal mode number in the diamagnetic frequencies

.gitignore

@@ -38,3 +38,6 @@ scratch/
 
 # Local profiling scratch (one-off study scripts, not part of the package)
 profiling/
+
+# Override-case rundirs materialized beside their example by the regression harness
+.regress-override-*

regression-harness/cases/diiid_slayer_n2.toml

@@ -0,0 +1,173 @@
+# Regression case: DIII-D-like H-mode n=2 SLAYER tearing-mode growth rates.
+# Reuses the n=1 SLAYER deck via [overrides] at toroidal mode number 2, where the deck's
+# qmin = 1.204 puts the 3/2 surface in the plasma. Exists to guard the n-dependence of the
+# layer build — in particular the diamagnetic frequencies ω_* ∝ n feeding Q_e/Q_i, which
+# no n=1 case can constrain — with the inner rationals 3/2, 4/2, 5/2 as the tracked roots.
+# Each [quantities.*] block names an HDF5 path in the run output, how to extract it,
+# and the noise floor below which a difference is treated as zero.
+[case]
+name = "diiid_slayer_n2"
+description = "DIII-D-like H-mode equilibrium, n=2, SLAYER tearing-mode analysis guarding the 3/2 surface and the n-scaling of Q_e/Q_i (reuses the n=1 deck via overrides)"
+example_dir = "examples/DIIID-like_SLAYER_example"
+
+# Run the shared SLAYER deck at n = 2 (no separate n=2 example directory).
+[overrides]
+"ForceFreeStates.nn_low" = 2
+"ForceFreeStates.nn_high" = 2
+
+# Per-surface SLAYER layer parameters (geometry + dimensionless)
+[quantities.slayer_ising]
+h5path = "Tearing/PerSurface/rational_index"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER surface indices"
+noise_threshold = 0
+order = 10
+
+[quantities.slayer_m]
+h5path = "Tearing/PerSurface/m"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER poloidal m"
+noise_threshold = 0
+order = 11
+
+[quantities.slayer_n]
+h5path = "Tearing/PerSurface/n"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER toroidal n"
+noise_threshold = 0
+order = 12
+
+[quantities.slayer_rs]
+h5path = "Tearing/PerSurface/rs"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER minor radius rs"
+noise_threshold = 1e-10
+order = 13
+
+[quantities.slayer_sval_r]
+h5path = "Tearing/PerSurface/sval_r"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER r-based shear"
+noise_threshold = 1e-10
+order = 14
+
+[quantities.slayer_lu]
+h5path = "Tearing/PerSurface/lu"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER Lundquist S"
+noise_threshold = 1e-8
+order = 15
+
+[quantities.slayer_D_norm]
+h5path = "Tearing/PerSurface/D_norm"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER D_norm"
+noise_threshold = 1e-10
+order = 16
+
+[quantities.slayer_P_perp]
+h5path = "Tearing/PerSurface/P_perp"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER P_perp"
+noise_threshold = 1e-8
+order = 17
+
+[quantities.slayer_tauk]
+h5path = "Tearing/PerSurface/tau_k"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER tauk"
+noise_threshold = 1e-12
+order = 18
+
+[quantities.slayer_Q_e]
+h5path = "Tearing/PerSurface/Q_e"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER Q_e"
+noise_threshold = 1e-12
+order = 20
+
+[quantities.slayer_Q_i]
+h5path = "Tearing/PerSurface/Q_i"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER Q_i"
+noise_threshold = 1e-12
+order = 21
+
+[quantities.slayer_iota_e]
+h5path = "Tearing/PerSurface/iota_e"
+type = "real_vector"
+extract = "all_real"
+label = "SLAYER iota_e"
+noise_threshold = 1e-12
+order = 19
+
+# Tearing eigenvalue (coupled mode → length 1). The headline deliverable:
+# a real, nonzero growth rate on a realistic equilibrium. Root-extraction
+# is sensitive to the AMR cell topology and ODE solver, so the Q/ω/γ
+# thresholds are absolute and modestly loose; re-pin intentionally if a
+# solver/AMR change shifts the root inventory.
+# Growth-rate / frequency / root outputs. Pinned for the inner three rational
+# surfaces only (3/2, 4/2, 5/2) via `first_3`: the Δ'/γ contour search is
+# numerically unreliable on the outermost surfaces near the edge, so those are
+# deliberately not golden-tracked.
+[quantities.slayer_Q]
+h5path = "Tearing/Roots/Q_root"
+type = "complex_vector"
+extract = "first_3_complex"
+label = "SLAYER Q_root [3/2,4/2,5/2]"
+noise_threshold = 1e-4
+order = 30
+
+[quantities.slayer_omega_Hz]
+h5path = "Tearing/Roots/omega"
+type = "real_vector"
+extract = "first_3"
+label = "SLAYER ω_Hz [3/2,4/2,5/2]"
+noise_threshold = 1.0
+order = 32
+
+[quantities.slayer_gamma_Hz]
+h5path = "Tearing/Roots/gamma"
+type = "real_vector"
+extract = "first_3"
+label = "SLAYER γ_Hz [3/2,4/2,5/2]"
+noise_threshold = 1e-1
+order = 33
+
+# no_root flag (1 = extraction failed). Pinned for the inner three surfaces
+# so the 3/2, 4/2, 5/2 root inventory cannot drift silently.
+[quantities.slayer_no_root]
+h5path = "Tearing/Roots/no_root"
+type = "real_vector"
+extract = "first_3"
+label = "SLAYER no_root flags [3/2,4/2,5/2]"
+noise_threshold = 0
+order = 34
+
+# Settings (catches accidental config drift)
+[quantities.slayer_enabled]
+h5path = "Tearing/enabled"
+type = "int_scalar"
+extract = "value"
+label = "SLAYER enabled flag"
+noise_threshold = 0
+order = 90
+
+[quantities.runtime]
+h5path = ""
+type = "runtime"
+extract = "value"
+label = "Runtime (s)"
+noise_threshold = 0.0
+order = 999

regression-harness/src/runner.jl

@@ -27,15 +27,17 @@ end
 Materialize the directory GPEC will actually run in.
 
 With no `overrides`, the example deck runs in place (returns it untouched). With overrides,
-the deck is copied to a throwaway temp dir and the named gpec.toml keys are patched there,
-so one shared example can serve several cases (e.g. a collisionless variant via
-`"KineticForces.nutype" => "zero"`). Override keys are dotted paths into the TOML; missing
-intermediate tables are created. Returns `(rundir, is_temp)`; the caller removes the temp
-tree when `is_temp`.
+the deck is copied to a throwaway sibling of the example dir and the named gpec.toml keys are
+patched there, so one shared example can serve several cases (e.g. a collisionless variant via
+`"KineticForces.nutype" => "zero"`). The copy sits beside the original so relative file
+references in the deck (e.g. `SLAYER.profile_file = "../<other_example>/..."`) still resolve.
+Override keys are dotted paths into the TOML; missing intermediate tables are created.
+Returns `(rundir, is_temp)`; the caller removes `rundir` when `is_temp`.
 """
 function _materialize_rundir(example_path::String, overrides::Dict{String,Any})
     isempty(overrides) && return (example_path, false)
-    rundir = joinpath(mktempdir(), "deck")
+    rundir = joinpath(dirname(example_path), ".regress-override-" * basename(example_path))
+    rm(rundir; recursive=true, force=true)   # stale leftover from a crashed run
     cp(example_path, rundir)
     rm(joinpath(rundir, "gpec.h5"); force=true)   # drop any stale output copied along
     cfg = TOML.parsefile(joinpath(rundir, "gpec.toml"))
@@ -523,7 +525,8 @@ function run_local(db::SQLite.DB, case_spec::CaseSpec, repo_root::String;
             rm(runinfo_file; force=true)
         end
         if rundir_is_temp && rundir !== nothing
-            rm(dirname(rundir); recursive=true, force=true)
+            # rundir sits beside the example; removing its parent would delete examples/ itself
+            rm(rundir; recursive=true, force=true)
         end
     end
 end
@@ -647,7 +650,8 @@ function run_at_commit(db::SQLite.DB, commit_hash::String, ref_name::String,
             rm(runinfo_file; force=true)
         end
         if rundir_is_temp && rundir !== nothing
-            rm(dirname(rundir); recursive=true, force=true)
+            # rundir sits beside the example; removing its parent would delete examples/ itself
+            rm(rundir; recursive=true, force=true)
         end
         if own_worktree && worktree_path !== nothing
             remove_worktree(worktree_path, repo_root)

src/InnerLayer/SLAYER/LayerInputs.jl

@@ -217,20 +217,23 @@ function build_slayer_inputs(equil, sings, profiles::KineticProfiles;
         da_dpsi = _da_dpsi_at(psi)
         sval_r = r_based_shear(rs, q, q1, da_dpsi)
 
-        prof = profiles(psi)
-        # Override ω_*e, ω_*i with spline-derivative values when requested.
-        ω_e_use, ω_i_use = if compute_omega_star
-            _omega_star_at(psi)
-        else
-            (prof.omega_e, prof.omega_i)
-        end
-
         # Resonant (m, n): take the first element of the mode-number vectors.
         # Parallel-FM `sing.m`/`sing.n` hold exactly one entry each; ideal
         # DCON may hold multiple — we pick the first and document the choice.
         m_res = sing.m[1]
         n_res = sing.n[1]
 
+        prof = profiles(psi)
+        # Override ω_*e, ω_*i with spline-derivative values when requested. In flux coordinates
+        # ω_* = n·(dp/dψ)/(e·n_e); `_omega_star_at` returns the n = 1 value, so restore the
+        # factor n here. Values supplied through `profiles` are taken to be physical already.
+        ω_e_use, ω_i_use = if compute_omega_star
+            ωe1, ωi1 = _omega_star_at(psi)
+            (n_res * ωe1, n_res * ωi1)
+        else
+            (prof.omega_e, prof.omega_i)
+        end
+
         # Pull geometric trapped-fraction inputs from ResistGeometry when
         # available (populated by ForceFreeStates.resist_eval_all!); else
         # fall back to nothing and let slayer_parameters compute them from

test/runtests_slayer_inputs.jl

@@ -183,4 +183,20 @@
         @test sl isa Vector{SLAYERParameters}
         @test isempty(sl)
     end
+
+    @testset "build_slayer_inputs: omega_star carries the toroidal mode number" begin
+        # In flux coordinates ω_* = n·(dp/dψ)/(e·n_e): resolving the same surface at n = 1
+        # and n = 2 must double Q/tauk = -ω_*, while the ratio iota_e must not move.
+        # Asserted through the returned parameters so the check survives a refactor of
+        # where the factor is applied.
+        s1 = [_mk_sing(psi=0.3, q=2.0, q1=1.5, m=2, n=1)]
+        s2 = [_mk_sing(psi=0.3, q=2.0, q1=1.5, m=4, n=2)]
+        sl1 = build_slayer_inputs(equil, s1, profiles; bt=2.0, dr_val=0.0)
+        sl2 = build_slayer_inputs(equil, s2, profiles; bt=2.0, dr_val=0.0)
+
+        @test sl2[1].Q_e / sl2[1].tauk ≈ 2 * (sl1[1].Q_e / sl1[1].tauk) rtol = 1e-12
+        @test sl2[1].Q_i / sl2[1].tauk ≈ 2 * (sl1[1].Q_i / sl1[1].tauk) rtol = 1e-12
+        @test sl2[1].iota_e ≈ sl1[1].iota_e rtol = 1e-12
+    end
+
 end