Growth rate calculation functionality added to gslayer.f

[d-burg]

The additions are structured as follows:

New block in slayer.f:

A simple block is added with approximate kinetic input data of the dimension(k) form that will be output by the upcoming build_inputs.f module (to interface with equil.f). Here k=2 rational surfaces are included. This block calls the gamma_match() subroutine, which takes in kinetic input data and outputs growth rates

New routines in gslayer.f:

The wrapper subroutine is gamma_match(). This is called by slayer.f.

gamma_match() calls these additional subroutines:

• Nested inside gamma_match() is gamma_stability_scan(). This sets up grid packing and ouputs a Re(Q) by Im(Q) scan of inner layer deltas
• Next used by gamma_match() is interpolate_slice_at_Q(). This subroutine outputs a deltas(Re(Q)=Q) column of growth rates
• Next used by gamma_match() is gamma_from_delta_match(). This subroutine extracts the gamma corresponding to a $\Delta$ = $\Delta$' match. These growth rates are returned by gamma_match()

[logan-nc]

Thanks for making the PR @d-burg!
Don't be afraid to post figures (even block diagrams or initial figures showing what interpolate_slice_at_Q means) and questions directly here (you can go into the "Files Changed" tab and make in-line comments like "I did this to get blah. Is there a better way?", "need blah here - where do I get it?", etc.). Having things on record is helpful for years down the road when we are trying to remember what we did and why we made the decisions we made.

[d-burg]

Appearance of `slice` at a given Re(Q) = omega_ExB

[d-burg]

Sorting approach taken to match inner layer delta with outer layer delta in a way that should be robust to negative numbers. This is the sorting key which re-sorts the gammas array correspondingly, meaning the index of the match is true for both deltas and gamma

[logan-nc]

How's it going @d-burg? Have kin and sq interfaces set up yet?

[d-burg]

@logan-nc it's going! Having some trouble parsing exactly which dependencies and function/routine calls are needed where (with all the nested equilibrium objects). My main questions are:

1. Do I need to read in the vmat file to get msing? (This is how I've seen it done so far in GPEC)
2. Does the way I've written the kin and sq initializations look about right to you? and
3. Could you point me to a location where a netcdf of the form output by STRIDE is read by a different code? I've gotten a bit lost trying to figure out the deltaprime matrix read-in, and STRIDE deallocates the matrix I'd want before concluding its run

These questions all pertain to lines ~30-110 of the new layerinputs.f. Thanks!

[logan-nc]

You need read_kin from this module as well

[logan-nc]

I think the only equilibrium quantity the read_kin subroutine uses is chi1 (the normalization factor poloidal flux and psi_n). This is a public variable of the pentrc inputs module, so you should be able to set it more efficiently than having to do all this set_eq stuff with all the matrices. If that is hard for any reason (I think you might have to rename the variable like how dcon.F deals with overlapping names), then just add op_chi1 as an optional variable in the subroutine and use that if it is included in the inputs. See the progressbar in inputs.f for an example of how to use optional arguments.

[logan-nc]

I don't think you need the action matrices or to initialize_pentrc. You are not actually going to run pentrc. You literally just want to read that ascii table and make the kin spline.

[logan-nc]

You never assign anything to vmat_filename? Isn't it just blank then?

[logan-nc]

Searching the repo for vmat_filename I only see it in rmatch/msing.f. It seems to be a special interface needed to do the eigenfunction inner/outer layer matching from resistive DCON. Not something standard. Not something in stride or normal dcon. It also doesn't seem to contain sq, which is what you need, right? Seems like you might be barking up the wrong tree here?

[logan-nc]

@logan-nc it's going! Having some trouble parsing exactly which dependencies and function/routine calls are needed where (with all the nested equilibrium objects). My main questions are:

1. Do I need to read in the vmat file to get msing? (This is how I've seen it done so far in GPEC)
2. Does the way I've written the kin and sq initializations look about right to you? and
3. Could you point me to a location where a netcdf of the form output by STRIDE is read by a different code? I've gotten a bit lost trying to figure out the deltaprime matrix read-in, and STRIDE deallocates the matrix I'd want before concluding its run

These questions all pertain to lines ~30-110 of the new layerinputs.f. Thanks!

Thanks for checking in! Here are some quick replies

1. I don't think vmat is what you want it to be. It is a custom rdcon thing as far as I can tell. To read the equilibrium, you want to emulate how dcon does it:
   

   GPEC/dcon/dcon.F

   Lines 97 to 103 in 377c0d6

   	c-----------------------------------------------------------------------
   	c open output files, read, process, and diagnose equilibrium.
   	c-----------------------------------------------------------------------
   	CALL ascii_open(out_unit,"dcon.out","UNKNOWN")
   	CALL equil_read(out_unit)
   	CALL equil_out_global
   	CALL equil_out_qfind

   
   then a little lower down, it also does CALL sing_find, which is where msing gets set. It is all very annoying because each subroutine sets a mystery subset of "global" variables. It takes time to trace everything around. Sorry! Part of the fun I suppose.

2. See (1) for how to set sq by calling the appropriate equil subroutines. See inline comments regarding kin.

3. We don't have any netcdf reading in the code yet! I would love to see you lead us on this front. The top two hits of googling "read a netcdf file in fortran" look good to me. I am not an expert and just copied examples to do the writing part :)

[d-burg]

Overview

@logan-nc -- this is a major extension of the SLAYER to support uncoupled and coupled multi-surface tearing growth-rate calculations via complex-plane dispersion scans with Adaptive Mesh Refinement (AMR). Previously, SLAYER only computed single-surface inner layer Delta/torque/b_crit; this branch adds the ability to find tearing mode growth rates by solving coupled dispersion relations across multiple rational surfaces.

17 files changed: +4,428 / -578 lines across 83 commits.

Key Changes

New Capabilities

• Growth rate solver: Finds tearing mode growth rates by matching the inner-layer Delta to Delta' from STRIDE, solving Det(Delta_hat - Delta') = 0 in the complex frequency plane.
• Coupled multi-surface dispersion: New dispersion_det function evaluates 2×2/3×3 coupled determinants across msing_max rational surfaces.
• AMR complex-plane scanning: Two AMR implementations (dispersion_AMR v1 hash-based, dispersion_AMR_v2 cell-based) adaptively refine the (Re(Q), Im(Q)) scan grid to locate dispersion-relation zeros efficiently. v1 may be removed, but is retained for now (and both work).
• Fitzpatrick formalism (Pperp_Ptor_flag): New riccati_f solver variant incorporating perpendicular (P_perp) and toroidal (P_tor) Prandtl numbers and anomalous diffusion, following R. Fitzpatrick's updated extended layer equation formalism. This is equivalent to the original Cole/Fitzpatrick model originally coded in SLAYER and used in riccati(), but without a c_beta dependence on P_tor and with improved boundary conditions for the ODE integration. The two formalisms could be united in the future, but considering they both rely on anomalous parameters (chi_perp and chi_tor for riccati_f(), inpr and thermal conductivity for riccati()), the numerically stable and robustly benchmarked riccati_f() is retained as default for now.
• Delta_crit computation: Three selectable models (dc_type = "toroidal" | "lar" | "rfitzp" for JW Connor, Lutjens, and Fitzpatrick definitions respectively) for the critical curvature stabilization threshold , including the new toroidal formula computed with STRIDE's help for the geometric factor.

New Files

• slayer/layerinputs.f — layerinputs_mod: reads STRIDE NetCDF output, kinetic profiles, and equilibrium data to build per-surface input arrays (slayer_inputs_type) for the dispersion solver.
• slayer/slayer_netcdf.f — slayer_netcdf_mod: writes SLAYER results (growth rates, AMR scan data, per-surface parameters) to a structured NetCDF output file.
• slayer/makefile — standalone Makefile for building the SLAYER module.

Significantly Reworked Files

• slayer/sglobal.f — Expanded from ~25 to ~193 lines. Adds new derived types (slayer_inputs_type, slayer_outputs_type, deltas_outputs_type, amr_cell_type), AMR storage arrays (hash tables, cell lists), and additional physics scalars (P_perp, P_tor, D_norm, d_beta, tau_r, dc_tmp, delta_eff, etc.).
• slayer/params.f — Extended parameter computation: now accepts anomalous diffusivities (chis), resistive interchange parameter (dr_val), and toroidal Delta_crit geometric factor (dgeo_val). Computes Braginskii collision times, Spitzer-Härm conductivity, ion skin depth, P_perp, P_tor, D_norm, and iterative Delta_crit.
• slayer/gslayer.f — Grew from ~110 to ~1,280 lines. Added ~10 new subroutines: output_gamma, allocate_inputs/allocate_outputs, shrink_array/grow_array, calc_determinant, dispersion_det, dispersion_AMR (v1 & v2), and associated helpers.
• slayer/delta.f — Added riccati_f (Fitzpatrick formulation with w_der_f ODE and jac_f Jacobian), improved documentation and variable annotations throughout.
• slayer/slayer.f — Restructured main driver to support read_eq mode (reading equilibrium from STRIDE/kinetic files), growth-rate matching workflows, and new output flags.

STRIDE Changes

• stride/free.f — Computes toroidal Delta_crit geometric quantities (flux-surface-averaged |∇ψ|², ⟨B²⟩, shear) at rational surfaces via new spline-based surface integrals.
• stride/stride_netcdf.f — Outputs additional per-surface data: shear, Delta_geo, resm (resonant m), dr (resistive interchange parameter).
• stride/stride.F — Updated fallback stride_netcdf_out call to pass the new shr/dgeo arguments (zero-filled when no free-boundary data is available).

Build System Fixes

• install/DEPENDENCIES.inc — Added missing SLAYER inter-module dependencies: slayer_netcdf.o, layerinputs.o (with pentrc/inputs.o and equil/*.o), and updated gslayer.o and slayer.o prerequisites. Added version.inc dependency for slayer_netcdf.o.
• install/RULES.inc — Added -I../slayer -I../pentrc to FCSLAYER so the compiler can find version.inc and inputs.mod.
• install/TARGETS.inc — Added ../slayer/version.inc generation target. Added -lpentrc -lharvest to SLAYER_LIBS and pentrc harvest as build prerequisites for the slayer target.

Input/Namelist Changes (input/slayer.in)

• New physics inputs: dr_val, dgeo_val, chi_p_prof, chi_t_prof, kappa_prof, delta_prime, ingamma
• New control flags: read_eq, Pperp_Ptor_flag, coupling_flag, dc_type, msing_max, Q_num, scan_width, AMR_passes
• New output flags: est_gamma_flag, match_gamma_flag, stabscan_flag, coupled_stabscan_flag, amr_flag
• Default parameter values updated to more realistic tokamak-scale values

Code Quality

• Extensive documentation added throughout (module headers, subroutine docstrings, variable annotations with units and intent)
• TODO comments flagging known issues (unused arguments, uninitialized variables)

[logan-nc]

@claude please review this pr

[claude]

Claude finished @logan-nc's task in 4m 50s —— View job

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PR Review: Growth Rate Calculation for SLAYER

Tasks:

• Gather context and understand PR scope
• Read and analyze changed files
• Review new files (layerinputs.f, slayer_netcdf.f, gslayer.f additions)
• Review modified files (delta.f, params.f, sglobal.f, slayer.f)
• Review STRIDE changes (free.f, stride_netcdf.f)
• Review build system changes
• Compile findings and post review

---

This is a substantial PR that successfully implements uncoupled and coupled multi-surface tearing growth-rate calculations via complex-plane dispersion scans with AMR. The core physics logic, the AMR design, and the NetCDF I/O structure are well thought out and well documented. Below I've organized findings by severity.

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Definite Bugs

1. stride/free.f — Wrong shear value stored (physics bug)

shr_spl is fit to ln_q = LOG(sq%fs(:,4)), so after CALL spline_eval(shr_spl, respsi, 1):

• shr_spl%f(1) = value of ln(q) at the surface (e.g., ln(2) ≈ 0.693 at q=2)
• shr_spl%f1(1) = d(ln q)/d(psi_n) at the surface

But the code sets:

shr(ising) = shr_spl%f(1)    ! line 395 — this is ln(q), NOT shear!

This is then written to NetCDF as shear and read back by layerinputs.f, where it becomes sval passed into params() — which uses it to compute b_l, tau_h, and delta_crit. The magnetic shear should be s = (psi_n/q) * dq/d(psi_n) = respsi * shr_spl%f1(1). Fix this →

2. stride/free.f — Memory leak (confirmed Copilot #14)

spline_alloc is called for psi_t, avg_dpsi_spl, avg_bsq_spl, v_spl, shr_spl but only fspl is deallocated. The four remaining splines leak on every call to free_run. Fix this →

3. slayer/layerinputs.f:83 — File opened in write mode for read (confirmed Copilot #9)

stat = nf90_open(path=ncfile, mode=NF90_WRITE, ncid=ncid)

read_stride_netcdf_diagonal only reads from the file. NF90_WRITE requires write permission on the file and is semantically wrong. Should be NF90_NOWRITE. Fix this →

4. slayer/params.f — Uninitialized pr causes division by zero (confirmed Copilot #3)

tau_v = tau_r / pr    ! line 131 — pr not initialized in new read_eq workflow

The module-level pr in sglobal_mod is never set in the new read_eq path (only the old single-surface path sets it via namelist). This will divide by zero or produce NaN for tau_v, visc, P_perp, and P_tor. The TODO comment at the top of sglobal.f acknowledges this. The most robust fix would be to pass pr as INTENT(IN) to params(), or guard with IF (pr > 0.0).

5. slayer/params.f:88 — Local Qconv shadows module-level (confirmed Copilot #4)

REAL(r8) :: Qconv  ! shadows sglobal_mod%Qconv
...
Qconv = lu**(1.0/3.0) * tau_h
tauk  = Qconv         ! tauk (=sglobal_mod%tauk) IS updated correctly

The module-level Qconv from sglobal_mod is never updated because the local variable shadows it. tauk is updated correctly as a workaround. If any downstream code reads sglobal_mod%Qconv directly (rather than tauk), it will get an uninitialized value. Rename the local to remove the shadow.

6. slayer/slayer_netcdf.f:301-302 — n_amr_pts dimension mismatch (confirmed Copilot #6)

CALL sl_check( nf90_def_var(ncid, "n_amr_pts", NF90_INT,
     $     (/qsing_dim/), var_npts_id) )   ! dimension = msing
...
CALL sl_check( nf90_put_var(ncid, var_npts_id, n_pts_arr) )  ! size = m_AMR

n_pts_arr is allocated with size m_AMR but the variable is defined on qsing_dim (size msing). When m_AMR ≠ msing, the write will fail or corrupt output. Fix: define n_amr_pts on nAMR_dim instead.

---

Design Issues / Code Quality

7. slayer/slayer_netcdf.f:250 — q_rational stored as integer

CALL sl_check( nf90_def_var(ncid, "q_rational", nf90_int, qsing_dim, qr_id) )

Safety factor values like q = 7/3 = 2.333 are truncated to integer. The slayer_inputs_type%qval_arr field is also INTEGER. The name q_rational suggests the actual rational q value; using an integer is confusing and lossy. Consider storing as nf90_double or renaming to q_integer.

8. slayer/slayer.f + slayer/layerinputs.f — chi_p_arr assignment before allocation

In slayer.f (around line 477):

sl_in%chi_p_arr = chi_p_prof   ! implicit alloc to size 8 via F2003 semantics
sl_in%chi_t_arr = chi_t_prof
sl_in%kappa_arr = kappa_prof
CALL build_inputs(infile,ncfile,sl_in)  ! accesses chi_p_arr(ising) for ising=1..msing

The Fortran 2003 automatic allocation makes the LHS array size 8 (from chi_p_prof). Inside build_inputs, the access sl_in%chi_p_arr(ising) where ising goes up to msing will go out-of-bounds if msing > 8. Also, allocate_inputs in gslayer.f does not allocate chi_p_arr / chi_t_arr / kappa_arr, making it inconsistent with build_inputs's expectations.

9. slayer/layerinputs.f:81 — Debug WRITE in production code

WRITE(*,*) '$^$ opening netcdf file', ncfile

The $^$ prefix is clearly a debug marker. Should be removed or gated behind n_trace > 0 before merge.

10. slayer/gslayer.f — Two AMR implementations

dispersion_AMR (v1, hash-based) and dispersion_AMR_v2 (cell-based) both exist. The PR description notes v1 may be removed. Having two implementations increases maintenance burden and binary size. Recommend deciding which to keep before merging (or at minimum, marking v1 with ! DEPRECATED prominently).

11. stride/free.f — Unconditional diagnostic writes in production loop

The outer psi loop and rational-surface loop contain (now-removed?) debug WRITE statements. The Copilot comment (#10) about this appears to have been partially addressed, but worth verifying the loop over ipsi = 0, mpsi doesn't emit per-point output.

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Copilot Comments Addressed in Current Code

The following Copilot comments appear to be false positives for the current state of the branch:

• P_tor_hat computation (w_der_del_s): Current code correctly has P_tor_hat = P_tor / D_norm**6.0, not from P_perp.
• inx as OPTIONAL (riccati_del_s): inx is not declared OPTIONAL in the current code; only iny is optional. The unconditional use of inx is correct.
• dr_rational dimension (stride_netcdf.f): Current diff shows r_dim (rational surface dim) is used correctly, not p_dim.
• ising as REAL (layerinputs.f): ising is declared INTEGER in the current code.
• Dimension guards in slayer_netcdf.f: The early RETURN for msing == 0 is now present before nf90_def_var calls that depend on it.

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Summary

The core AMR scan logic, dispersion determinant formulation, and NetCDF I/O framework are solid. The most critical issue before merge is bug #1 (shear stored as ln(q)), which affects the physics of every growth rate computed in read_eq mode. Bugs #3–#6 and the pr initialization issue (#4) should also be resolved. The memory leak (#2) should be fixed but won't silently corrupt results.

[d-burg]

@claude can you check whether all changes in the latest commit address your latest PR review?

[claude]

Claude finished @d-burg's task in 2m 49s —— View job

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Review of Latest Commit Against Previous Issues

Tasks:

• Gather context from previous review
• Check Bug Public Release #1: stride/free.f — shear stored as ln(q) instead of actual shear
• Check Bug brzphi_flag bug #2: stride/free.f — memory leak (splines not deallocated)
• Check Bug Reluctance Eigenvectors #3: slayer/layerinputs.f — NF90_WRITE → NF90_NOWRITE
• Check Bug mthsurf #4: slayer/params.f — uninitialized pr divide-by-zero
• Check Bug Normalized Reluctance Eigenvalues #5: slayer/params.f — local Qconv shadowing module-level
• Check Bug Complex plasma response with torque and kinetic grid. #6: slayer/slayer_netcdf.f — n_amr_pts dimension mismatch
• Check Design Control Surface Pitch #7: q_rational stored as integer
• Check Design ASCII output overflow bug #8: chi_p_arr assignment before allocation
• Check Design pypec synthetics broken by new interp #9: debug WRITE in layerinputs.f
• Check Design Output Coordinates need to be Clear #10: two AMR implementations
• Check Design KPEC Testing: fkg_mats_flag understanding & expansion #11: Q variable defined but never written in NetCDF
• Compile findings and post

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Commit 7de735c ("address PR review bugs and suggestions") touches exactly the 5 files that needed changes. Here is the status of every item from the previous review.

All 6 Definite Bugs — FIXED ✅

#	File	Issue	Fix
1	stride/free.f:395	Shear stored as ln(q)	Now correctly respsi * shr_spl%f1(1)
2	stride/free.f	Memory leak — 4 splines never deallocated	spline_dealloc added for psi_t, avg_dpsi_spl, avg_bsq_spl, v_spl, shr_spl
3	slayer/layerinputs.f:81	File opened with NF90_WRITE for a read-only operation	Changed to NF90_NOWRITE
4	slayer/params.f	tau_v = tau_r / pr divides by zero when pr is unset	Guarded: IF (pr > 0.0_r8) sets tau_v/visc; else both zero
5	slayer/params.f:88	Local REAL(r8) :: Qconv shadowed module-level Qconv	Local declaration removed; module-level Qconv is now directly assigned
6	slayer/slayer_netcdf.f:299	n_amr_pts defined on qsing_dim but data has size m_AMR	Now correctly defined on nAMR_dim

All Design Issues — Resolved ✅

#	File	Issue	Resolution
7	slayer/slayer_netcdf.f	q_rational stored as nf90_int (lossy)	Changed to nf90_double
8	slayer/layerinputs.f	chi_p_arr(ising) out-of-bounds when msing > 8	MIN(ising, SIZE(arr)) guard added
9	slayer/layerinputs.f:81	Debug WRITE(*,*) '$^$' in production path	Removed
10	slayer/gslayer.f	Two AMR implementations coexisting	dispersion_AMR (v1) prominently marked DEPRECATED
11	slayer/slayer_netcdf.f	Q variable defined but nf90_put_var never called	Q_id removed entirely (flagged in file comment as FLAG 3)

Copilot comment #15 (riccati_del_s relying on stale module globals for tau, D_norm, P_tor) has been documented rather than refactored — lines 166–169 now explicitly state the caller's responsibility. That is acceptable.

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One Remaining Issue

docs/examples/a10_ideal_example/slayer.in:59 still contains:

    growthrates_flag=t   ! Calculate growthrates on each rational surface

The flag growthrates_flag no longer exists in the updated namelist reader. An unknown namelist variable typically causes a fatal runtime error (compiler-dependent, but common with gfortran). It should be replaced with one of the current output flags, e.g.:

    est_gamma_flag=t     ! Calculate estimated growth rates on each rational surface

This was flagged in both my previous review and Copilot comment #17 and was not addressed in 7de735c. Fix this →

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Summary: 11/12 items addressed in 7de735c. Only the stale growthrates_flag in the example input file remains.

[d-burg]

@logan-nc STRIDE on this branch has broken for some reason despite scouring it for bugs and confirming that none of these changes are interfering with the ODE solve. Please hold off further action while I investigate

[d-burg]

@logan-nc the STRIDE bug has been fixed, further strengthening of STRIDE against similar automatic array errors has been moved to a question at #244. I believe this is ready for further review