Fix warnings and stabilize orbit diagnostics by krystophny · Pull Request #299 · itpplasma/SIMPLE

krystophny · 2026-01-06T10:09:24Z

User description

Summary

clean up warning sites in orbit integration, diagnostics, samplers, and classification
fix cut detector stencil initialization ordering to avoid out-of-bounds access
adjust boozer converter imports and shift calculation to remove warnings

Testing

make test (timed out while running test_netcdf_results) [log: /tmp/simple_make_test_2026-01-06b.log]
make test TEST=test_netcdf_results [log: /tmp/simple_test_netcdf_results_2026-01-06.log]
make test TEST=test_engineering [log: /tmp/simple_test_engineering_2026-01-06.log]

PR Type

Bug fix, Enhancement

Description

Replace local dp kind definitions with intrinsic iso_fortran_env import
Fix cut detector stencil initialization to avoid out-of-bounds array access
Remove unused variables and clean up compiler warnings across modules
Improve code formatting and fix floating-point comparison logic

Diagram Walkthrough

flowchart LR
  A["Local dp definitions"] -->|Replace with| B["iso_fortran_env import"]
  C["Cut detector loop logic"] -->|Refactor into| D["Two-phase initialization"]
  E["Unused variables"] -->|Remove| F["Clean codebase"]
  G["Floating-point comparison"] -->|Fix| H["Proper zero check"]

File Walkthrough

Relevant files

Cleanup

2 files

simple_diag_orbit.f90 `Remove local dp definition and unused variable`	+1/-5
diag_orbit.f90 `Remove unused ierr_orbit variable declaration`	+2/-2

Enhancement

4 files

classification.f90 `Add iso_fortran_env import, remove local dp definition`	+2/-4
orbit_symplectic.f90 `Add iso_fortran_env import, remove unused variables`	+10/-12
samplers.f90 `Add iso_fortran_env import, remove local dp definition`	+2/-4
sub_alpha_lifetime_can.f90 `Add iso_fortran_env import, improve subroutine signatures`	+6/-9

Bug fix

3 files

cut_detector.f90 `Fix stencil initialization and refactor loop logic`	+77/-19
netcdf_results_output.f90 `Fix floating-point zero comparison logic`	+1/-1
boozer_converter.F90 `Remove unused import and fix shift calculation`	+3/-3

qodo-code-review · 2026-01-06T10:09:49Z

PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
🟢	No security concerns identified No security vulnerabilities detected by AI analysis. Human verification advised for critical code.
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qodo-code-review · 2026-01-06T10:11:39Z

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Restore missing solver variables Restore the declaration of `pivot` and `info` variables, which were removed in the PR. These are necessary for the `dgesv` LAPACK solver call and their absence will cause a compilation error. src/orbit_symplectic.f90 [425] real(dp) :: fvec(n), fjac(n,n), jinv(n,n) +integer :: pivot(n), info `[To ensure code accuracy, apply this suggestion manually]` Suggestion importance[1-10]: 9 __ Why: The PR incorrectly removed the `pivot` and `info` variable declarations, which are required by the `dgesv` LAPACK routine, causing a compilation error. This suggestion correctly restores them.	High
Possible issue	Remove dead code from loop Remove the unreachable cut detection logic from the initialization loop in `advance_to_cut`. The condition `if(i.gt.nplagr ...)` is always false within this loop, making the code dead. src/cut_detector.f90 [88-149] do i = 1, nplagr call tstep(si, f, z, ierr) if (ierr.ne.0) exit self%par_inv = self%par_inv + z(5)*2 ! parallel adiabatic invariant self%orb_sten(1:5, i) = z self%orb_sten(6, i) = self%par_inv !------------------------------------------------------------------------- - ! Tip detection and interpolation - + ! Tip detection if(self%alam_prev.lt.0.d0.and.z(5).gt.0.d0) then self%itip=0 !<=tip has been passed end if self%itip=self%itip+1 self%alam_prev=z(5) - - !<=use only initialized stencil - if(i.gt.nplagr .and. self%itip.eq.nplagr/2) then - cut_type = 0 - call plag_coeff(nplagr, nder, 0d0, self%orb_sten(5, self%ipoi), & - self%coef) - var_cut = matmul(self%orb_sten(:, self%ipoi), self%coef(0,:)) - var_cut(2) = modulo(var_cut(2), twopi) - var_cut(3) = modulo(var_cut(3), twopi) - self%par_inv = self%par_inv - var_cut(6) - return - end if - - ! End tip detection and interpolation + ! End tip detection !------------------------------------------------------------------------- - ! Periodic boundary footprint detection and interpolation - + ! Periodic boundary footprint detection if(z(3).gt.dble(self%kper+1)self%fper) then self%iper=0 !<=periodic boundary has been passed phiper=dble(self%kper+1)self%fper self%kper=self%kper+1 elseif(z(3).lt.dble(self%kper)self%fper) then self%iper=0 !<=periodic boundary has been passed phiper=dble(self%kper)self%fper self%kper=self%kper-1 endif self%iper=self%iper+1 - - !<=use only initialized stencil - if(i.gt.nplagr .and. self%iper.eq.nplagr/2) then - cut_type = 1 - !<=stencil around periodic boundary is complete, interpolate - call plag_coeff(nplagr, nder, 0d0, self%orb_sten(3, self%ipoi) - & - phiper, self%coef) - var_cut = matmul(self%orb_sten(:, self%ipoi), self%coef(0,:)) - var_cut(2) = modulo(var_cut(2), twopi) - var_cut(3) = modulo(var_cut(3), twopi) - return - end if - - ! End periodic boundary footprint detection and interpolation + ! End periodic boundary footprint detection !------------------------------------------------------------------------- - end do + end do Apply / Chat* Suggestion importance[1-10]: 7 __ Why: The suggestion correctly identifies dead code within the first `do` loop, where the condition `i.gt.nplagr` can never be met, making the enclosed logic unreachable.	Medium
General	Use tolerance for zero check Replace the direct comparison of floating-point values with zero with a check against a small tolerance (e.g., `1.0e-12_dp`) for robustness. src/netcdf_results_output.f90 [321] -zend_is_zero = all(abs(zend(1:3, i)) <= 0.0_dp) +zend_is_zero = all(abs(zend(1:3, i)) <= 1.0e-12_dp) Apply / Chat Suggestion importance[1-10]: 5 __ Why: The suggestion correctly points out that comparing floating-point numbers directly to zero is fragile and recommends using a small tolerance, which is a standard best practice.	Low
Update

qodo-code-review · 2026-01-06T10:49:38Z

CI Feedback 🧐

A test triggered by this PR failed. Here is an AI-generated analysis of the failure:

Action: Build and Test
Failed stage: Run Fast Tests (Fortran only) [❌]
Failed test name: test_chartmap_ncsx_map2disc_wall_offset
Failure summary: The action failed during the CTest phase because 1 out of 47 tests failed: - `test_chartmap_ncsx_map2disc_wall_offset` (shown as test `#4`) failed with an assertion/tolerance check: `chartmap wall deviates from buffered VMEC boundary: max_to_buffer=6.801169e-03 m (tol` `1.000000e-03) at phi=0.253866` This caused `ctest` to return a non-zero exit status (`Errors while` `running CTest`), which then made the `make test-fast` target fail (`Makefile:47: test-fast`), and the GitHub Action step exited with code `2` (`Process completed with exit code 2`).
Relevant error logs: 1: Runner name: 'debian' 2: Runner group name: 'default' ... 25: ssh-user: git 26: persist-credentials: true 27: clean: true 28: sparse-checkout-cone-mode: true 29: fetch-tags: false 30: show-progress: true 31: lfs: false 32: submodules: false 33: set-safe-directory: true 34: env: 35: LIBNEO_BRANCH: feature/fpm-bind 36: ##[endgroup] 37: Syncing repository: itpplasma/SIMPLE 38: ##[group]Getting Git version info 39: Working directory is '/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE' 40: Unexpected error attempting to determine if executable file exists '/home/ert/.npm-global/bin/git': Error: EACCES: permission denied, stat '/home/ert/.npm-global/bin/git' 41: Unexpected error attempting to determine if executable file exists '/home/ert/code/.venv/bin/git': Error: EACCES: permission denied, stat '/home/ert/code/.venv/bin/git' 42: Unexpected error attempting to determine if executable file exists '/home/ert/code/scripts/git': Error: EACCES: permission denied, 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2290: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_io.f90:126:49: 2291: 126 \| subroutine savefig(filename, dpi, transparent, bbox_inches) 2292: \| 1 2293: Warning: Unused dummy argument ‘transparent’ at (1) [-Wunused-dummy-argument] 2294: [673/957] Building Fortran object _deps/fortplot-build/CMakeFiles/fortplot.dir/src/fortplot_animation_pipeline.f90.o 2295: [674/957] Building Fortran object _deps/fortplot-build/CMakeFiles/fortplot.dir/src/fortplot_matplotlib_plotting.f90.o 2296: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:333:59: 2297: 333 \| subroutine add_3d_plot(x, y, z, label, linestyle, color, linewidth, marker, markersize) 2298: \| 1 2299: Warning: Unused dummy argument ‘color’ at (1) [-Wunused-dummy-argument] 2300: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:259:91: 2301: 259 \| subroutine add_errorbar(x, y, xerr, yerr, fmt, label, capsize, linestyle, marker, color) 2302: \| 1 ... 2358: \| 1 2359: Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable] 2360: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:54:57: 2361: 54 \| subroutine bar(x, height, width, bottom, label, color, edgecolor, align) 2362: \| 1 2363: Warning: Unused dummy argument ‘color’ at (1) [-Wunused-dummy-argument] 2364: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:54:68: 2365: 54 \| subroutine bar(x, height, width, bottom, label, color, edgecolor, align) 2366: \| 1 2367: Warning: Unused dummy argument ‘edgecolor’ at (1) [-Wunused-dummy-argument] 2368: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:65:20: 2369: 65 \| integer :: i 2370: \| 1 2371: Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable] 2372: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:41:61: 2373: 41 \| subroutine errorbar(x, y, xerr, yerr, fmt, label, capsize, linestyle, marker, color) 2374: \| 1 2375: Warning: Unused dummy argument ‘capsize’ at (1) [-Wunused-dummy-argument] 2376: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:41:87: 2377: 41 \| subroutine errorbar(x, y, xerr, yerr, fmt, label, capsize, linestyle, marker, color) 2378: \| 1 2379: Warning: Unused dummy argument ‘color’ at (1) [-Wunused-dummy-argument] 2380: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:41:45: 2381: 41 \| subroutine errorbar(x, y, xerr, yerr, fmt, label, capsize, linestyle, marker, color) 2382: \| 1 2383: Warning: Unused dummy argument ‘fmt’ at (1) [-Wunused-dummy-argument] 2384: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:41:80: 2385: 41 \| subroutine errorbar(x, y, xerr, yerr, fmt, label, capsize, linestyle, marker, color) 2386: \| 1 2387: Warning: Unused dummy argument ‘marker’ at (1) [-Wunused-dummy-argument] 2388: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:41:34: 2389: 41 \| subroutine errorbar(x, y, xerr, yerr, fmt, label, capsize, linestyle, marker, color) 2390: \| 1 2391: Warning: Unused dummy argument ‘xerr’ at (1) [-Wunused-dummy-argument] 2392: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/fortplot-src/src/fortplot_matplotlib_plotting.f90:41:40: 2393: 41 \| subroutine errorbar(x, y, xerr, yerr, fmt, label, capsize, linestyle, marker, color) 2394: \| 1 ... 2769: Constructing wrapper function "f2py_vmec_wrappers.vmec_field_wrapper"... 2770: a_theta,a_phi,da_theta_ds,da_phi_ds,aiota,sqg,alam,dl_ds,dl_dt,dl_dp,bctrvr_vartheta,bctrvr_varphi,bcovar_s,bcovar_vartheta,bcovar_varphi = vmec_field_wrapper(s,theta,varphi) 2771: Constructing wrapper function "f2py_vmec_wrappers.vmec_field_cylindrical_wrapper"... 2772: br,bphi,bz,bmag = vmec_field_cylindrical_wrapper(s,theta,varphi) 2773: Wrote C/API module "_magfie" to file "./_magfiemodule.c" 2774: Fortran 90 wrappers are saved to "./_magfie-f2pywrappers2.f90" 2775: [729/957] Building Fortran preprocessed _deps/libneo-build/CMakeFiles/_magfie.dir/src/f2py_interfaces/f2py_vmec_support.f90-pp.f90 2776: [730/957] Building Fortran preprocessed _deps/libneo-build/CMakeFiles/_magfie.dir/_magfie-f2pywrappers2.f90-pp.f90 2777: [731/957] Building Fortran preprocessed _deps/libneo-build/CMakeFiles/_magfie.dir/src/magfie/magfie_vmec.f90-pp.f90 2778: [732/957] Building Fortran preprocessed _deps/libneo-build/CMakeFiles/_magfie.dir/_magfie-f2pywrappers.f-pp.f 2779: [733/957] Building Fortran preprocessed _deps/libneo-build/CMakeFiles/_magfie.dir/src/f2py_interfaces/f2py_vmec_wrappers.f90-pp.f90 2780: [734/957] Building Fortran preprocessed _deps/libneo-build/CMakeFiles/_magfie.dir/src/f2py_interfaces/f2py_magfie.f90-pp.f90 2781: [735/957] Generating Fortran dyndep file _deps/libneo-build/CMakeFiles/_magfie.dir/Fortran.dd 2782: [736/957] Building Fortran object _deps/libneo-build/CMakeFiles/_magfie.dir/_magfie-f2pywrappers.f.o 2783: [737/957] Generating _efit_to_boozermodule.c, _efit_to_boozer-f2pywrappers.f, _efit_to_boozer-f2pywrappers2.f90 2784: OSError: [Errno 2] No such file or directory: '/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/src/magfie/field_divB0.f90'. Skipping file "/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/src/magfie/field_divB0.f90". 2785: OSError: [Errno 2] No such file or directory: '/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/src/magfie/field_eq_mod.f90'. Skipping file "/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/src/magfie/field_eq_mod.f90". 2786: OSError: [Errno 2] No such file or directory: '/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/src/spl_three_to_five.f90'. Skipping file "/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/src/spl_three_to_five.f90". 2787: OSError: [Errno 2] No such file or directory: '/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/src/plag_coeff.f90'. Skipping file "/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/src/plag_coeff.f90". 2788: OSError: [Errno 2] No such file or directory: '/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/src/binsrc.f90'. Skipping file "/home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/src/binsrc.f90". 2789: get_useparameters: mapping for {'only': 1, 'map': {'psimax': 'psimax'}} not impl. ... 3306: LIBNEO_BRANCH: feature/fpm-bind 3307: ##[endgroup] 3308: cmake --build build --config Release 3309: [1/1] cd /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/libneo-src/extra/MyMPILib && /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/_deps/libneo-src/extra/MyMPILib/Scripts/do_versioning.sh 3310: Versioning MyMPILib... 3311: cd build && ctest --test-dir test --output-on-failure -LE "slow\|regression" 3312: Internal ctest changing into directory: /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/test 3313: Test project /home/github-runner/actions-runner/_work/SIMPLE/SIMPLE/build/test 3314: Start 1: generate_chartmap_map2disc 3315: 1/47 Test #1: generate_chartmap_map2disc ...................... Passed 8.21 sec 3316: Start 2: generate_chartmap_ncsx_map2disc 3317: 2/47 Test #2: generate_chartmap_ncsx_map2disc ................. Passed 8.80 sec 3318: Start 3: generate_chartmap_ncsx_map2disc_wall 3319: 3/47 Test #3: generate_chartmap_ncsx_map2disc_wall ............ Passed 9.82 sec 3320: Start 4: test_chartmap_ncsx_map2disc_wall_offset 3321: 4/47 Test #4: test_chartmap_ncsx_map2disc_wall_offset .........**Failed 0.64 sec 3322: chartmap wall deviates from buffered VMEC boundary: max_to_buffer=6.801169e-03 m (tol 1.000000e-03) at phi=0.253866 ... 3394: 40/47 Test #54: test_orbit_refcoords_rk45_plot .................. Passed 0.89 sec 3395: Start 55: test_orbit_chartmap_comparison 3396: 41/47 Test #55: test_orbit_chartmap_comparison .................. Passed 6.04 sec 3397: Start 56: test_chartmap_refcoords_config 3398: 42/47 Test #56: test_chartmap_refcoords_config .................. Passed 0.36 sec 3399: Start 59: test_orbit_chartmap_comparison_plot 3400: 43/47 Test #59: test_orbit_chartmap_comparison_plot ............. Passed 0.77 sec 3401: Start 60: test_orbit_chartmap_comparison_map2disc 3402: 44/47 Test #60: test_orbit_chartmap_comparison_map2disc ......... Passed 6.20 sec 3403: Start 61: test_orbit_chartmap_comparison_plot_map2disc 3404: 45/47 Test #61: test_orbit_chartmap_comparison_plot_map2disc .... Passed 0.81 sec 3405: Start 62: test_chartmap_refcoords_config_map2disc 3406: 46/47 Test #62: test_chartmap_refcoords_config_map2disc ......... Passed 0.36 sec 3407: Start 73: test_engineering 3408: 47/47 Test #73: test_engineering ................................ Passed 1.37 sec 3409: 98% tests passed, 1 tests failed out of 47 3410: Label Time Summary: 3411: engineering = 1.37 secproc (1 test) 3412: integration = 175.88 secproc (23 tests) 3413: performance = 0.53 secproc (1 test) 3414: plot = 4.52 secproc (7 tests) 3415: python = 80.49 secproc (15 tests) 3416: system = 18.80 secproc (3 tests) 3417: unit = 5.57 secproc (5 tests) 3418: Total Test time (real) = 221.03 sec 3419: The following tests FAILED: 3420: 4 - test_chartmap_ncsx_map2disc_wall_offset (Failed) integration plot python 3421: Errors while running CTest 3422: make: *** [Makefile:47: test-fast] Error 8 3423: ##[error]Process completed with exit code 2. 3424: ##[group]Run actions/upload-artifact@v4 3425: with: 3426: name: test-results 3427: path: build/Testing/ 3428: 3429: if-no-files-found: warn 3430: compression-level: 6 3431: overwrite: false 3432: include-hidden-files: false 3433: env: 3434: LIBNEO_BRANCH: feature/fpm-bind 3435: ##[endgroup] 3436: ##[warning]No files were found with the provided path: build/Testing/. No artifacts will be uploaded. 3437: Post job cleanup. 3438: Unexpected error attempting to determine if executable file exists '/home/ert/.npm-global/bin/git': Error: EACCES: permission denied, stat '/home/ert/.npm-global/bin/git' 3439: Unexpected error attempting to determine if executable file exists '/home/ert/code/.venv/bin/git': Error: EACCES: permission denied, stat '/home/ert/code/.venv/bin/git' 3440: Unexpected error attempting to determine if executable file exists '/home/ert/code/scripts/git': Error: EACCES: permission denied, stat '/home/ert/code/scripts/git' 3441: [command]/usr/bin/git version

Fix warning cleanups and orbit utilities

6492fc3

krystophny temporarily deployed to github-pages January 6, 2026 10:09 — with GitHub Actions Inactive

qodo-code-review bot added the Review effort 3/5 label Jan 6, 2026

Remove local CODE libneo overrides

7b3e7df

krystophny temporarily deployed to github-pages January 6, 2026 10:45 — with GitHub Actions Inactive

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Fix warnings and stabilize orbit diagnostics#299

Fix warnings and stabilize orbit diagnostics#299
krystophny wants to merge 2 commits intomainfrom
feature/fpm-bind

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