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

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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

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

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

krystophny added 2 commits March 27, 2026 18:41

Fix warning cleanups and orbit utilities

48b918b

Remove local CODE libneo overrides

4e1ed99

krystophny force-pushed the feature/fpm-bind branch from 7b3e7df to 4e1ed99 Compare March 27, 2026 17:41

krystophny temporarily deployed to github-pages March 27, 2026 17:41 — with GitHub Actions Inactive

krystophny temporarily deployed to github-pages March 27, 2026 17:42 — 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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