Test with Probe

[XZTian64]

User description

Description

To test mfc probe output.

Fixes #455

Type of change

Please delete options that are not relevant.

• Bug fix
• Add probe check in ./mfc.sh test
• Rewrite all of the golden data
• Need to do more about the out of tolerance issue
• Something else

Scope

• This PR comprises a set of related changes with a common goal

If you cannot check the above box, please split your PR into multiple PRs that each have a common goal.

How Has This Been Tested?

Please describe the tests that you ran to verify your changes.
Provide instructions so we can reproduce.
Please also list any relevant details for your test configuration

• Test A
• Test B

Test Configuration:

• What computers and compilers did you use to test this:

Checklist

• I have added comments for the new code
• I added Doxygen docstrings to the new code
• I have made corresponding changes to the documentation (docs/)
• I have added regression tests to the test suite so that people can verify in the future that the feature is behaving as expected
• I have added example cases in examples/ that demonstrate my new feature performing as expected.
  They run to completion and demonstrate "interesting physics"
• I ran ./mfc.sh format before committing my code
• New and existing tests pass locally with my changes, including with GPU capability enabled (both NVIDIA hardware with NVHPC compilers and AMD hardware with CRAY compilers) and disabled
• This PR does not introduce any repeated code (it follows the DRY principle)
• I cannot think of a way to condense this code and reduce any introduced additional line count

If your code changes any code source files (anything in src/simulation)

To make sure the code is performing as expected on GPU devices, I have:

• Checked that the code compiles using NVHPC compilers
• Checked that the code compiles using CRAY compilers
• Ran the code on either V100, A100, or H100 GPUs and ensured the new feature performed as expected (the GPU results match the CPU results)
• Ran the code on MI200+ GPUs and ensure the new features performed as expected (the GPU results match the CPU results)
• Enclosed the new feature via nvtx ranges so that they can be identified in profiles
• Ran a Nsight Systems profile using ./mfc.sh run XXXX --gpu -t simulation --nsys, and have attached the output file (.nsys-rep) and plain text results to this PR
• Ran a Rocprof Systems profile using ./mfc.sh run XXXX --gpu -t simulation --rsys --hip-trace, and have attached the output file and plain text results to this PR.
• Ran my code using various numbers of different GPUs (1, 2, and 8, for example) in parallel and made sure that the results scale similarly to what happens if you run without the new code/feature

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PR Type

Enhancement, Tests, Bug fix

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Description

• Enhanced probe output functionality with MHD support and precision-dependent formatting
• Added automatic probe configuration for test cases based on dimensionality (1D, 2D, 3D)
• Implemented special handling for probe files in data packing by discarding time column
• Fixed Silo database function name from DBADDIOPT to DBADDIAOPT
• Updated extensive golden reference data across multiple test cases to include probe output files
• Added magnetic pressure computation and acceleration calculations for 2D simulations
• Improved probe positioning logic and default finite difference order settings

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Changes walkthrough 📝

	Relevant files
Enhancement	3 files m_data_output.fpp Enhanced probe output with MHD support and precision formatting src/simulation/m_data_output.fpp • Added MHD support to probe output by computing magnetic pressure and passing it to pressure computation • Implemented precision-dependent formatting for probe output using dynamic format strings • Fixed chemistry variable initialization to occur within proper conditional blocks • Added acceleration computation for 2D simulations and enhanced probe output formatting for different physics models +92/-33  case.py Automated probe setup for test case generation                      toolchain/mfc/test/case.py • Added automatic probe configuration for test cases based on dimensionality • Implemented probe positioning logic for 1D, 2D, and 3D simulations • Added default finite difference order setting and probe write enablement +33/-3    pack.py Enhanced data packing for probe output files                          toolchain/mfc/packer/pack.py • Added special handling for probe files in data packing by discarding time column • Modified data extraction logic to handle probe output format differently from regular grid data +11/-6
Bug fix	1 files m_data_output.fpp Fixed Silo database function name for option handling        src/post_process/m_data_output.fpp • Fixed function name from DBADDIOPT to DBADDIAOPT for Silo database option handling +4/-4
Tests	4 files golden.txt Updated golden reference data with probe outputs                  tests/2F35A1FE/golden.txt • Updated golden reference data with minor numerical precision changes • Added new probe output data files to test expectations +7/-5      golden.txt Added probe data to golden reference                                          tests/AE9A7D73/golden.txt • Added probe output data to golden reference file +2/-1      golden.txt Update golden test data with probe output files                    tests/2A6136EF/golden.txt • Minor numerical precision adjustments in several data files (D/cons.3.00.000050.dat, D/cons.4.00.000050.dat, D/prim.3.00.000050.dat) • Addition of two new probe data files (D/probe1_prim.dat and D/probe2_prim.dat) containing primitive variable data • Updated golden reference values to reflect probe output testing functionality +5/-3      golden.txt Update golden test data with probe output files                    tests/C79E1D3C/golden.txt • Updated numerical values in D/cons.3.00.000050.dat line with minor precision changes • Updated numerical values in D/cons.4.00.000050.dat line with minor precision changes • Updated numerical values in D/prim.3.00.000050.dat line with minor precision changes • Added two new probe data files: D/probe1_prim.dat and D/probe2_prim.dat with numerical output data +5/-3
Additional files	101 files m_derived_variables.f90 +0/-2      golden-metadata.txt +74/-73  golden.txt +9/-7      golden-metadata.txt +87/-51  golden.txt +14/-6    golden-metadata.txt +113/-43 golden.txt +7/-5      golden-metadata.txt +80/-86  golden.txt +11/-9    golden-metadata.txt +74/-73  golden.txt +14/-5    golden-metadata.txt +74/-73  golden.txt +9/-7      golden-metadata.txt +86/-76  golden.txt +9/-7      golden-metadata.txt +90/-54  golden.txt +12/-4    golden-metadata.txt +84/-111 golden.txt +9/-5      golden-metadata.txt +113/-43 golden.txt +10/-6    golden-metadata.txt +86/-80  golden.txt +13/-5    golden-metadata.txt +83/-80  golden.txt +6/-4      golden-metadata.txt +86/-76  golden.txt +12/-8    golden-metadata.txt +74/-80  golden.txt +13/-5    golden-metadata.txt +87/-51  golden.txt +13/-5    golden-metadata.txt +83/-80  golden.txt +12/-4    golden-metadata.txt +90/-54  golden.txt +14/-6    golden-metadata.txt +77/-83  golden.txt +13/-5    golden-metadata.txt +113/-43 golden.txt +14/-12  golden-metadata.txt +85/-112 golden.txt +13/-5    golden-metadata.txt +87/-51  golden.txt +14/-6    golden-metadata.txt +113/-43 golden.txt +12/-4    golden-metadata.txt +113/-43 golden.txt +11/-3    golden-metadata.txt +77/-76  golden.txt +14/-5    golden-metadata.txt +99/-65  golden.txt +7/-5      golden-metadata.txt +89/-83  golden.txt +7/-3      golden-metadata.txt +74/-73  golden.txt +19/-8    golden-metadata.txt +81/-71  golden.txt +16/-1    golden-metadata.txt +90/-54  golden.txt +12/-4    golden-metadata.txt +90/-54  golden.txt +14/-6    golden-metadata.txt +83/-71  golden.txt +8/-4      golden-metadata.txt +89/-79  golden.txt +14/-6    golden-metadata.txt +113/-43 golden.txt +14/-12  golden-metadata.txt +85/-79  golden.txt +8/-6      golden-metadata.txt +84/-48  golden.txt +10/-2    golden-metadata.txt +86/-113 golden.txt +8/-6      golden-metadata.txt +77/-76  golden.txt +9/-5      golden-metadata.txt +86/-113 golden.txt +6/-4      golden-metadata.txt +84/-48  golden.txt +9/-5      golden-metadata.txt +113/-43 golden.txt +11/-7    golden-metadata.txt +74/-80  golden.txt +8/-4      golden-metadata.txt +83/-80  golden.txt +16/-8    golden-metadata.txt +87/-51  golden.txt +14/-6    golden-metadata.txt +113/-43 golden.txt +11/-3    golden-metadata.txt +100/-66 golden.txt +22/-3    golden-metadata.txt +84/-111 golden.txt +8/-4      golden-metadata.txt +84/-48  golden.txt +9/-5      golden-metadata.txt +84/-111 golden.txt +10/-6    golden-metadata.txt +89/-83  golden.txt +8/-6      golden-metadata.txt +113/-43 Additional files not shown

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PR Reviewer Guide 🔍

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🎫 Ticket compliance analysis 🔶 455 - Partially compliant Compliant requirements: • Add tests to cover lines of code not currently covered by test suite Non-compliant requirements: • Consider using a fuzzer across inputs to ensure user doesn't use nonsense or incompatible initial conditions Requires further human verification: • Improve test code coverage from current 50% level (requires running coverage analysis to verify improvement)

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🧪 PR contains tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Code Duplication Significant code duplication in probe output formatting logic across different dimensional cases (1D, 2D, 3D) and physics models (bubbles_euler, elasticity, MHD). The same magnetic pressure calculation and pressure computation patterns are repeated multiple times. else if (mhd) then pres_mag = 0.5_wp*(Bx0**2 + q_cons_vf(B_idx%beg)%sf(j - 2, k, l)**2 + q_cons_vf(B_idx%beg + 1)%sf(j - 2, k, l)**2) call s_compute_pressure( & q_cons_vf(1)%sf(j - 2, k, l), & q_cons_vf(alf_idx)%sf(j - 2, k, l), & dyn_p, pi_inf, gamma, rho, qv, rhoYks(:), pres, T, & pres_mag=pres_mag) else call s_compute_pressure( & q_cons_vf(1)%sf(j - 2, k, l), & q_cons_vf(alf_idx)%sf(j - 2, k, l), & dyn_p, pi_inf, gamma, rho, qv, rhoYks(:), pres, T) end if if (model_eqns == 4) then lit_gamma = 1._wp/fluid_pp(1)%gamma + 1._wp else if (elasticity) then tau_e(1) = q_cons_vf(stress_idx%end)%sf(j - 2, k, l)/rho end if if (bubbles_euler) then alf = q_cons_vf(alf_idx)%sf(j - 2, k, l) if (num_fluids == 3) then alfgr = q_cons_vf(alf_idx - 1)%sf(j - 2, k, l) end if do s = 1, nb nR(s) = q_cons_vf(bub_idx%rs(s))%sf(j - 2, k, l) nRdot(s) = q_cons_vf(bub_idx%vs(s))%sf(j - 2, k, l) end do if (adv_n) then nbub = q_cons_vf(n_idx)%sf(j - 2, k, l) else nR3 = 0._wp do s = 1, nb nR3 = nR3 + weight(s)*(nR(s)**3._wp) end do nbub = sqrt((4._wp*pi/3._wp)*nR3/alf) end if #ifdef DEBUG print *, 'In probe, nbub: ', nbub #endif if (qbmm) then M00 = q_cons_vf(bub_idx%moms(1, 1))%sf(j - 2, k, l)/nbub M10 = q_cons_vf(bub_idx%moms(1, 2))%sf(j - 2, k, l)/nbub M01 = q_cons_vf(bub_idx%moms(1, 3))%sf(j - 2, k, l)/nbub M20 = q_cons_vf(bub_idx%moms(1, 4))%sf(j - 2, k, l)/nbub M11 = q_cons_vf(bub_idx%moms(1, 5))%sf(j - 2, k, l)/nbub M02 = q_cons_vf(bub_idx%moms(1, 6))%sf(j - 2, k, l)/nbub M10 = M10/M00 M01 = M01/M00 M20 = M20/M00 M11 = M11/M00 M02 = M02/M00 varR = M20 - M10**2._wp varV = M02 - M01**2._wp end if R(:) = nR(:)/nbub Rdot(:) = nRdot(:)/nbub ptilde = ptil(j - 2, k, l) ptot = pres - ptilde end if ! Compute mixture sound Speed call s_compute_speed_of_sound(pres, rho, gamma, pi_inf, & ((gamma + 1._wp)*pres + pi_inf)/rho, alpha, 0._wp, 0._wp, c) accel = accel_mag(j - 2, k, l) end if elseif (p == 0) then ! 2D simulation if ((probe(i)%x >= x_cb(-1)) .and. (probe(i)%x <= x_cb(m))) then if ((probe(i)%y >= y_cb(-1)) .and. (probe(i)%y <= y_cb(n))) then do s = -1, m distx(s) = x_cb(s) - probe(i)%x if (distx(s) < 0._wp) distx(s) = 1000._wp end do do s = -1, n disty(s) = y_cb(s) - probe(i)%y if (disty(s) < 0._wp) disty(s) = 1000._wp end do j = minloc(distx, 1) k = minloc(disty, 1) if (j == 1) j = 2 ! Pick first point if probe is at edge if (k == 1) k = 2 ! Pick first point if probe is at edge l = 0 if (chemistry) then do d = 1, num_species rhoYks(d) = q_cons_vf(chemxb + d - 1)%sf(j - 2, k - 2, l) end do end if ! Computing/Sharing necessary state variables call s_convert_to_mixture_variables(q_cons_vf, j - 2, k - 2, l, & rho, gamma, pi_inf, qv, & Re, G, fluid_pp(:)%G) do s = 1, num_vels vel(s) = q_cons_vf(cont_idx%end + s)%sf(j - 2, k - 2, l)/rho end do dyn_p = 0.5_wp*rho*dot_product(vel, vel) if (elasticity) then if (cont_damage) then damage_state = q_cons_vf(damage_idx)%sf(j - 2, k - 2, l) G = G*max((1._wp - damage_state), 0._wp) end if call s_compute_pressure( & q_cons_vf(1)%sf(j - 2, k - 2, l), & q_cons_vf(alf_idx)%sf(j - 2, k - 2, l), & dyn_p, pi_inf, gamma, rho, qv, & rhoYks, & pres, & T, & q_cons_vf(stress_idx%beg)%sf(j - 2, k - 2, l), & q_cons_vf(mom_idx%beg)%sf(j - 2, k - 2, l), G) else if (mhd) then pres_mag = 0.5_wp*(q_cons_vf(B_idx%beg)%sf(j - 2, k - 2, l)**2 + q_cons_vf(B_idx%beg + 1)%sf(j - 2, k - 2, l)**2 + q_cons_vf(B_idx%beg + 2)%sf(j - 2, k - 2, l)**2) call s_compute_pressure(q_cons_vf(E_idx)%sf(j - 2, k - 2, l), & q_cons_vf(alf_idx)%sf(j - 2, k - 2, l), & dyn_p, pi_inf, gamma, rho, qv, & rhoYks, pres, T, pres_mag=pres_mag) else call s_compute_pressure(q_cons_vf(E_idx)%sf(j - 2, k - 2, l), & q_cons_vf(alf_idx)%sf(j - 2, k - 2, l), & dyn_p, pi_inf, gamma, rho, qv, & rhoYks, pres, T) end if if (model_eqns == 4) then lit_gamma = 1._wp/fluid_pp(1)%gamma + 1._wp else if (elasticity) then do s = 1, 3 tau_e(s) = q_cons_vf(s)%sf(j - 2, k - 2, l)/rho end do end if if (bubbles_euler) then alf = q_cons_vf(alf_idx)%sf(j - 2, k - 2, l) do s = 1, nb nR(s) = q_cons_vf(bub_idx%rs(s))%sf(j - 2, k - 2, l) nRdot(s) = q_cons_vf(bub_idx%vs(s))%sf(j - 2, k - 2, l) end do if (adv_n) then nbub = q_cons_vf(n_idx)%sf(j - 2, k - 2, l) else nR3 = 0._wp do s = 1, nb nR3 = nR3 + weight(s)*(nR(s)**3._wp) end do nbub = sqrt((4._wp*pi/3._wp)*nR3/alf) end if R(:) = nR(:)/nbub Rdot(:) = nRdot(:)/nbub end if ! Compute mixture sound speed call s_compute_speed_of_sound(pres, rho, gamma, pi_inf, & ((gamma + 1._wp)*pres + pi_inf)/rho, alpha, 0._wp, 0._wp, c) accel = accel_mag(j - 2, k - 2, l) end if end if else ! 3D if ((probe(i)%x >= x_cb(-1)) .and. (probe(i)%x <= x_cb(m))) then if ((probe(i)%y >= y_cb(-1)) .and. (probe(i)%y <= y_cb(n))) then if ((probe(i)%z >= z_cb(-1)) .and. (probe(i)%z <= z_cb(p))) then do s = -1, m distx(s) = x_cb(s) - probe(i)%x if (distx(s) < 0._wp) distx(s) = 1000._wp end do do s = -1, n disty(s) = y_cb(s) - probe(i)%y if (disty(s) < 0._wp) disty(s) = 1000._wp end do do s = -1, p distz(s) = z_cb(s) - probe(i)%z if (distz(s) < 0._wp) distz(s) = 1000._wp end do j = minloc(distx, 1) k = minloc(disty, 1) l = minloc(distz, 1) if (j == 1) j = 2 ! Pick first point if probe is at edge if (k == 1) k = 2 ! Pick first point if probe is at edge if (l == 1) l = 2 ! Pick first point if probe is at edge ! Computing/Sharing necessary state variables call s_convert_to_mixture_variables(q_cons_vf, j - 2, k - 2, l - 2, & rho, gamma, pi_inf, qv, & Re, G, fluid_pp(:)%G) do s = 1, num_vels vel(s) = q_cons_vf(cont_idx%end + s)%sf(j - 2, k - 2, l - 2)/rho end do dyn_p = 0.5_wp*rho*dot_product(vel, vel) if (chemistry) then do d = 1, num_species rhoYks(d) = q_cons_vf(chemxb + d - 1)%sf(j - 2, k - 2, l - 2) end do end if if (elasticity) then if (cont_damage) then damage_state = q_cons_vf(damage_idx)%sf(j - 2, k - 2, l - 2) G = G*max((1._wp - damage_state), 0._wp) end if call s_compute_pressure( & q_cons_vf(1)%sf(j - 2, k - 2, l - 2), & q_cons_vf(alf_idx)%sf(j - 2, k - 2, l - 2), & dyn_p, pi_inf, gamma, rho, qv, & rhoYks, pres, T, & q_cons_vf(stress_idx%beg)%sf(j - 2, k - 2, l - 2), & q_cons_vf(mom_idx%beg)%sf(j - 2, k - 2, l - 2), G) else if (mhd) then pres_mag = 0.5_wp*(q_cons_vf(B_idx%beg)%sf(j - 2, k - 2, l - 2)**2 + q_cons_vf(B_idx%beg + 1)%sf(j - 2, k - 2, l - 2)**2 + q_cons_vf(B_idx%beg + 2)%sf(j - 2, k - 2, l - 2)**2) call s_compute_pressure(q_cons_vf(E_idx)%sf(j - 2, k - 2, l), & q_cons_vf(alf_idx)%sf(j - 2, k - 2, l), & dyn_p, pi_inf, gamma, rho, qv, & rhoYks, pres, T, pres_mag=pres_mag) else call s_compute_pressure(q_cons_vf(E_idx)%sf(j - 2, k - 2, l - 2), & q_cons_vf(alf_idx)%sf(j - 2, k - 2, l - 2), & dyn_p, pi_inf, gamma, rho, qv, & rhoYks, pres, T) end if ! Compute mixture sound speed call s_compute_speed_of_sound(pres, rho, gamma, pi_inf, & ((gamma + 1._wp)*pres + pi_inf)/rho, alpha, 0._wp, 0._wp, c) accel = accel_mag(j - 2, k - 2, l - 2) end if end if end if end if if (num_procs > 1) then #:for VAR in ['rho','pres','gamma','pi_inf','qv','c','accel'] tmp = ${VAR}$ call s_mpi_allreduce_sum(tmp, ${VAR}$) #:endfor do s = 1, num_vels tmp = vel(s) call s_mpi_allreduce_sum(tmp, vel(s)) end do if (bubbles_euler) then #:for VAR in ['alf','alfgr','nbub','nR(1)','nRdot(1)','M00','R(1)','Rdot(1)','ptilde','ptot'] tmp = ${VAR}$ call s_mpi_allreduce_sum(tmp, ${VAR}$) #:endfor if (qbmm) then #:for VAR in ['varR','varV','M10','M01','M20','M02'] tmp = ${VAR}$ call s_mpi_allreduce_sum(tmp, ${VAR}$) #:endfor end if end if if (elasticity) then do s = 1, (num_dims*(num_dims + 1))/2 tmp = tau_e(s) call s_mpi_allreduce_sum(tmp, tau_e(s)) end do end if if (cont_damage) then tmp = damage_state call s_mpi_allreduce_sum(tmp, damage_state) end if end if if (precision == 1) then FMT_glb = "F30.7" else FMT_glb = "F40.14" end if if (proc_rank == 0) then if (n == 0) then if (bubbles_euler .and. (num_fluids <= 2)) then if (qbmm) then FMT = '(6X,f12.6,14'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & rho, & vel(1), & pres, & alf, & R(1), & Rdot(1), & nR(1), & nRdot(1), & varR, & varV, & M10, & M01, & M20, & M02 else FMT = '(6X,f12.6,8'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & rho, & vel(1), & pres, & alf, & R(1), & Rdot(1), & nR(1), & nRdot(1) ! ptilde, & ! ptot end if else if (bubbles_euler .and. (num_fluids == 3)) then FMT = '(6X,f12.6,11'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & rho, & vel(1), & pres, & alf, & alfgr, & nR(1), & nRdot(1), & R(1), & Rdot(1), & ptilde, & ptot else if (bubbles_euler .and. num_fluids == 4) then FMT = '(6X,f12.6,13'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & q_cons_vf(1)%sf(j - 2, 0, 0), & q_cons_vf(2)%sf(j - 2, 0, 0), & q_cons_vf(3)%sf(j - 2, 0, 0), & q_cons_vf(4)%sf(j - 2, 0, 0), & q_cons_vf(5)%sf(j - 2, 0, 0), & q_cons_vf(6)%sf(j - 2, 0, 0), & q_cons_vf(7)%sf(j - 2, 0, 0), & q_cons_vf(8)%sf(j - 2, 0, 0), & q_cons_vf(9)%sf(j - 2, 0, 0), & q_cons_vf(10)%sf(j - 2, 0, 0), & nbub, & R(1), & Rdot(1) else FMT = '(6X,f12.6,3'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & rho, & vel(1), & pres end if elseif (p == 0) then if (bubbles_euler) then FMT = '(6X,f12.6,9'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & rho, & vel(1), & vel(2), & pres, & alf, & nR(1), & nRdot(1), & R(1), & Rdot(1) else if (elasticity) then FMT = '(6X,F12.6,7'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & rho, & vel(1), & vel(2), & pres, & tau_e(1), & tau_e(2), & tau_e(3) else FMT = '(6X,F12.6,3'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & rho, & vel(1), & pres print *, 'time =', nondim_time, 'rho =', rho, 'pres =', pres end if else if (bubbles_euler) then FMT = '(6X,F12.6,10'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & rho, & vel(1), & vel(2), & vel(3), & pres, & alf, & nR(1), & nRdot(1), & R(1), & Rdot(1) else if (elasticity) then FMT = '(6X,F12.6,8'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & rho, & vel(1), & vel(2), & vel(3), & pres, & tau_e(1), & tau_e(2), & tau_e(3) else FMT = '(6X,F12.6,11'//FMT_glb//')' write (i + 30, FMT) & nondim_time, & rho, & vel(1), & vel(2), & vel(3), & pres, & ! Out of tolerance gamma, & pi_inf, & qv end if end if Possible Issue In the 3D case MHD pressure calculation, the magnetic field indices appear inconsistent. Line 1405 uses l - 2 for array indexing while line 1406-1409 use l for some variables, which could lead to accessing wrong array elements. else if (mhd) then pres_mag = 0.5_wp*(q_cons_vf(B_idx%beg)%sf(j - 2, k - 2, l - 2)**2 + q_cons_vf(B_idx%beg + 1)%sf(j - 2, k - 2, l - 2)**2 + q_cons_vf(B_idx%beg + 2)%sf(j - 2, k - 2, l - 2)**2) call s_compute_pressure(q_cons_vf(E_idx)%sf(j - 2, k - 2, l), & q_cons_vf(alf_idx)%sf(j - 2, k - 2, l), & dyn_p, pi_inf, gamma, rho, qv, & rhoYks, pres, T, pres_mag=pres_mag) Logic Error The probe positioning logic uses hardcoded array indexing that could cause index out of bounds errors. The f-string formatting uses variables i, j, k in nested loops but the probe array indexing calculations may not match the intended probe numbering scheme. mods[f'probe({{i+1}})%x'] = case['x_domain%beg'] + (i+1) * dx elif case['p'] == 0: mods['num_probes'] = 4 dx = (case['x_domain%end'] - case['x_domain%beg']) / 3 dy = (case['y_domain%end'] - case['y_domain%beg']) / 3 for i in range(2): for j in range(2): mods[f'probe({{i*2+j+1}})%x'] = case['x_domain%beg'] + (i+1) * dx mods[f'probe({{i*2+j+1}})%y'] = case['y_domain%beg'] + (j+1) * dy else: mods['num_probes'] = 8 dx = (case['x_domain%end'] - case['x_domain%beg']) / 3 dy = (case['y_domain%end'] - case['y_domain%beg']) / 3 dz = (case['z_domain%end'] - case['z_domain%beg']) / 3 for i in range(2): for j in range(2): for k in range(2): mods[f'probe({{i*4+j*2+k+1}})%x'] = case['x_domain%beg'] + (i+1) * dx mods[f'probe({{i*4+j*2+k+1}})%y'] = case['y_domain%beg'] + (j+1) * dy mods[f'probe({{i*4+j*2+k+1}})%z'] = case['z_domain%beg'] + (k+1) * dz

[qodo-merge-pro]

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[wilfonba]

Did you make these golden files with '--generate' or with '--add-new-variables'? This feature should be compatible with '--add-new-variables' if it isn't, and the new golden files should be generated with '--add-new-variables' so that the existing golden data isn't changed, just appended to.

[XZTian64]

Did you make these golden files with '--generate' or with '--add-new-variables'? This feature should be compatible with '--add-new-variables' if it isn't, and the new golden files should be generated with '--add-new-variables' so that the existing golden data isn't changed, just appended to.

I used --generate. I will try add-new-variables tonight.

[codecov]

Codecov Report

Attention: Patch coverage is 63.33333% with 22 lines in your changes missing coverage. Please review.

Project coverage is 45.53%. Comparing base (565178a) to head (b8c3ccf).
Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
src/simulation/m_data_output.fpp	63.33%	20 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #943      +/-   ##
==========================================
+ Coverage   44.06%   45.53%   +1.46%     
==========================================
  Files          68       68              
  Lines       18220    18138      -82     
  Branches     2292     2283       -9     
==========================================
+ Hits         8029     8259     +230     
+ Misses       8821     8521     -300     
+ Partials     1370     1358      -12     

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[sbryngelson]

remove your updates to goldenfile_metadata (only commit these if you update the goldenfile itself).

[XZTian64]

remove your updates to goldenfile_metadata (only commit these if you update the goldenfile itself).

I used the --add-new-variables flag, so the golden files were updated accordingly. As a result, the goldenfile_metadata files were also regenerated. Do you want me to roll back the golden_metadata, and update in a separate commit?

[sbryngelson]

Nevermind, I thought you didn't change the actual goldenfiles.