Fix 6 low-risk pre-process bugs (batch)

[sbryngelson]

User description

Summary

Batches 6 low-risk bug fixes in pre-process code paths. These fix real numerical issues in IC generation but don't touch simulation GPU kernels or MPI hot paths.

Included fixes

• moncon_cutoff type (Fix moncon_cutoff declared as integer, truncating 1e-8 to 0 #1174): Declared as integer, silently truncating 1e-8 to 0 — disabled MUSCL-THINC monotonicity limiter
• Grid stretching bounds (Fix grid stretching using wrong array bounds for y_cc and z_cc #1179): y_cc(0:m) and z_cc(0:m) used x-dimension bound instead of 0:n/0:p
• Duplicate R3bar (Remove duplicate R3bar accumulation line that doubles bubble perturbation #1183): Copy-paste duplicate line doubled bubble perturbation magnitude in QBMM IC
• Perturbation velocity order (Fix y-velocity perturbation using already-modified x-velocity #1216): y-velocity perturbation read already-modified x-velocity
• Hyper-cleaning 3D init (Fix hyper_cleaning psi initialization only covering k=0 plane #1217): psi initialization only covered k=0 plane in 3D MHD cases
• IB patch broadcast loop (Fix IB patch vel/angular_vel/angles broadcast inside wrong loop #1188): vel/angular_vel/angles broadcast was inside the wrong loop

Supersedes

Closes #1174, closes #1179, closes #1183, closes #1216, closes #1217, closes #1188

Test plan

• All GitHub CI checks pass (ubuntu MPI debug, ubuntu no-mpi, macOS)
• All changes are in pre-process or MPI setup — no simulation hot-path modifications
• Verify with stretched grid, QBMM, MHD, and IB test cases if available

🤖 Generated with Claude Code

Summary by CodeRabbit

• Bug Fixes

  • Fixed grid cell-center indexing in y/z for accurate grid generation.
  • Removed a redundant momentum accumulation step.

• Improvements

  • Enhanced initialization to better support 3D configurations.
  • Improved numerical precision for monotonicity constraint handling.

• Chores

  • Reorganized MPI communication sequence for immersed-boundary variables.

---

CodeAnt-AI Description

Fix several pre-process bugs that caused incorrect initial conditions and grid errors

What Changed

• THINC monotonicity limiter now uses a tiny real threshold so the limiter is applied correctly (previously treated as zero and effectively disabled)
• Stretched grid cell-center coordinates for y and z now use the correct dimension bounds so stretched grids produce correct cell centers when dimensions differ
• QBMM bubble size accumulator corrected so initial bubble perturbation magnitudes are not doubled
• Random flow perturbation now updates the intended velocity component in the correct order so velocity perturbations use the original values
• Hyper-cleaning psi initialization now fills all 3D planes, uses consistent precision, and avoids accessing z-coordinates in 2D runs
• Immersed-boundary patch velocity/angle data are broadcast across MPI in the correct loop so all ranks receive IB motion data

Impact

✅ Correct THINC monotonicity behavior during interface reconstruction
✅ Accurate stretched grid coordinates when x/y/z sizes differ
✅ Correct initial bubble perturbation magnitudes for QBMM cases

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📝 Walkthrough

Walkthrough

Six targeted bug fixes across preprocessing and constants: corrected a constant type, removed a duplicate accumulation, fixed grid center index bounds, moved MPI broadcasts to the correct loop, adjusted perturbation assignments, and expanded 3D startup psi initialization to all z-planes.

Changes

Cohort / File(s)	Summary
Constants src/common/m_constants.fpp	Changed moncon_cutoff from integer to real(wp) so 1e-8_wp is retained as a real value.
QBMM / Perturbation src/pre_process/m_assign_variables.fpp	Removed duplicate R3bar accumulation line in QBMM branch that previously doubled the contribution.
Grid generation src/pre_process/m_grid.f90	Fixed cell-center assignments to use correct dimension bounds: y_cc(0:n) and z_cc(0:p) (previously used m).
MPI / IB broadcasts src/pre_process/m_mpi_proxy.fpp	Moved broadcasts of patch_ib(%vel), patch_ib(%angular_vel), and patch_ib(%angles) out of the BC-patch loop into the IB-patch broadcast blocks using correct sizes.
Perturbation ordering src/pre_process/m_perturbation.fpp	Adjusted assignment order so y-velocity perturbation reads the original x-velocity before x-velocity is modified (prevents unintended coupling).
Startup / 3D init src/pre_process/m_start_up.fpp	Extended hyper_cleaning psi initialization to loop over l = 0..p, initializing psi across all z-planes and using z_cc(l) in the Gaussian expression.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Possibly related issues

• MFlowCode/MFC#1197: Same moncon_cutoff fix — changes moncon_cutoff to real(wp) to avoid truncation-to-zero.
• MFlowCode/MFC#1208: Same IB broadcast relocation — moves vel/angular_vel/angles broadcasts into correct IB-patch loop.

Possibly related PRs

• MFlowCode/MFC#1116: Modifies IB-variable MPI broadcast logic in m_mpi_proxy.fpp, strongly related to the broadcast reorganization here.
• MFlowCode/MFC#1063: Changes s_perturb_primitive in m_assign_variables.fpp; related to the QBMM / perturbation adjustments in this PR.

Suggested labels

Review effort 1/5, size:L

Suggested reviewers

• wilfonba

Poem

🐰 I hopped through code and found the spots,
Constants mended, grids set in their slots.
Broadcasts moved to the proper loop,
Perturbations fixed — no sneaky dup or loop.
Psi now fills every z-plane — hop, hop, hooray!

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title clearly summarizes a batch of low-risk pre-process bug fixes, accurately representing the primary changes across multiple files.
Linked Issues check	✅ Passed	All code changes directly address the primary coding requirements from the six linked issues: moncon_cutoff type correction, grid bounds fixes, duplicate removal, velocity order correction, psi 3D initialization, and IB broadcast loop relocation.
Out of Scope Changes check	✅ Passed	All six file changes are scoped to the linked issues: constant declaration, grid computation, QBMM accumulation, perturbation order, hyper-cleaning initialization, and MPI broadcast loop—no out-of-scope changes detected.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description check	✅ Passed	The pull request description includes all required template sections: summary of changes, issue references, type of change (Refactor), testing notes, and a comprehensive checklist with GPU considerations noted.

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[cubic-dev-ai]

No issues found across 6 files

Confidence score: 5/5

• Automated review surfaced no issues in the provided summaries.
• No files require special attention.

[codeant-ai]

Nitpicks 🔍

🔒 No security issues identified

⚡ Recommended areas for review IB broadcast placement The broadcast of IB patch arrays (vel, angular_vel, angles) has been moved into the IB broadcast block. Verify there are no remaining duplicated broadcasts, that the size/count (3) matches the array shapes everywhere, and that ordering of broadcasts matches the data layout expected on receivers. Monotonicity cutoff type The parameter moncon_cutoff was changed from an integer to a real. Verify every usage site expects a real (comparisons, arithmetic, interfaces). Mixed-type assumptions elsewhere could silently convert or truncate values or change logic in monotonicity checks. Y cell-center bounds The y cell-center calculation was corrected to use the y-dimension range. Validate index ranges of y_cb and y_cc (uses of -1:n-1) are consistent with alloc/usage elsewhere, and that the min cell size dy and subsequent MPI reduction use the updated values. Z cell-center bounds The z cell-center calculation was corrected to use the z-dimension range. Confirm z_cb/z_cc indexing and dz computation are correct for both serial and parallel grid routines and consistent with any callers. Perturbation assignment order The order of assignments for perturbed momenta was changed so mom_idx%end is set from the original mom_idx%beg before mom_idx%beg is scaled. Confirm no other code in the same loop reads mom_idx%beg after it is updated (should use original value) and consider making the use of the original value explicit to avoid future ordering bugs.

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[Copilot]

Pull request overview

This PR batches 6 bug fixes in pre-process code paths that address real numerical issues in initial condition generation. The fixes correct type declarations, array bounds, duplicate operations, statement ordering, loop coverage, and MPI broadcast placement.

Changes:

• Fixed moncon_cutoff declared as integer instead of real(wp), which silently truncated 1e-8 to 0 and disabled MUSCL-THINC monotonicity limiting
• Corrected grid stretching array bounds for y_cc and z_cc using wrong dimension (m instead of n and p)
• Removed duplicate R3bar accumulation line that doubled bubble perturbation magnitude in QBMM initial conditions
• Reordered perturbation statements so y-velocity uses original x-velocity before x-velocity is modified
• Extended hyper-cleaning psi initialization to cover all z-planes in 3D (was only initializing k=0 plane)
• Moved IB patch velocity/angular_vel/angles broadcasts from wrong loop to correct loop

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/common/m_constants.fpp	Changed moncon_cutoff from integer to real(wp) to prevent truncation
src/pre_process/m_grid.f90	Fixed y_cc and z_cc array bounds to use correct dimensions (n and p instead of m)
src/pre_process/m_assign_variables.fpp	Removed duplicate R3bar accumulation line in QBMM branch
src/pre_process/m_perturbation.fpp	Swapped statement order so y-velocity perturbation uses unmodified x-velocity
src/pre_process/m_start_up.fpp	Added outer z-loop for 3D psi initialization and replaced double-precision literal
src/pre_process/m_mpi_proxy.fpp	Moved patch_ib vel/angular_vel/angles broadcasts to num_patches_max loop

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[codecov]

Codecov Report

❌ Patch coverage is 27.27273% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 44.05%. Comparing base (df28255) to head (068c79c).
⚠️ Report is 10 commits behind head on master.

Files with missing lines	Patch %	Lines
src/pre_process/m_start_up.fpp	28.57%	5 Missing ⚠️
src/pre_process/m_grid.f90	0.00%	2 Missing ⚠️
src/pre_process/m_perturbation.fpp	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1241      +/-   ##
==========================================
- Coverage   44.05%   44.05%   -0.01%     
==========================================
  Files          70       70              
  Lines       20496    20499       +3     
  Branches     1989     1992       +3     
==========================================
+ Hits         9030     9031       +1     
- Misses      10328    10330       +2     
  Partials     1138     1138              

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/pre_process/m_start_up.fpp`:
- Around line 790-797: Add a validator in the CaseValidator
(toolchain/mfc/case_validator.py) to forbid enabling hyper_cleaning in 2D: call
self.prohibit(hyper_cleaning and p is not None and p == 0, "Hyperbolic cleaning
is not supported for 2D simulations") in the validation routine that checks
dimensionality (the same place that already forbids 1D via n==0); this prevents
m_start_up.fpp from accessing unallocated z_cc when p==0 by rejecting
hyper_cleaning for 2D cases.

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ℹ️ Review info

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between e8d2790 and 553161d.

📒 Files selected for processing (6)

• src/common/m_constants.fpp
• src/pre_process/m_assign_variables.fpp
• src/pre_process/m_grid.f90
• src/pre_process/m_mpi_proxy.fpp
• src/pre_process/m_perturbation.fpp
• src/pre_process/m_start_up.fpp

💤 Files with no reviewable changes (1)

• src/pre_process/m_assign_variables.fpp

🚧 Files skipped from review as they are similar to previous changes (2)

• src/common/m_constants.fpp
• src/pre_process/m_mpi_proxy.fpp

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