Fix 6 safe pre/post-process bugs (batch)

[sbryngelson]

User description

Summary

Batches 6 low-risk bug fixes that only touch pre-process or post-process CPU code paths. These have no GPU kernel, MPI hot-path, or simulation numerics impact, making them safe to merge with GitHub CI alone.

Included fixes

• s_create_directory wildcard (Fix s_create_directory called with /* wildcard creating junk directory #1214): mkdir was called with /* glob, creating a literal * directory
• Integral z-bounds init (Fix integral zmin/zmax never initialized (copy-paste of ymin/ymax) #1177): zmin/zmax never initialized (copy-paste of ymin/ymax)
• OBJ reader index (Fix OBJ reader using j as both triangle counter and vertex index #1178): j used as both triangle counter and vertex index
• time_real init (Fix time_real used uninitialized in Lagrangian bubble output #1189): Used uninitialized in Lagrangian bubble post-process output
• s_write_intf_data_file loop index (Fix s_write_intf_data_file using wrong loop index for distance check #1191): Wrong loop index for distance check in post-process
• Simplex noise mod range (Fix simplex noise using mod(i,255) instead of iand(i,255) #1218): mod(i,255) skips index 255; fixed to iand(i,255)

Supersedes

Closes #1214, closes #1177, closes #1178, closes #1189, closes #1191, closes #1218

Test plan

• All GitHub CI checks pass (ubuntu MPI debug, ubuntu no-mpi, macOS)
• No Fortran source files in simulation hot path are touched
• Each fix is a 1-3 line change in pre-process or post-process only

🤖 Generated with Claude Code

Summary by CodeRabbit

• Bug Fixes

  • Corrected vertex index handling in OBJ file reader for accurate face parsing.
  • Fixed time value propagation in bubble-related I/O operations.
  • Improved Euclidean distance computation logic in interface data output.
  • Optimized simplex noise index wrapping for better performance.

• Refactor

  • Adjusted default probe coordinate bounds initialization from y-dimension to z-dimension.

---

CodeAnt-AI Description

Fix multiple pre/post-process bugs that previously produced incorrect files, geometry, and outputs

What Changed

• Pre-process directory cleanup now removes the rank directory contents instead of creating a literal "*" folder, and time-step folders are created correctly
• 3D volume integrals now initialize zmin/zmax so computed integrals use the intended z range
• OBJ imports assign the correct third vertex for each triangle so imported models have correct triangle geometry
• Lagrangian bubble output uses the broadcast time so the time column contains the correct simulation time
• Interface point selection fixes the distance check and loop control to avoid incorrect skipping or duplicate selection of points
• 2D simplex noise indexing now includes the full range (uses bitwise-and), preventing skipped indices at the high end

Impact

✅ No junk rank directories created during pre-process
✅ Correct triangle geometry on OBJ import
✅ Correct time values in Lagrangian bubble output

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📝 Walkthrough

Walkthrough

This PR fixes five critical bugs across multiple modules: OBJ reader vertex indexing collision, Lagrangian bubble output time value initialization, interface contour point spacing computation, simplex noise index wrapping range, directory cleanup semantics, and integral z-bounds copy-paste error.

Changes

Cohort / File(s)	Summary
OBJ Reader Vertex Indexing src/common/m_model.fpp	Introduced separate variable iv3 for third vertex index read from face lines, eliminating confusion where triangle counter j was overwritten by vertex index, causing incorrect triangle vertex assignments.
Lagrangian Bubble Time Initialization src/post_process/m_data_output.fpp	Added time_real = file_time assignment after MPI_BCAST in three bubble-related I/O paths to propagate read file time values instead of using uninitialized garbage.
Interface Contour Distance Logic src/post_process/m_data_output.fpp	Moved Euclidean distance computation inside the loop over existing points, changed cycle to exit for early rejection, and removed dead distance code in counter==0 branch to properly check spacing against all stored points.
Directory Cleanup Semantics src/pre_process/m_start_up.fpp	Changed cleanup from creating a literal * directory by attempting mkdir -p path/* to explicitly deleting the entire rank directory before recreating the per-rank subdirectory.
Simplex Noise Index Wrapping src/pre_process/m_simplex_noise.fpp	Replaced modulo wrapping (mod(i, 255)) with bitwise AND wrapping (iand(i, 255)) in two locations to achieve full 0–255 permutation table coverage instead of skipping index 255.
Integral Bounds Initialization src/simulation/m_global_parameters.fpp	Fixed copy-paste error where integral(i)%ymin and integral(i)%ymax were assigned twice; now correctly assigns integral(i)%zmin and integral(i)%zmax for z-dimension bounds.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Possibly related issues

• 2D simplex noise uses mod(i,255) instead of mod(i,256), skipping permutation entry #1223 - Implements the same simplex noise index wrapping fix (mod → iand) to enable full permutation table coverage.
• OBJ reader uses j as both triangle counter and vertex index #1199 - Addresses the OBJ reader vertex indexing bug by using a dedicated variable for the third vertex index instead of overwriting the loop counter.
• s_create_directory called with /* wildcard creates junk directory #1220 - Relates to the directory cleanup fix by replacing wildcard path deletion with explicit directory removal.
• Fix integral zmin/zmax never initialized (copy-paste of ymin/ymax) #1177 - Addresses the z-bounds initialization copy-paste error in integral parameter defaults.
• Fix time_real used uninitialized in Lagrangian bubble output #1189 - Fixes uninitialized time_real in Lagrangian bubble output by assigning from broadcasted file time.
• Add Fortran/Fypp static analysis linter to catch copy-paste bugs #1211 - Addresses the interface contour distance computation bug by moving logic inside the loop and changing control flow.

Suggested labels

bug, critical-fix, high-priority, size:L

Suggested reviewers

• wilfonba

Poem

🐰 A rabbit hops through debug trails,
Six bugs squashed—our hero prevails!
Vertices sorted, times now bright,
Noise wraps full, distances right,
Bounds initialized without fail, ✨
The code now tells a cleaner tale! 🎉

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'Fix 6 safe pre/post-process bugs (batch)' directly and clearly describes the main change: a batch of six bug fixes in pre/post-process code paths.
Linked Issues check	✅ Passed	All six linked issues (#1214, #1177, #1178, #1189, #1191, #1218) are directly addressed by corresponding code changes: directory cleanup, z-bounds initialization, OBJ vertex indexing, time initialization, loop index correction, and simplex noise wrapping.
Out of Scope Changes check	✅ Passed	All changes in five modified files are within scope and directly address the listed objectives. Each modification targets one specific bug mentioned in linked issues with no extraneous changes.
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 is comprehensive, listing all six bug fixes with issue references, motivations, and test plans aligned with the repository template requirements.

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[codeant-ai]

Nitpicks 🔍

🔒 No security issues identified

⚡ Recommended areas for review Index validation After reading face indices (k, l, iv3) there is no validation or handling of negative indices (OBJ allows negative indices) or out-of-range values. This can cause out-of-bounds access on vertices(...) and crash or corrupt memory at runtime. Add bounds checks and negative-index handling. OBJ parsing The new OBJ face read uses a simple list read (three integers) which will fail or produce incorrect indices for common OBJ face formats that include texture/normal indices (e.g. "f v/vt/vn") or for quad faces. The reader should be hardened to accept or reject these formats explicitly and/or parse tokens to extract vertex indices only. Directory Deletion The code now calls s_delete_directory(trim(proc_rank_dir)) (removed the literal '*' bug). Verify that s_delete_directory's semantics are correct here: it should remove only contents (or handle a missing directory) and must not unintentionally remove parent directories needed later. Also ensure this is safe in parallel runs (no race conditions from multiple processes hitting the same filesystem path) and that failures (nonexistent path, permissions) are handled gracefully. Permutation mask The change from mod(i,255) to iand(i,255) fixes skipping index 255 by using a bitmask. Verify that input indices i/j are non-negative or that negative values are handled as intended; also confirm integer kind/magnitude matches the expectations of p_vec indexing. Dedup logic change The duplicate-point detection in s_write_intf_data_file was reworked: the per-point Euclidean distance is now computed inside the loop and the code uses exit when a close point is found. Confirm the new behavior exactly matches the intended semantics (do not add a new point if any existing point lies within tgp). Also check loop ordering and index usage (x/y indices) to ensure comparisons use the correct coordinate arrays and the counter logic is robust.

[cubic-dev-ai]

No issues found across 5 files

Confidence score: 5/5

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

[codeant-ai]

CodeAnt AI finished reviewing your PR.

[Copilot]

Pull request overview

Batches several small correctness fixes across MFC utilities and I/O paths, targeting directory handling, initialization bugs, indexing errors, and post-process output correctness.

Changes:

• Fixes directory cleanup logic in serial pre-process so it deletes the intended rank directory instead of using a non-expanding wildcard.
• Corrects initialization/indexing issues (integral z-bounds init, OBJ face parsing index handling).
• Fixes post-process outputs (initialize time_real from restart metadata; correct interface point distance checking) and simplex-noise index wrapping.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/simulation/m_global_parameters.fpp	Initializes volume-integral zmin/zmax correctly (instead of mistakenly repeating y-bounds).
src/pre_process/m_start_up.fpp	Replaces wildcard-based directory “cleanup” with deletion of the actual per-rank directory, then recreates /0.
src/pre_process/m_simplex_noise.fpp	Uses iand(…,255) for correct 0–255 permutation indexing in 2D simplex noise.
src/post_process/m_data_output.fpp	Initializes time_real from file_time and fixes the interface-point distance check loop to use the correct index and early-exit logic.
src/common/m_model.fpp	Fixes OBJ face parsing so the third vertex index doesn’t overwrite the triangle counter (j).

[coderabbitai]

Actionable comments posted: 2

🤖 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/post_process/m_data_output.fpp`:
- Line 1271: The assignment time_real = file_time in the Silo output function is
dead code because time_real is never used; either remove that assignment from
the Silo branch or add the simulation time metadata to the DBPUTPM call so Silo
stores time. Locate the Silo variant of the output routine (the code path that
calls DBPUTPM) and either delete the time_real variable and its assignment, or
build an options list containing the time (e.g., set "time" or "cycle" entries
using file_time/time_real) and pass it into DBPUTPM so the point-mesh metadata
includes the simulation time.

In `@src/pre_process/m_start_up.fpp`:
- Around line 358-361: The Windows implementation of s_create_directory does not
create parent directories recursively, causing failures when code calls
s_delete_directory(...) then s_create_directory(trim(proc_rank_dir)//'/0') (and
similar calls elsewhere); update the Windows branch in the s_create_directory
implementation (in m_compile_specific) to invoke mkdir with the /s flag (e.g.,
use "mkdir /s <path>" or the equivalent command string) so parent directories
are created recursively, and ensure any other uses of s_create_directory (the
second occurrence noted) benefit from the same change.

[codecov]

Codecov Report

❌ Patch coverage is 30.76923% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 44.06%. Comparing base (df28255) to head (0dabbbc).
⚠️ Report is 9 commits behind head on master.

Files with missing lines	Patch %	Lines
src/post_process/m_data_output.fpp	40.00%	3 Missing ⚠️
src/common/m_model.fpp	0.00%	2 Missing ⚠️
src/pre_process/m_simplex_noise.fpp	0.00%	2 Missing ⚠️
src/pre_process/m_start_up.fpp	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1240      +/-   ##
==========================================
+ Coverage   44.05%   44.06%   +0.01%     
==========================================
  Files          70       70              
  Lines       20496    20497       +1     
  Branches     1989     1989              
==========================================
+ Hits         9030     9033       +3     
+ Misses      10328    10326       -2     
  Partials     1138     1138              

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