Extrusion v3#1349
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March 30, 2026 22:18
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Review Summary by QodoAdd premixed flame IC cases and refactor extrusion workflow with configurable paths
WalkthroughsDescription• Add two new hardcoded IC cases (271, 272) for premixed flame simulations - Case 271: Premixed flame vortex interaction with dual counter-rotating vortices - Case 272: Premixed flame instability with sinusoidal front perturbation • Refactor IC extrusion workflow to use configurable files_dir and file_extension parameters - Replace hardcoded path and filename pattern with user-configurable parameters - Improve MPI communication for new parameters via broadcast • Add three reference example cases with complete configuration files - 1D flamelet case with San Diego mechanism - 2D premixed flame vortex interaction case - 2D premixed flame Landau instability case • Update parameter definitions and test suite for new IC extrusion examples Diagramflowchart LR
A["Hardcoded IC Cases<br/>271, 272"] -->|"Vortex & Instability<br/>Perturbations"| B["2D Premixed<br/>Flame Simulations"]
C["Configurable<br/>files_dir & file_extension"] -->|"Replace hardcoded<br/>init_dir"| D["Flexible IC<br/>Extrusion"]
E["Reference Examples<br/>1D, 2D cases"] -->|"Complete setup<br/>with case.py"| F["User-friendly<br/>Workflow"]
D --> B
F --> B
File Changes1. src/common/include/2dHardcodedIC.fpp
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Code Review by Qodo
1. files_extension parameter typo
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📝 WalkthroughWalkthroughThis pull request introduces a new 1D flamelet example case and updates related documentation. A 🚥 Pre-merge checks | ✅ 2 | ❌ 1❌ Failed checks (1 inconclusive)
✅ Passed checks (2 passed)
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Actionable comments posted: 2
🧹 Nitpick comments (1)
.gitignore (1)
57-57: Redundant ignore pattern (no functional change).Line 57 is already covered by
examples/**/*.dat(Line 64), so this new rule is a no-op. Consider removing it to keep ignore rules minimal.
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⛔ Files ignored due to path filters (42)
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📒 Files selected for processing (17)
.gitignoredocs/documentation/case.mdexamples/1D_flamelet/case.pyexamples/1D_flamelet/sandiego.yamlexamples/2D_premixed_flame_vortex/case.pyexamples/2D_premixed_landau_insta/case.pysrc/common/include/2dHardcodedIC.fppsrc/common/include/ExtrusionHardcodedIC.fppsrc/pre_process/m_global_parameters.fppsrc/pre_process/m_mpi_proxy.fppsrc/pre_process/m_start_up.fpptests/0D1E22F3/golden-metadata.txttests/0D1E22F3/golden.txttoolchain/mfc/params/definitions.pytoolchain/mfc/params/descriptions.pytoolchain/mfc/params/namelist_parser.pytoolchain/mfc/test/cases.py
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #1349 +/- ##
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- Coverage 64.88% 64.13% -0.75%
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Files 70 70
Lines 18249 18337 +88
Branches 1507 1511 +4
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- Hits 11841 11761 -80
- Misses 5446 5534 +88
- Partials 962 1042 +80 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Code Review by Qodo
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| #:enddef | ||
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| #:def HardcodedReadValues() | ||
| if (.not. files_loaded) then | ||
| max_files = merge(sys_size, sys_size - 1, num_dims == 1) | ||
| do f = 1, max_files | ||
| write (file_num_str, '(I0)') f | ||
| fileNames(f) = trim(init_dir) // "prim." // trim(file_num_str) // ".00." // zeros_default // ".dat" | ||
| fileNames(f) = trim(files_dir) // "/" // "prim." // trim(file_num_str) // ".00." // trim(file_extension) // ".dat" |
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1. files_dir undefined in simulation 📘 Rule violation ≡ Correctness
ExtrusionHardcodedIC.fpp now references files_dir and file_extension, but the simulation-side m_global_parameters/namelist/MPI broadcast do not define or distribute these parameters. This can break simulation compilation or cause rank-to-rank mismatches at runtime when using extrusion-based ICs.
Agent Prompt
## Issue description
The new parameters `files_dir` and `file_extension` are used by code included in the simulation build (`ExtrusionHardcodedIC.fpp`), but they are only declared/bound/broadcast in `src/pre_process`. Simulation must also declare them in `m_global_parameters`, read them from `simulation.inp` via the `user_inputs` namelist, and broadcast them to all ranks.
## Issue Context
`src/simulation/m_ib_patches.fpp` includes `ExtrusionHardcodedIC.fpp`, which now constructs file names using `files_dir` and `file_extension`.
## Fix Focus Areas
- src/simulation/m_global_parameters.fpp[24-35]
- src/simulation/m_start_up.fpp[84-114]
- src/simulation/m_mpi_proxy.fpp[58-70]
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| #:enddef | ||
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| #:def HardcodedReadValues() | ||
| if (.not. files_loaded) then | ||
| max_files = merge(sys_size, sys_size - 1, num_dims == 1) | ||
| do f = 1, max_files | ||
| write (file_num_str, '(I0)') f | ||
| fileNames(f) = trim(init_dir) // "prim." // trim(file_num_str) // ".00." // zeros_default // ".dat" | ||
| fileNames(f) = trim(files_dir) // "/" // "prim." // trim(file_num_str) // ".00." // trim(file_extension) // ".dat" |
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2. Extrusion reads rank-00 only 🐞 Bug ≡ Correctness
The extrusion reader hard-codes the middle filename field to .00. (prim.<var>.00.<ext>.dat), so it cannot read data produced with parallel I/O that is split across ranks (prim.<var>.<rank>.<tstep>.dat). This can lead to incomplete/incorrect extruded initial conditions or runtime failures when users follow the documented prim.XX.YY.file_extension.dat naming.
Agent Prompt
### Issue description
IC extrusion currently assumes the source data files have processor-rank field `YY=00` in `prim.XX.YY.<ext>.dat`. This prevents extruding from source datasets produced with MPI/parallel I/O where data is split across multiple `YY` files.
### Issue Context
- The repository writes files as `prim.<var>.<proc_rank>.<t_step>.dat`.
- Documentation states the format is `prim.XX.YY.file_extension.dat` without stating `YY` must be `00`.
### Fix Focus Areas
- src/common/include/ExtrusionHardcodedIC.fpp[59-67]
- src/pre_process/m_data_output.fpp[162-166]
- docs/documentation/case.md[259-267]
### Fix options (pick one)
1) **Implement support**: read and merge/sort data across all available `YY` partitions for each `XX` (most robust).
2) **Add a parameter**: e.g., `files_rank` (I2.2) and build filenames with that rank instead of hard-coding `00`.
3) **Clarify & enforce**: update docs to require `YY=00` / serial output, and add an explicit runtime check + clear abort message when expected files are missing.
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Code Review by Qodo
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Comment on lines
98
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| ! Calculate offsets | ||
| domain_xstart = x_coords(1) | ||
| x_step = x_cc(1) - x_cc(0) | ||
| delta_x = merge(x_cc(0) - domain_xstart + x_step/2.0, x_cc(index_x) - domain_xstart + x_step/2.0, num_dims == 1) | ||
| delta_x = merge(x_cc(0) - domain_xstart, x_cc(index_x) - domain_xstart + x_step/2.0, num_dims == 1) | ||
| global_offset_x = nint(abs(delta_x)/x_step) |
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1. 1d extrusion index shift 🐞 Bug ≡ Correctness
HardcodedReadValues() now computes global_offset_x for 1D using x_cc(0) - x_coords(1) without the half-cell correction, but x_coords comes from files written with x_cb coordinates. This makes global_offset_x round to 1 instead of 0 (via nint), shifting all 1D extruded IC samples by one index.
Agent Prompt
### Issue description
1D IC extrusion computes `global_offset_x` using `delta_x = x_cc(0) - x_coords(1)` (where `x_coords` is read from the first column of `prim.*.dat`). Because `prim.*` files write `x_cb(j)` as the coordinate while `x_cc` is cell-centered, this introduces a half-cell mismatch and `nint` rounds it to a full index shift.
### Issue Context
- `x_cc(0:m) = (x_cb(0:m) + x_cb(-1:(m-1)))/2` (cell centers)
- `prim.*` output uses `x_cb(j)` as the x-coordinate
- `HardcodedReadValues()` uses `global_offset_x = nint(abs(delta_x)/x_step)` and then indexes `stored_values` with `idx = i + 1 + global_offset_x`
### Fix Focus Areas
- src/common/include/ExtrusionHardcodedIC.fpp[98-103]
### Suggested fix
- For `num_dims == 1`, reintroduce the half-step correction when comparing `x_cc` to file coordinates, e.g.:
- `delta_x = x_cc(0) - domain_xstart + x_step/2.0_wp`
- Add a short comment explaining that the first column in `prim.*` is `x_cb` while values are cell-centered.
- (Optional but ideal) add a small regression test covering hcid=170 on a uniform grid that verifies no one-cell shift occurs when extruding from a serial `prim.*` output.
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Member
Claude Code ReviewPR #1349 — Extrusion v3 Critical Issues1. 2D index calculation is constant — all cells read the same data row
idx = i + 1 + global_offset_x - index_xsimplifies to 2. The offset is calculated inside 3. logical :: files_loaded = .false.Fortran 2008 §5.2.4: a local variable with an initializer implicitly has the Important Issues4. Asymmetric deallocation of
5.
6. Both construct 7. Both 2D example case files reference Suggestions
Strengths
The 2D extruded IC (hcid 270/271/272) is currently broken due to issue #1: every cell gets the same row of data, producing a uniform field. Issues #2 and #3 compound this. These must be fixed before merge. |
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Description
Summarize your changes and the motivation behind them.
IC Extrusion: The workflow for extending Initial Conditions to higher dimensions has been simplified. The updated methodology is now more robust and user-friendly.
Documentation & Examples: To assist users with this new methodology, three new reference examples have been uploaded to the repository (one 1D case and two 2D cases)
Fixes #(issue)
Type of change
-[x] A current methodology being more user-friendly
Testing
How did you test your changes?
Flame_Vortex_Interaction.mp4
-[x] 3rd Test, 2D Premixed Flame with perturbed flame front
Flame_Insta.mp4
Checklist
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