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Initial Condition Extrusion + Chem Examples #1109

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f1d47b9
Extrusion_ic
Dec 15, 2025
389e8e7
Extrusion V2
Jan 6, 2026
4c26059
IC files for extrusion
Jan 7, 2026
2404925
IC files
Jan 7, 2026
9ff179e
Re-committing without large core files
Jan 13, 2026
f233473
Extrusion IC for 2D Chem Cases
Jan 13, 2026
83b20f9
Small fixes
Jan 13, 2026
8513cc8
space
Jan 13, 2026
99f8829
Spell Check
Jan 13, 2026
7194c0b
Small errors
Jan 13, 2026
4203aae
...
Jan 14, 2026
c790a73
....
Jan 14, 2026
a853cad
aaaaa
Jan 14, 2026
3310f56
Fixed folder names
Jan 14, 2026
5038dcf
IC files
Jan 14, 2026
a8126e6
...
Jan 14, 2026
c1e4a40
Minor changes
Jan 16, 2026
5baa703
format
Jan 16, 2026
0918651
..
Jan 29, 2026
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4 changes: 2 additions & 2 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ __pycache__
toolchain/mfc/_version.py

.DS_Store

!examples/**/IC/*.dat
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@coderabbitai coderabbitai bot Jan 28, 2026

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⚠️ Potential issue | 🟡 Minor

Gitignore negation pattern is in wrong position and will be ineffective.

The negation !examples/**/IC/*.dat on line 26 appears before the broader ignore pattern examples/**/*.dat on line 47. In .gitignore, later patterns override earlier ones, so IC .dat files will still be ignored.

Move this line after line 47 (or after line 64 where similar negations exist) to ensure IC data files are properly tracked.

Suggested fix

Move line 26 to after line 64, grouping it with similar negation patterns:

 examples/**/*.f90
 !examples/3D_lag_bubbles_shbubcollapse/input/lag_bubbles.dat
 !examples/3D_lag_bubbles_bubblescreen/input/lag_bubbles.dat
+!examples/**/IC/*.dat
 workloads/

And remove the current line 26.

🤖 Prompt for AI Agents 
In @.gitignore at line 26, The negation pattern "!examples/**/IC/*.dat" is
placed before the broader ignore "examples/**/*.dat" so it is ineffective;
relocate the line containing "!examples/**/IC/*.dat" to after the broader ignore
pattern "examples/**/*.dat" (or after the block of similar negations) and remove
the original occurrence so the IC .dat files are actually un-ignored.

/tests/*/**
!/tests/*/golden.txt
!/tests/*/golden-metadata.txt
Expand Down Expand Up @@ -92,4 +92,4 @@ benchmarks/*.png
*.avi

**isolation_rules/
**.supercode/
**.supercode/
4 changes: 2 additions & 2 deletions docs/documentation/case.md
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Expand Up @@ -251,8 +251,8 @@ The code provides three pre-built patches for dimensional extrusion of initial c
- `case(270)`: Extrude 1D data to 2D domain
- `case(370)`: Extrude 2D data to 3D domain

Setup: Only requires specifying `init_dir` and filename pattern via `zeros_default`. Grid dimensions are automatically detected from the data files.
Implementation: All variables and file handling are managed in `src/pre_process/include/ExtrusionHardcodedIC.fpp` with no manual grid configuration needed.
Setup: Only requires specifying `files_dir` and filename pattern via `file_extension`. The files are located, for example, at `examples/2D_case/IC`, and their format is `prim.XX.YY.files_extension.dat`.
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Suggestion: Clarify the example filename format in the documentation to show a concrete example, such as prim.XX.YY.dat, instead of using file_extension as a literal part of the name. [general, importance: 4]

Suggested change
Setup: Only requires specifying `files_dir` and filename pattern via `file_extension`. The files are located, for example, at `examples/2D_case/IC`, and their format is `prim.XX.YY.files_extension.dat`.
Setup: Only requires specifying `files_dir` and filename pattern via `file_extension`. The files are located, for example, at `examples/2D_case/IC`, and their format is `prim.XX.YY.dat` (assuming `file_extension` is set to `.dat`).

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@cubic-dev-ai cubic-dev-ai bot Jan 28, 2026 •
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P3: The filename example uses files_extension while the text defines the key as file_extension. This mismatch is likely a typo and could mislead users about the required filename pattern.

Prompt for AI agents 
Check if this issue is valid — if so, understand the root cause and fix it. At docs/documentation/case.md, line 254:

<comment>The filename example uses `files_extension` while the text defines the key as `file_extension`. This mismatch is likely a typo and could mislead users about the required filename pattern.</comment>

<file context>
@@ -251,8 +251,8 @@ The code provides three pre-built patches for dimensional extrusion of initial c
 
-Setup: Only requires specifying `init_dir` and filename pattern via `zeros_default`. Grid dimensions are automatically detected from the data files.
-Implementation: All variables and file handling are managed in `src/pre_process/include/ExtrusionHardcodedIC.fpp` with no manual grid configuration needed.
+Setup: Only requires specifying `files_dir` and filename pattern via `file_extension`. The files are located, for example, at `examples/2D_case/IC`, and their format is `prim.XX.YY.files_extension.dat`.
+Implementation: All variables and file handling are managed in the `case.py` file of the simulation.
 Usage: Ideal for initializing simulations from lower-dimensional solutions, enabling users to add perturbations or modifications to the base extruded fields for flow instability studies.
</file context>
Suggested change
Setup: Only requires specifying `files_dir` and filename pattern via `file_extension`. The files are located, for example, at `examples/2D_case/IC`, and their format is `prim.XX.YY.files_extension.dat`.
Setup: Only requires specifying `files_dir` and filename pattern via `file_extension`. The files are located, for example, at `examples/2D_case/IC`, and their format is `prim.XX.YY.file_extension.dat`.
Fix with Cubic

Implementation: All variables and file handling are managed in the `case.py` file of the simulation.
Usage: Ideal for initializing simulations from lower-dimensional solutions, enabling users to add perturbations or modifications to the base extruded fields for flow instability studies.

#### Parameter Descriptions
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72 changes: 72 additions & 0 deletions examples/1D_flamelet/case.py
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@@ -0,0 +1,72 @@
#!/usr/bin/env python3
import json
import argparse
import math
import os
import cantera as ct

current_dir = os.path.dirname(os.path.abspath(__file__))
ctfile = "sandiego.yaml"
sol_L = ct.Solution(ctfile)
sol_L.TPX = 300, 8000, "O2:2,N2:2,H2O:5"
L = 0.016
Nx = 1199
dx = L / Nx
dt = 1e-8
Tend = 0.60e-3
NT = int(Tend / dt)
SAVE_COUNT = 1000
NS = 1000
case = {
"run_time_info": "T",
"x_domain%beg": -L / 2,
"x_domain%end": +L / 2,
"m": Nx,
"n": 0,
"p": 0,
"dt": float(dt),
"t_step_start": 0,
"t_step_stop": NT,
"t_step_save": NS,
"t_step_print": 100,
"parallel_io": "F",
"model_eqns": 2,
"num_fluids": 1,
"num_patches": 1,
"mpp_lim": "F",
"mixture_err": "F",
"time_stepper": 3,
"weno_order": 5,
"weno_eps": 1e-16,
"weno_avg": "F",
"mapped_weno": "T",
"mp_weno": "T",
"riemann_solver": 2,
"wave_speeds": 2,
"avg_state": 1,
"bc_x%beg": -8,
"bc_x%end": -8,
"viscous": "F",
"files_dir": os.path.join(current_dir, "IC"),
"file_extension": "000000",
"chemistry": "T",
"chem_params%diffusion": "T",
"chem_params%reactions": "T",
"chem_params%transport_model": 2,
"format": 1,
"precision": 2,
"prim_vars_wrt": "T",
"patch_icpp(1)%geometry": 1,
"patch_icpp(1)%hcid": 170,
"patch_icpp(1)%x_centroid": 0,
"patch_icpp(1)%length_x": L,
"patch_icpp(1)%vel(1)": "0",
"patch_icpp(1)%pres": 1.01325e5,
"patch_icpp(1)%alpha(1)": 1,
"patch_icpp(1)%alpha_rho(1)": "1",
Comment on lines +63 to +66
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Suggestion: Several fields in the case dict that represent numeric configuration values are provided as strings (for example patch_icpp(1)%vel(1) and patch_icpp(1)%alpha_rho(1)), which can cause downstream config parsers to treat them as strings and fail numeric operations; make these entries numeric (remove the quotes). [type error]

Severity Level: Major ⚠️ 
- ❌ Simulation config fields parsed as wrong types.
- ⚠️ Downstream numeric operations may misbehave.
Suggested change
"patch_icpp(1)%vel(1)": "0",
"patch_icpp(1)%pres": 1.01325e5,
"patch_icpp(1)%alpha(1)": 1,
"patch_icpp(1)%alpha_rho(1)": "1",
"patch_icpp(1)%vel(1)": 0,
"patch_icpp(1)%alpha_rho(1)": 1,
Steps of Reproduction ✅ 
1. Run the example script to emit JSON: `python examples/1D_flamelet/case.py`; the script
prints the `case` dict as JSON.

2. Parse the output JSON (e.g., `json.loads(...)`) and inspect keys "patch_icpp(1)%vel(1)"
and "patch_icpp(1)%alpha_rho(1)" defined at lines 63 and 66; both values are strings ("0"
and "1").

3. If a downstream consumer expects numeric types (e.g., performing arithmetic on these
config entries), it will receive strings and either convert them or raise a type-related
error in the consumer.

4. Observed result: mis-typed configuration values in produced JSON; behavior depends on
downstream code but can lead to incorrect numeric operations.
Prompt for AI Agent 🤖 
This is a comment left during a code review.

**Path:** examples/1D_flamelet/case.py
**Line:** 63:66
**Comment:**
	*Type Error: Several fields in the `case` dict that represent numeric configuration values are provided as strings (for example `patch_icpp(1)%vel(1)` and `patch_icpp(1)%alpha_rho(1)`), which can cause downstream config parsers to treat them as strings and fail numeric operations; make these entries numeric (remove the quotes).

Validate the correctness of the flagged issue. If correct, How can I resolve this? If you propose a fix, implement it and please make it concise.

"fluid_pp(1)%gamma": 1.0e00 / (1.5e00 - 1.0e00),
"fluid_pp(1)%pi_inf": 0,
"cantera_file": ctfile,
}
if __name__ == "__main__":
print(json.dumps(case))
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