Added a PFR reactor to the flux diagram generator

[alongd]

No description provided.

[alongd]

Rebased onto main (673b866); the three original commits are preserved. Conflicts were all in t3/utils/flux.py, where main had since rewritten the typing (PEP 585/604) and added the molecule-image / logger parameters — the PFR parameters are merged in alongside those, and the new set_pfr / run_pfr now use list / dict / tuple / | None annotations.

Two things surfaced while verifying the rebase, fixed in a fourth commit:

• PFR pressure was off by 1e5. set_pfr and run_pfr did gas.TPX = T, P, ..., but P travels in bar throughout this module — set_jsr and run_batch_p both convert with P * 1e5. A PFR requested at 1 bar was simulated at 1 Pa.
• ct.PressureController(master=...) no longer exists. It was renamed primary= in Cantera 3.x, and environment.yml pins cantera >=3.2.0, so run_pfr raised TypeError on its first call. The PFR path could not have run against the pinned Cantera.

With both fixed, a PFR at P=1 now returns 1.0000e+05 Pa, matching the JSR path on the same input. tests/test_utils/test_flux.py is 26 passed, same as main. The three create_digraph tests main added needed reactor_type='JSR' added at the call site, since this PR makes reactor_type a required parameter — folded into the first commit.

⚠️ The surface_names path in run_pfr is untested. No model in tests/data/models carries a surface phase, so surface(surface_names.index(surface.name)).thermo was never exercised; it's left exactly as authored. Given that the gas-phase path was written against a pre-3.x Cantera, that line is worth a look before this merges.

[Copilot]

Pull request overview

Adds Plug Flow Reactor (PFR) support to T3’s flux diagram generation utilities by introducing a PFR simulation path and threading reactor-type metadata through diagram generation so outputs are labeled appropriately.

Changes:

• Added reactor_type, surface_names, and n_cells plumbing into generate_flux() / simulation profile generation, including a new run_pfr() / set_pfr() implementation.
• Updated flux diagram generation APIs (generate_flux_diagrams(), create_digraph()) to accept reactor_type and include it in diagram labels.
• Updated unit tests to pass reactor_type into create_digraph() calls.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 5 comments.

File	Description
tests/test_utils/test_flux.py	Updates test invocations to match the updated create_digraph() signature.
t3/utils/flux.py	Adds PFR simulation support and threads reactor_type through flux diagram generation and labeling.

Suppressed comments (2)

t3/utils/flux.py:171

• Same issue as in generate_flux: n_cells is annotated as optional, but the PFR path requires a positive integer. The signature should reflect the actual contract.

                                 n_cells: int | None = 100,

t3/utils/flux.py:477

• run_pfr() divides by tau to compute flow_rate; if any requested residence time is 0 or negative, this will crash (or yield meaningless results). Add input validation similar to run_batch_p().

    profiles = dict()
    stoichiometry = get_rxn_stoichiometry(gas)
    for tau in times:

---

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[alongd]

Confirmed, and the second half of your comment is the more serious part — deliberately left as-authored for now rather than fixed blind. set_pfr builds its own ct.Interface per cell and attaches those to the reactors, so the surfaces list run_pfr reads ROPs from was never attached to anything and never advanced: even with the call fixed, those ROPs would come from an unintegrated phase still at the inlet state. No model in tests/data/models carries a surface phase, so any rewrite here would be untestable in this repo. Flagging rather than guessing; this wants either a surface-bearing test fixture or set_pfr returning the interfaces it created.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 72.76%. Comparing base (673b866) to head (5949ba1).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #162      +/-   ##
==========================================
- Coverage   72.77%   72.76%   -0.01%     
==========================================
  Files          37       37              
  Lines        5932     6004      +72     
  Branches     1289     1307      +18     
==========================================
+ Hits         4317     4369      +52     
- Misses       1170     1187      +17     
- Partials      445      448       +3     

Flag	Coverage Δ
unittests	72.76% <ø> (-0.01%)	⬇️

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