13c-metabolic-flux
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Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use for combustion kinetics, closed adiabatic ideal-gas constant-volume or constant-pressure ignition, temperature histories, or
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Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use for combustion kinetics, closed adiabatic ideal-gas constant-volume or constant-pressure ignition, temperature histories, or
name: cantera description: Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use for combustion kinetics, closed adiabatic ideal-gas constant-volume or constant-pressure ignition, temperature histories, or mechanism-specific ignition-delay comparisons. license: MIT compatibility: Requires Python 3.12-3.14, Cantera 3.2.0, and NumPy. Installation needs network access; simulations run locally without credentials. Custom mechanisms must be available as Cantera YAML files. metadata: version: "1.1" skill-author: K-Dense Inc. tested-package-version: "3.2.0" last-reviewed: "2026-09-30"
Use for a closed, adiabatic, homogeneous ideal-gas reactor with a known kinetic mechanism, initial temperature, pressure, and mole composition. The bundled helper runs both constant volume and constant pressure cases and reports a precisely defined temperature-based delay. It is not a flame solver or a general reactor-network builder.
A calculation completing successfully establishes numerical execution, not mechanism validity for the fuel, pressure, temperature, diluent, or measured ignition observable. Read [references/interpretation.md](references/interpretation.md) when choosing a mechanism, comparing experiments, or interpreting unresolved/two-stage ignition.
1. Identify the mechanism and its validated condition range. Preserve its source, version, citation, and any modifications. Check that its phase is `ideal-gas` and that every reactant, diluent, and tracked species exists. For custom YAML with imports, retain the original dependency files as well as the generated phase snapshot. Custom Python rate extensions additionally need their original code and environment for replay. 2. Choose constant volume or constant pressure from the physical experiment. Supply K, Pa, seconds, and mole amounts explicitly. `mole_amounts` is normalized to mole fractions; it is not a mass-fraction mapping. The report includes the normalized initial composition. 3. Copy [assets/hydrogen-ignition.json](assets/hydrogen-ignition.json) and change its conditions. The supplied H2/O2/Ar case uses Cantera's bundled `h2o2.yaml` for an executable numerical example; it is not a recommendation for every hydrogen experiment. 4. Set a time horizon long enough to observe the temperature rise and the decline of the heating-rate peak. Choose output spacing fine enough to locate that peak. Set a minimum temperature rise to distinguish ignition from negligible heating or numerical noise. 5. Run the helper and inspect all four histories and the report. Refine again if the delay changes materially, if the maximum approaches a time boundary, or if conservation fails. Compare the temperature and tracked-species histories with the actual ignition definition. 6. Report the condition set, mechanism hash, reactor constraint, delay definition, output spacing, numerical changes, and scientific limits together with the delay.
From the collection root:
uv run --no-project --python 3.12 --with cantera==3.2.0 --with numpy==2.5.3 \ python skills/cantera/scripts/ignition_delay.py \ skills/cantera/assets/hydrogen-ignition.json hydrogen-result
Tested on Python 3.12, Cantera 3.2.0, and NumPy 2.5.3. No external solver executable or credentials are needed. Local relative mechanism paths resolve against the configuration file directory before Cantera's built-in data search. Use a new output directory each run.
The 1000 K, 101325 Pa, H2:O2:Ar = 2:1:7 constant-volume example gives about **0.313 ms** using the stated `max(dT/dt)` definition. At 3 ms its temperature is approximately 2920.67 K and agrees with a separate `UV` equilibrium calculation. These are package regression values, not experimental validation data.
Delay is the time of the global maximum of `numpy.gradient(T, time, edge_order=2)` on a uniform output grid. It is reported only if the maximum temperature rise reaches `minimum_temperature_rise_k` and the maximum is at least two sample indices from each boundary. Otherwise `delay_s` is null and a status explains why. No delay beyond the simulation horizon is extrapolated.
The helper explicitly uses Cantera 3.2's `clone=True` and reads evolving properties from `reactor.phase`. The original `Solution` retains the initial state; do not read it as the reactor's final state. `ReactorNet.advance(t)` requests an absolute time, and no advance limits are configured, so the output grid remains uniform.
It runs four independent fresh reactors:
| Run | Change from configured conditions | | --- | --- | | baseline | Original settings | | finer_output | Half output spacing, same horizon and solver controls | | tighter_solver | Both solver tolerances divided by ten; maximum internal time step halved | | longer_horizon | Twice the horizon with the original output spacing |
`numerically_resolved` requires all runs to yield delays, relative delay changes within `delay_relative_tolerance`, and all conservation checks to pass. Agreement on a discrete grid is not a statistical error bar: also report the output spacing. The baseline samples must be between 11 and 50000, leaving room for refinement. Runtime grows with mechanism size, stiffness, and the chosen horizon; integration failures retain Cantera's error text.
normalized starting composition, four delay estimates, numerical changes, conservation, and mechanism thermodynamic temperature bounds.
temperature, pressure, volume, mass, total internal energy, total enthalpy, and requested species mole fractio
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