Mechanisms and preprocessing

CreateSolution("mechanism.yaml") parses gas species, thermodynamics, and supported reaction data from YAML in Julia. The input path is composed from separate native kinetics, YAML thermo/species, and optional transport-fit readers. A .yaml.npz sidecar is optional and supplies pre-fitted transport properties when present. Cantera and Python are not required to load gas chemistry.

Native gas kinetics support elementary and three-body Arrhenius reactions, Lindemann and Troe falloff, pressure-dependent Arrhenius (PLOG) rates, linear-Burke/Lindemann mixture rules, Blowers–Masel rates, explicit reaction orders, and NASA7, NASA9, Shomate, and constant-cp thermodynamic models. SRI, Tsang, chemically-activated, and Chebyshev rate forms are not supported by the native reader.

YAML phase definitions may select local or imported species and reaction sections. Imported files are resolved relative to the mechanism file; optional data_paths can provide additional search directories:

gas = CreateSolution("mechanism.yaml"; data_paths=["shared-data"])

Transport sidecars are optional for chemistry but should be regenerated after changing the mechanism or an imported YAML file when fitted transport data are needed. For multicomponent diffusion or Soret diffusion, export matching collision-integral data with mechanism/exportmulticomponent.py; see flame transport. Use `kineticsreader=:sidecar` only when comparing against legacy kinetics arrays.

Mechanism checks and an opt-in NASA7 continuity refit are available in Julia:

report = audit_mechanism("mechanism.yaml")
report.issues
refit_nasa7_continuity("mechanism.yaml", "mechanism-refit.yaml")

The audit checks balance, unused species, duplicate candidates, NASA polynomial continuity, negative pre-exponential declarations, collision-limit screens, broad transport parameter ranges, and PLOG rate underflow risks. PLOG findings report tabulated pressure bounds and use the intersection of participating species' thermo ranges when available; where ranges are absent, the temperature field is left undeclared. Collision and transport thresholds are heuristic review flags. Duplicate groups are candidates and may include false positives because the screen does not fully reproduce Cantera's rate-type and third-body comparisons.

The refit adjusts each high-temperature NASA7 cp/R polynomial by constrained least squares so cp/R and its first derivative match at Tmid, then anchors h/RT and s/R there. It writes a separate YAML file and reports the largest changes to cp/R, h/RT, s/R, and g/RT. By default, each species is refused if any dimensionless change exceeds 0.05; use force=true only after reviewing the reported deltas. Refused species retain their original coefficients. The output removes note annotation fields because YAML.jl does not preserve multiline note indentation.

Common-midpoint NASA7 refit

For a single shared NASA7 split temperature, use the opt-in refit:

report, output = refit_nasa7_common_tmid("mechanism.yaml", "mechanism-common-tmid.yaml")

It requires the chosen Tmid to lie inside the shared interval of all supported NASA7 species. It jointly fits both cp/R segments, enforces value and first-derivative continuity, preserves h/RT and s/R at each species' lower temperature bound, and anchors their continuity at the shared midpoint. The report gives maximum absolute changes in cp/R, h/RT, s/R, and g/RT. By default, each species is refused if any change exceeds 0.05; refused species retain their original data and midpoint. force=true overrides this safeguard explicitly. The output is separate; unsupported NASA7 layouts are listed as skipped. The fit is an opt-in least-squares transformation, so inspect its reported changes before using the generated mechanism.

Mechanism-audit context: Killingsworth et al. describe automated kinetic-mechanism analysis and debugging in Combustion and Flame 221 (2020), 170–179; related Cantera enhancement discussion: ChemCheck issue #42.

@article{Killingsworth2020CloudMechanismAnalysis,
  author  = {Killingsworth, Nick J. and McNenly, Matthew J. and Whitesides, Russell A. and Wagnon, Scott W.},
  title   = {Cloud based tool for analysis of chemical kinetic mechanisms},
  journal = {Combustion and Flame},
  volume  = {221},
  pages   = {170--179},
  year    = {2020},
  doi     = {10.1016/j.combustflame.2020.06.010}
}

PLOG-to-Chebyshev export

An optional refit writes a separate Cantera mechanism and does not alter its input:

report, output = refit_plog_to_chebyshev(
    "mechanism.yaml", "mechanism-chebyshev.yaml", 12;
    temperature_range=(300.0, 2500.0), temperature_order=6,
    pressure_order=4, max_log10_error=0.05)

The fitter evaluates summed PLOG Arrhenius terms with log-sum-exp, fits the Chebyshev surface over the requested temperature/pressure box, and checks maximum absolute log10(k) error on a denser validation grid. It writes the refit only when the error is within the stated bound, unless force=true is supplied. The output uses Cantera's Chebyshev format; the native reader still rejects Chebyshev rates. This fit does not support collider-specific or Linear-Burke PLOG reactions.

The Chebyshev representation over a stated (T,P) box follows Venkatesh et al. (AIChE Journal 43 (1997), 1331–1340). The rate-refit design was informed by the differentiable PLOG-to-Troe software KiRATE at commit d5e8e12df9e9bb3073bba1378e74b8bdbcee4177.

@article{Venkatesh1997PressureTemperatureKinetics,
  author  = {Venkatesh, Prasana K. and Chang, Albert Y. and Dean, Anthony M. and Cohen, Morrel H. and Carr, Robert W.},
  title   = {Parameterization of pressure- and temperature-dependent kinetics in multiple well reactions},
  journal = {AIChE Journal},
  volume  = {43},
  number  = {5},
  pages   = {1331--1340},
  year    = {1997},
  doi     = {10.1002/aic.690430522}
}