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Network Configuration (jaff.toml)

A jaff.toml carries network-scoped settings that belong to a network rather than to a code-generation run — the per-reaction and global temperature-cutoff behaviour and the duplicate policy. It lives alongside the network file and is independent of jaffgen.toml, which configures the jaffgen pipeline.

JAFF loads it from, in order:

  1. the config= argument to Network (or --network-config on jaffgen);
  2. otherwise a jaff.toml auto-detected in the network file's directory.

All keys live under the [network] table.

Temperature cutoffs

Every reaction carries a temperature validity range [Tmin, Tmax]. What happens when the gas temperature tgas falls outside that range is controlled by the reaction's temperature cutoff behaviour:

Cutoff Behaviour outside [Tmin, Tmax]
clip tgas is clamped to the nearest bound, so the rate is frozen at its boundary value
extrapolate tgas is left untouched, so the rate expression is evaluated (extrapolated) as-is

clip is the default. Under clip, tgas in each rate expression is replaced by max(min(tgas, Tmax), Tmin) (only the bounds that are defined are applied). Under extrapolate, no clamp is inserted and the raw tgas symbol survives into the generated code.

# Global default applied to every reaction
[network.rates]
T_cutoff = "clip"          # "clip" (default) or "extrapolate"

# Per-reaction override, keyed by the reaction's serialized form
[network.reactions."CO._PHOTON__C.O"]
T_cutoff = "extrapolate"

Values are case-insensitive; anything other than clip or extrapolate raises a ParserError.

Reaction keys are serialized names

The per-reaction key is the reaction's serialized form: <reactants>__<products>, where each side is a .-joined list of species names sorted alphabetically. Special pseudo-species keep their underscore prefix (e.g. _PHOTON, _CR). For CO + PHOTON -> C + O this is CO._PHOTON__C.O. The . separators mean the key must be quoted in the TOML table header. The cutoff is baked into the rate expression at load time, so a .jaff file saved afterwards already carries the resolved behaviour and does not need the config on reload.

For a reaction defined over a single temperature range, clip replaces tgas with max(min(tgas, Tmax), Tmin) as above. When a reaction is defined over multiple disjoint ranges (merged into a piecewise rate — see Temperature ranges and piecewise rates), T_cutoff governs only the outer edges: below the first range and above the last, clip holds the boundary rate while extrapolate lets the end segments run on. Gaps between adjacent ranges are always linearly interpolated, independent of T_cutoff.

Resolution order

The same settings can also appear in jaffgen.toml under an identical [network.rates] / [network.reactions."<srxn>"] schema. When both files supply a value, they are resolved per reaction as (highest wins):

  1. jaffgen.toml per-reaction T_cutoff
  2. jaff.toml per-reaction T_cutoff
  3. jaffgen.toml global ([network.rates]) T_cutoff
  4. jaff.toml global ([network.rates]) T_cutoff
  5. built-in default clip

A per-reaction setting always wins over any global one; within the same scope, jaffgen.toml overrides jaff.toml. In short: jaffgen.toml lets a particular code-generation run override the network's own defaults, without editing jaff.toml.

Duplicate policy

When two rate coefficients share the same reaction, mechanism (type), and temperature range [Tmin, Tmax], duplicate_policy decides how the clash is resolved during network construction:

Policy Behaviour
preserve-first Keep the first coefficient seen; drop later duplicates (default)
preserve-last Keep the last coefficient seen; discard earlier ones
error Raise a ParserError — the clash must be fixed in the source network 
[network]
duplicate_policy = "preserve-last"

Resolution order (highest wins):

  1. --duplicate-policy CLI flag (jaffgen / jaffx)
  2. jaffgen.toml [network].duplicate_policy (jaffgen only)
  3. jaff.toml [network].duplicate_policy
  4. built-in default preserve-first

Unlike T_cutoff, this is a single network-wide key — there is no per-reaction form.