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jaffx

jaffx is JAFF's command-line tool for quick network inspection and rate-coefficient export. Think of it as a thin shell around Network: every invocation loads a network and calls one of its methods, then exits. It deliberately does not run the code-generation pipeline. Use jaffgen when you want generated source.

jaffx <command> <subcommand> --network <file> [options]

How it maps to Network

There is nothing in jaffx that you cannot do from Python — each subcommand is a one-line wrapper. Holding that mapping in mind is the whole mental model:

CLI invocation Equivalent Python
jaffx get num-species Network(...).species.count
jaffx get num-reactions Network(...).reactions.count
jaffx export hdf5 -f f.h5 Network(...).to_hdf5("f.h5", ...)
jaffx export txt -f f.txt Network(...).to_txt("f.txt", ...)
jaffx export jaff -f f.jaff Network(...).to_jaff("f.jaff")

Every run first loads the network (printing the JAFF banner and the usual load log), so the load-time validation warnings you'd see from Network(...) show up here too.

Shared network arguments

Every subcommand loads a network, so all of them accept the same loading options. These mirror the Network constructor:

Argument Description
--network Path to the network file (required in practice)
--label Override the network label (defaults to the file stem)
--funcfile Path to a .jfunc auxiliary file; auto-detected from the network dir if omitted
--replace-nh --replace-nh / --no-replace-nh — expand nh/nhe density shorthands

jaffx get

Query a scalar property of the network. Output is written through the logger, so it carries the usual INFO prefix.

get num-species

jaffx get num-species --network networks/GOW/GOW.jet

INFO     Total number of species: 18

get num-reactions

jaffx get num-reactions --network networks/GOW/GOW.jet

INFO     Total number of reactions: 50

jaffx export

Export the network in one of three formats. The first two tabulate rate coefficients against temperature; the third serializes the whole network.

export hdf5 and export txt

export hdf5 writes an HDF5 rate table; export txt writes the same data as a whitespace-separated text table. Both take the identical option set and forward it straight to Network.to_hdf5 / Network.to_txt:

Argument Description
--file, -f Output file path (required)
--tmin Minimum tabulation temperature (default: minimum over reactions)
--tmax Maximum tabulation temperature (default: maximum over reactions)
--nT Initial number of temperature points (before adaptive refinement)
--err-tol Relative interpolation error tolerance; adaptive sampling is off when unset
--rate-min Adaptive refinement is not applied to rates below this floor
--rate-max Rates above this ceiling are clipped to prevent overflow
--fast-log Sample equally in fast_log2(T) space instead of log(T)
--include-all Include every reaction, marking non-tabulatable ones NaN
--verbose, -v Print progress during adaptive refinement 
# HDF5 table, adaptively refined to 0.1% interpolation error
jaffx export hdf5 \
    --network networks/GOW/GOW.jet \
    --file    rates.hdf5           \
    --tmin    10                   \
    --tmax    1e4                  \
    --nT      200                  \
    --err-tol 1e-3

# Plain-text table, fixed 100-point grid (no --err-tol → no refinement)
jaffx export txt \
    --network networks/GOW/GOW.jet \
    --file    rates.txt            \
    --tmin 10 --tmax 1e4 --nT 100

Only rates that depend solely on temperature are tabulated; reactions involving av, crate, or undefined functions are dropped (or set to NaN under --include-all).

export jaff

Serialize the entire parsed network to a gzip-compressed JSON .jaff file — exactly Network.to_jaff. Re-loading it with Network("...jaff") skips parsing and the expensive SymPy assembly, so this is the recommended cache for large networks.

jaffx export jaff \
    --network networks/GOW/GOW.jet \
    --file    GOW.jaff

Same serialization limit as Network.to_jaff

Networks whose rates contain an undefined function — most often an unresolved photorates(...) (a photo-reaction loaded without rad_bands) or a custom interp(...) — cannot be serialized and will raise an error.

Examples

# Quick species count
jaffx get num-species --network networks/h_photoionization/h_photo.jet

# 500-point HDF5 table with tight adaptive sampling
jaffx export hdf5 \
    --network networks/GOW/GOW.jet \
    --file    GOW_rates.hdf5       \
    --tmin 10 --tmax 1e5 --nT 500  \
    --err-tol 1e-4

# Text table including all reactions (NaN for non-tabulatable)
jaffx export txt \
    --network    networks/GOW/GOW.jet \
    --file       GOW_rates.txt        \
    --include-all

# Cache the network for fast re-loading
jaffx export jaff \
    --network networks/GOW/GOW.jet \
    --file    GOW.jaff