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Network Formats

JAFF can currently parse five file formats that are standard in the astrochemical modelling community. Format detection is automatic — JAFF inspects the file content and picks the correct parser without requiring a format flag.

You never declare the format

Detection is per line, not per file. JAFF classifies each reaction line on its own, so a single file can mix formats freely (see Using these formats in JAFF). The file extension is ignored.

Supported Formats

Format Origin Paper
KIDA Kinetic Database for Astrochemistry A&A 689, A63 (2024)
UDFA UMIST Database for Astrochemistry (Rate22) A&A 682, A109 (2024)
PRIZMO Protoplanetary disk photochemistry code MNRAS 494, 4471 (2020)
KROME Astrophysical chemistry & microphysics lib MNRAS 439, 2386 (2014)
UCLCHEM Gas-grain astrochemical Python code AJ 154, 38 (2017)

Rate Expression Variables

All rate expressions are parsed as SymPy expressions. The following physical symbols are available across all formats:

Symbol Description Units
tgas Gas temperature K
av Visual extinction magnitudes
crate Primary cosmic-ray ionisation rate per H nucleus s⁻¹
chi Radiation field strength (Draine 1978 units) dimensionless
ntot Total number density cm⁻³
nh H nucleus number density cm⁻³
d2g Dust-to-gas mass ratio dimensionless
tdust Dust grain temperature K

Format-specific shorthand variables (e.g. t32, te, invtgas from KROME files) are automatically rewritten to the canonical symbols above during parsing.

KIDA Format

Source: kida.astrochem-tools.org/

KIDA (Kinetic Database for Astrochemistry) distributes networks as fixed-width files: each field occupies a fixed character range, not just a whitespace gap. Each data line encodes one reaction with its Arrhenius parameters, uncertainty estimate, formula index, and temperature range.

Columns are fixed-width, not just whitespace-separated

The reactant and product blocks are read by character position. Reactants occupy the first 34 columns and products the next 57; species names are padded with spaces to fit. Keep the column alignment of an existing KIDA file intact — adding or dropping spaces shifts the fields and misreads the reaction.

Column layout

Reactant1  Reactant2          Product1   Product2   α         β         γ        F    g   err  ni  Tmin  Tmax  frml  ID  ...

Example

A comprehensive example of the KIDA format implementation can be found in networks/GOW/GOW.jet

! comment lines start with '!'
! alpha, beta, gamma: Arrhenius coefficients
! frml: rate-formula index (see KIDA documentation)
! Tmin, Tmax: valid temperature range

H          CR                     H+         e-        0.000e+00  0.000e+00  0.000e+00 2.00e+00 0.00e+00 logn  1  -9999   9999  7     1 1  1
H2         CR                     H2+        e-        0.000e+00  0.000e+00  0.000e+00 2.00e+00 0.00e+00 logn  1  -9999   9999  7     2 1  1
He         CR                     He+        e-        1.100e+00  0.000e+00  0.000e+00 2.00e+00 0.00e+00 logn  1  -9999   9999  1     3 1  1

UDFA Format

Source: umistdatabase.uk

The UMIST Database for Astrochemistry (Rate22) uses a colon-delimited format with a leading integer ID and reaction-type tag. Up to two reactants and four products are supported; unused slots are left empty between consecutive colons.

Column layout

ID:type:R1:R2:P1:P2:P3:P4:α:β:γ:Tmin:Tmax:...
Field Description
ID Integer reaction index
type Reaction class code (e.g. AD, IN, RA, DR)
R1–R2 Reactants (empty if fewer than 2)
P1–P4 Products (empty if fewer than 4)
α β γ Arrhenius parameters
Tmin Tmax Valid temperature range (K)

Example

A comprehensive example of the UDFA format implementation can be found in networks/rate22_final/rate22_final.rates.jet

1:AD:C-:C:C2:e-:::1:5.00e-10:0.00:0.0:10:41000:L:C:"10.1086/190665":"Prasad and Huntress 1980":
2:AD:C-:CH2:C2H2:e-:::1:5.00e-10:0.00:0.0:10:41000:L:C:"10.1086/190665":"Prasad and Huntress 1980":
3:AD:C-:CH:C2H:e-:::1:5.00e-10:0.00:0.0:10:41000:L:C:"10.1086/190665":"Prasad and Huntress 1980":

PRIZMO Format

Source: jaff-chemistry.prizmo

PRIZMO networks are Fortran-flavoured text files with an optional VARIABLES{} block at the top. Inside the block, shorthand aliases are defined and then used in the rate expressions on subsequent reaction lines. JAFF converts Fortran double-precision literals (d exponent) and exponent operators (**) to Python/SymPy automatically.

VARIABLES{} block

VARIABLES{
    variable_name = expression
    ...
}

Variables can reference each other and the standard physical symbols (tgas, av, etc.).

Reaction line syntax

Reactant1 [+ Reactant2] -> Product1 [+ Product2 ...]    rate_expression

Photoreaction syntax

Photo reactions can be specified by using the PHOTO keyword in the rate expression separated by a comma. The PHOTO keyword is case sensitive. The value after the comma is the photon energy threshold in eV.

H -> H+ + E    []    PHOTO, 13.60

Example

# custom variables can be defined this way
VARIABLES{
    invt  = 1d0 / Tgas
    t32   = Tgas / 3d2
    sqrtt = sqrt(Tgas)
}

H + O -> OH        1.2d-10 * sqrtt
CO -> C + O        1.0d-10 * exp(-3.53d0 * av)

KROME Format

Source: kromepackage.org

KROME files open with a @format: header that specifies column semantics, followed by comma-separated reaction lines. Global Fortran-style variable aliases can be defined with @var:. Other KROME declaratives are ignored.

@format: header

@format:idx,R,R,R,P,P,P,P,tmin,tmax,rate

Tokens: idx (index), R (reactant), P (product), tmin/tmax (temperature bounds, K), rate (reaction rate coefficient).

Variable aliases

@var:te      = tgas * 8.617343e-5    ! electron temperature in eV
@var:invtgas = 1e0 / tgas
@var:t32     = tgas / 3e2

Example

A comprehensive example can be found at networks/COthin/react_COthin.jet

#rates for CO network similar to Glover+2010
@var:Hnuclei = get_Hnuclei(n(:))
@common: user_crate, user_Av, user_Tdust

@var:Te = Tgas * 8.617343d-5

1,H,,,OH,,,, 10,1e4, 1.2e-10 * (tgas/300)**0.5
2,H2,O,,OH,H,, 10,1e4, 3.4e-11 * exp(-500/tgas)

UCLCHEM Format

Source: uclchem.github.io

UCLCHEM networks are comma-separated, produced by the UCLCHEM Python tool. Every reaction always carries three reactant and four product slots; empty slots are filled with the NAN sentinel (this NAN is what identifies the format). Gas-phase species have no prefix; ice-surface species are prefixed with #, bulk-ice species with @.

Column layout

R1,R2,R3,P1,P2,P3,P4,α,β,γ,Tmin,Tmax,reduced_mass,extrapolate
Field Description
R1–R3 Reactants; unused slots are NAN
P1–P4 Products; unused slots are NAN
α β γ Arrhenius parameters
Tmin Tmax Valid temperature range (K)
reduced_mass Reduced mass of the reactants
extrapolate True/False — allow rate use outside [Tmin, Tmax]

Example

A comprehensive example can be found at networks/uclchem_small_gas/uclchem_small_gas_network.jet

!
! Small gas network from UCLCHEM v3.5.1
! Species notation: @ = bulk ice, # = surface ice, no prefix = gas phase
!

H,CRP,NAN,H+,E-,NAN,NAN,5.98e-18,0.0,0.0,10.0,41000.0,0.0,False
C,PHOTON,NAN,C+,E-,NAN,NAN,3.5e-10,0.0,3.76,10.0,41000.0,0.0,False
C,CO+,NAN,CO,C+,NAN,NAN,1.1e-10,0.0,0.0,10.0,41000.0,0.0,False
@C,BULKSWAP,NAN,#C,NAN,NAN,NAN,1.0,0.0,0.0,0.0,10000.0,0.0,False

Using these formats in JAFF

Since these formats are simple text files, JAFF can read any of these formats irrespective of the file name extension. However, it is recommended to use the .jet extension for JAFF networks for the sole purpose of consistency. Network formats in JAFF can also be combined in a single file and JAFF will be able to correctly detect and parse that format.

Example

An example of combined reaction formats can be found at networks/demos/demo1.jet

VARIABLES{
    invt = 1d0 / Tgas
    t32 = Tgas / 3d2
}

H+ + E -> H                    [0, 300]   3.61e-12*t32**(-0.75)

# KIDA format
N2         CR                     N          N                                             5.000e+00  0.000e+00  0.000e+00 1.25e+00 0.00e+00 logn  1  -9999   9999  1     1 1  1

# UMIST format
326:CE:CO:N2+:N2:CO+:::1:7.40e-11:0.00:0.0:10:41000:M:A:"10.1063/1.438893"::

# KROME format (default)
16,H2,E,,H,H,E,,NONE,NONE,5.6e-11*exp(-102124e0*invT)*Tgas**0.5

# KROME format (custom)
@format:R,R,P,P,rate
CO,N2+,N2,CO+,4.3e-13