Network File Formats

Overview

JAFF supports multiple file formats used in astrochemistry. Each format has its own syntax and conventions, but JAFF automatically detects and parses them correctly.

Supported Formats:

JAFF supports SymPy expressions with these variables:

• tgas: Gas temperature (K)
• av: Visual extinction
• crate: Cosmic rate ionization of \(H_2\) in \(s^{-1}\)
• ntot: Total number density in \(cm^{-1}\)
• hnuclei: H nuclei number density in \(cm^{-1}\)
• d2g: Dust-to-gas mass ratio again

KROME Format

Format used by the KROME astrochemistry package.

Syntax

@format:idx,R,R,R,P,P,P,P,tmin,tmax,rate
idx,Reactant1,Reactant2,Reactant3,Product1,Product2,Product3,Product4,Tmin,Tmax,Rate

Format Specification

The @format: line defines column meanings:

• idx: Reaction index (integer)
• R: Reactant (up to 3)
• P: Product (up to 4)
• tmin: Minimum temperature (K)
• tmax: Maximum temperature (K)
• rate: Rate expression

Example

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

# Reaction data
1,H,O,,,OH,,,10,1e4,1.2e-10*(T/300)**0.5
2,H2,O,,,OH,H,,10,1e4,3.4e-11*exp(-500/T)
3,C,O2,,,CO,O,,10,1e4,5.6e-12

# Three-body reactions (third body is last reactant)
4,H,H,H2,H2,,,,10,300,1.0e-32*(T/300)**(-0.6)

Variables

KROME supports variable definitions:

@var:te=tgas*8.617343e-5
@var:invtgas=1.0/tgas
@var:sqrtgas=sqrt(tgas)

1,H,O,,,OH,,,10,1e4,1.2e-10*sqrtgas

Temperature Limits

Rate expressions are clamped to [tmin, tmax]:

# This reaction only applies between 100K and 1000K
1,H,O,,,OH,,,100,1000,1.2e-10*(T/300)**0.5

When temperature is outside range:

• T < Tmin: Rate evaluated at Tmin
• T > Tmax: Rate evaluated at Tmax

KIDA Format

Format from the Kinetic Database for Astrochemistry.

Syntax

Reactants -> Products : α : β : γ

Rate formula: \(k(T) = \alpha \times (T/300)^\beta \times e^{(-\gamma/T)}\)

Example

H + O -> OH : 1.2e-10 : 0.5 : 0.0
H2 + O -> OH + H : 3.4e-11 : 0.0 : 500.0
C + O2 -> CO + O : 5.6e-12 : 0.0 : 0.0

Parameters

• \(\alpha\): Pre-exponential factor (cm³/s for 2-body)
• \(\beta\): Temperature exponent
• \(\gamma\): Activation energy parameter (K)

Temperature Dependence

# No temperature dependence (β=0, γ=0)
C + O -> CO : 5.0e-11 : 0 : 0

# Power law only (γ=0)
H + O -> OH : 1.2e-10 : 0.5 : 0

# Exponential only (β=0)
H2 + O -> OH + H : 3.4e-11 : 0 : 500

# Both power law and exponential
OH + H2 -> H2O + H : 2.1e-11 : 0.5 : 1000

UDFA Format

Format from the UMIST Database for Astrochemistry.

Syntax

R1:R2:R3:P1:P2:P3:P4:α:β:γ:Tmin:Tmax

Colon-separated format with all fields.

Example

H:O:::OH::::1.2e-10:0.5:0.0:10:1e4
H2:O:::OH:H:::3.4e-11:0.0:500.0:10:1e4
C:O2:::CO:O:::5.6e-12:0.0:0.0:10:1e4

Field Order

• 1-3: Reactants (empty if fewer than 3)
• 4-7: Products (empty if fewer than 4)
• 8: \(\alpha\) (pre-exponential factor)
• 9: \(\beta\) (temperature exponent)
• 10: \(\gamma\) (activation energy)
• 11: Tmin (minimum temperature)
• 12: Tmax (maximum temperature)

Empty Fields

Use empty strings for missing reactants/products:

# Single reactant, single product
CO::::C:O:::1.0e-10:0:0:10:1e4

# Two reactants, two products
H:O2:::OH:O:::2.0e-11:0:100:10:1e4

PRIZMO Format

Format used by the PRIZMO code.

Syntax

VARIABLES{
    variable1 = expression1
    variable2 = expression2
}

Reactants -> Products, rate_expression

Example

VARIABLES{
    k1 = 1.2e-10
    k2 = 3.4e-11
    sqrtt = sqrt(tgas)
    expt = exp(-500/tgas)
}

H + O -> OH, k1 * sqrtt
H2 + O -> OH + H, k2 * expt
C + O2 -> CO + O, 5.6e-12

Variable Block

Variables defined in VARIABLES{} block:

VARIABLES{
    # Temperature variables
    t32 = tgas / 300
    invt = 1.0 / tgas

    # Common rate factors
    k_neutral = 1.0e-10 * sqrt(tgas)
    k_ion = 1.0e-9
}

Variables can reference each other:

VARIABLES{
    t32 = tgas / 300
    sqrtt32 = sqrt(t32)
    rate_base = 1.0e-10 * sqrtt32
}

Fortran Expressions

PRIZMO uses Fortran syntax:

VARIABLES{
    # Fortran-style exponentiation
    t32 = tgas / 3.0e2

    # Double precision literals
    k1 = 1.0d-10
    k2 = 3.4d-11
}

JAFF automatically converts this to Python syntax.

UCLCHEM Format

Format from the UCLCHEM code.

Syntax

R1,R2,R3,P1,P2,P3,P4,α,β,γ

Comma-separated with NAN placeholders.

Example

H,O,NAN,OH,NAN,NAN,NAN,1.2e-10,0.5,0.0
H2,O,NAN,OH,H,NAN,NAN,3.4e-11,0.0,500.0
C,O2,NAN,CO,O,NAN,NAN,5.6e-12,0.0,0.0

NAN Placeholders

Use NAN for empty slots:

# Single reactant
CO,NAN,NAN,C,O,NAN,NAN,1.0e-10,0,0

# Two reactants, single product
H,H,NAN,H2,NAN,NAN,NAN,1.0e-32,-0.6,0

Field Order

Fields: R1, R2, R3, P1, P2, P3, P4, α, β, γ

Always 10 comma-separated values per line.

Format Comparison

Rate Expression Styles

Photoreactions

Different formats handle photoreactions differently.

JAFF Format

CO + Photon -> C + O, photo(CO, 1e-10)
H2O + hν -> OH + H, photo(H2O, 2e-10)

KROME Format

@format:idx,R,R,P,P,rate
1,CO,Photon,C,O,photo(1e-10,1e99)

KIDA Format

CO + Photon -> C + O : photo : 1e-10 : 0

See Also

• Loading Networks - How to load networks
• Network API - Network class reference

Next: Learn about Working with Species.