Loading Networks

Overview

JAFF can load chemical reaction networks from multiple file formats commonly used in astrochemistry. The Network class automatically detects the format and parses the file appropriately.

from jaff import Network

# Load a network - format is auto-detected
net = Network("networks/react_COthin")

Basic Loading

Simple Loading

The simplest way to load a network:

from jaff import Network

# Load network from file
net = Network("path/to/network.dat")

# Access network properties
print(f"Loaded: {net.label}")
print(f"Species: {len(net.species)}")
print(f"Reactions: {len(net.reactions)}")

With Error Checking

Enable validation to catch issues:

# Enable error checking
net = Network("mynetwork.dat", errors=True)

This will raise exceptions if the network has:

Species that only appear as reactants (sinks)
Species that only appear as products (sources)
Duplicate reactions
Isomer issues
Invalid reaction formatting

Custom Labels

Specify a custom label for the network:

# Default label is the filename
net1 = Network("networks/react_COthin")
print(net1.label)  # "react_COthin"

# Custom label
net2 = Network("networks/react_COthin", label="CO_chemistry")
print(net2.label)  # "CO_chemistry"

Supported Formats

JAFF automatically detects and parses multiple network file formats.

KROME Format

KROME network files with format specification:

@format:idx,R,R,R,P,P,P,P,tmin,tmax,rate
1,H,O,,,OH,,,0,1e4,1.2e-10*(tgas/300)**0.5
2,H2,O,,,OH,H,,0,1e4,3.4e-11*exp(-500/Tgas)

# Variables
@var:te=tgas*8.617343e-5
@var:invtgas=1.0/tgas

KIDA Format

Kinetic Database for Astrochemistry format:

H + O -> OH : 1.2e-10 : 0.5 : 0.0
H2 + O -> OH + H : 3.4e-11 : 0.0 : 500.0

Format: Reactants -> Products : α : β : γ

Where rate = \(\alpha \left(\frac{T}{300}\right)^\beta e^{\left(-\frac{\gamma}{T}\right)}\)

UDFA Format

UMIST Database for Astrochemistry format:

H:O:OH:1.2e-10:0.5:0.0:0:1e4
H2:O:OH:H:3.4e-11:0.0:500.0:0:1e4

PRIZMO Format

PRIZMO format with variable blocks:

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

H + O -> OH, k1 * sqrtt
H2 + O -> OH + H, k2 * exp(-500/tgas)

UCLCHEM Format

UCL_CHEM format with NAN placeholders:

H,O,NAN,OH,NAN,NAN,1.2e-10,0.5,0.0
H2,O,NAN,OH,H,NAN,3.4e-11,0.0,500.0

Advanced Loading

Auxiliary Function Files

Use custom rate function definitions:

# Load with auxiliary functions
net = Network(
    "network.dat",
    funcfile="aux_functions.txt"
)

Auxiliary function file format:

# Define custom functions
@function function_name(arg1, arg2)
expression # Eg: arg1 + arg2
return expression

JAFF also detects ausilary function files automatically if the file name extension ends with _functions Example: network.dat will have a network file as network.dat_functions

Hydrogen Nuclei Replacement

Control replacement of hydrogen nuclei density symbol with the total computed abundance over species:

# Enable replacement (default)
net = Network("network.dat", replace_nH=True)

# Disable replacement
net = Network("network.dat", replace_nH=False)

JAFF Binary Format

For faster loading of large networks, save to JAFF binary format:

# First load and save
net = Network("large_network.dat")
net.to_jaff_file("large_network.jaff")

# Future loads are much faster
net = Network("large_network.jaff")

Error Handling

Validation Warnings

When errors=False (default), validation issues produce warnings:

net = Network("network.dat", errors=False)
# Output:
# WARNING: Species 'X' only appears as reactant
# WARNING: Duplicate reaction found: H + O -> OH