JAFF

(Just Another Fancy Format)

An astrochemical network parser that supports multiple reaction network formats including KIDA, UDFA, PRIZMO, KROME, and UCLCHEM.

Installation

From source

git clone https://github.com/tgrassi/jaff.git
cd jaff
pip install .

For development

git clone https://github.com/tgrassi/jaff.git
cd jaff
pip install -e .  # Editable install

Quick Start

Command Line Usage

After installation, you can use the jaff command:

# Load and validate a network file
jaff networks/gas_reactions_kida.uva.2024.in

# List all species and reactions
jaff networks/test.dat --list-species --list-reactions

Python API Usage

from jaff import Network

# Load a chemical network
network = Network("networks/react_COthin")

# Access species
for species in network.species:
    print(f"{species.name}: mass={species.mass}, charge={species.charge}")

# Access reactions
for reaction in network.reactions:
    print(f"{reaction.get_sympy()}")

Features

• Multi-format support: Automatically detects and parses KIDA, UDFA, PRIZMO, KROME, and UCLCHEM formats
• Validation: Checks for mass and charge conservation in reactions
• Species analysis: Automatic extraction of elemental composition and properties
• Rate calculations: Temperature-dependent rate coefficient evaluation
• ODE generation: Creates differential equations for chemical kinetics

Supported Network Formats

• KIDA: Kinetic Database for Astrochemistry format Reference: A&A, 689, A63 (2024)
• UDFA: UMIST Database for Astrochemistry format Reference: A&A, 682, A109 (2024)
• PRIZMO: Uses -> separator with VARIABLES{} blocks Reference:MNRAS 494, 4471–4491 (2020)
• KROME: Comma-separated values with @format: header Reference: MNRAS 439, 2386–2419 (2014)
• UCLCHEM: Comma-separated with ,NAN, marker (UNDER CONSTRUCTION)
  Reference: J. Holdship et al 2017 AJ 154 38

Primitive Variables

The following variables are recognized in rate expressions:

• tgas: gas temperature, K
• av: visual extinction, Draine units
• crate: cosmic rays ionization rate of H2, 1/s
• ntot: total number density, 1/cm3
• hnuclei: H nuclei number density, 1/cm3
• d2g: dust-to-gas mass ratio

Examples

Example network files can be found in the networks/ directory.

Development

To contribute or modify JAFF:

# Install in development mode with dev dependencies
pip install -e ".[dev]"

# Run tests
pytest

# Format code
ruff format

# Lint code
ruff check src/jaff

# Organize imports
ruff check --select I --fix

JAFF Schema Validation

JAFF network exports are JSON payloads serialized to .jaff (optionally gzip-compressed as .jaff.gz). To validate a decompressed payload against the schema:

check-jsonschema --schemafile jaff.network.schema.json test.jaff

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