Overview

This section provides detailed documentation for all public APIs, classes, and functions in the JAFF library.

Core Modules

Network Management

Network - Chemical reaction network loading and management

The Network class is the foundation of JAFF, providing methods to load, parse, and manage chemical reaction networks from various formats.

from jaff import Network

net = Network("networks/react_COthin")
print(f"{len(net.species)} species, {len(net.reactions)} reactions")

Key Features:

• Multi-format support (KIDA, UDFA, PRIZMO, KROME, UCLCHEM)
• Automatic format detection
• Mass and charge conservation validation
• Species and reaction indexing

Species & Reactions

Species - Individual chemical species representation

Access detailed information about chemical species including mass, charge, elemental composition, and more.

species = net.species[0]
print(f"{species.name}: mass={species.mass}, charge={species.charge}")

Reaction - Chemical reaction representation and rate calculations

Work with individual reactions, calculate rate coefficients, and analyze stoichiometry.

reaction = net.reactions[0]
k = reaction.rate(T=100.0)  # Calculate rate at 100K
print(reaction.get_sympy())  # Symbolic representation

Code Generation

Codegen - Multi-language code generator

Generate optimized code for reaction rates, ODEs, Jacobians, and more in C, C++, or Fortran.

from jaff import Codegen

cg = Codegen(network=net, lang="cxx")
rate_code = cg.get_rates(idx_offset=0, rate_var="rate", brac_format="[]")

Supported Languages:

• C++ (cxx)
• C (c)
• Fortran 90/95 (f90)

JAFF Types - Type definitions for indexed expressions

Specialized data structures for organizing code generation output with indexed values.

from jaff.jaff_types import IndexedValue, IndexedList

# IndexedValue represents array[index] = value
iv = IndexedValue([0], "x + y")

# IndexedList is a type-safe collection of IndexedValue objects
items = IndexedList([IndexedValue([0], "expr1"), IndexedValue([1], "expr2")])

File Parser - Template-based code generation

Parse template files containing JAFF directives to generate customized code.

from jaff.file_parser import Fileparser
from pathlib import Path

parser = Fileparser(net, Path("template.cpp"))
output = parser.parse_file()

Analysis Tools

Elements - Element extraction and matrix generation

Extract chemical elements from species and generate element-related matrices for conservation analysis.

from jaff.elements import Elements

elem = Elements(net)
print(f"Elements: {elem.elements}")
truth_matrix = elem.get_element_truth_matrix()
density_matrix = elem.get_element_density_matrix()

Module Structure

classDiagram
    class jaff {
        \__init\__.py*
    }

    %% Define categories as separate classes
    class Core {
        network.py
        species.py
        reaction.py
        elements.py
        parsers.py
    }

    class CLI {
        cli.py
        generate.py
    }

    class Code_generation {
        jaff_types.py
        file_parser.py
        codegen.py
        preprocessor.py
        builder.py
        templates/preprocessor/
        templates/generator/
        plugins/
    }


    %% Connect categories to jaff
    jaff --> Core
    jaff --> CLI
    jaff --> Code_generation

All the above files can be found in the src/jaff folder. The templates folder contains to sub-folders - preprocessor & generator. The preprocessor folder contains templates than can be generated by the preprocessor. The generator contains templates than can gen generated by the jaffgen command.

The Core files contain the classes and parsers required to parse and store Network tokens. The CLI file handles command line tasks. The Code_generation files contains classes for handeling code-generation using different methods.

Quick API Reference

Common Imports

# Core functionality
from jaff import Network, Codegen

# Type definitions
from jaff.jaff_types import IndexedValue, IndexedList

# Template parsing
from jaff.file_parser import Fileparser

# Element analysis
from jaff.elements import Elements

# Direct imports
from jaff.species import Species
from jaff.reaction import Reaction

Network Operations

Code Generation

Element Analysis

Next Steps

Choose a module to explore:

Getting Help

• User Guide: Read the User Guide
• Examples: Check the examples/ directory
• Issues: Report bugs on GitHub