Jaffgen Command

Overview

jaffgen is the command-line interface for JAFF code generation. It processes template files containing JAFF directives and generates code for chemical reaction networks in multiple programming languages.

Basic Usage

jaffgen --network <network_file> [options]

Required Arguments

Argument	Description
`--network`	Path to chemical reaction network file

Optional Arguments

Argument	Description	Default
`--outdir`	Output directory for generated files	`src/jaff/generated`
`--indir`	Directory containing template files (Does recursive templating)	None
`--files`	Individual template files to process	None
`--template`	Name of predefined template collection	None
`--lang`	Default language for files without language detection	Auto-detect

Input Sources

You can combine multiple input sources in a single command:

1. Template Directory (`--indir`)

Process all files in a directory:

jaffgen --network networks/react_COthin --indir templates/ --outdir output/

2. Predefined Templates (`--template`)

Use built-in template collections from jaff/templates/generator/:

jaffgen --network networks/react_COthin --template kokkos_ode --outdir output/

Available Templates:

kokkos_ode - Kokkos-based ODE solver templates
microphysics - Microphysics integration templates
python_solve_ivp - Simple initial value proble using python
fortran_dlsodes - Fortran dlsodes template

3. Individual Files (`--files`)

Process specific template files:

jaffgen --network networks/test.dat --files rates.cpp odes.cpp --outdir output/

4. Combined Sources

Mix different input sources:

jaffgen --network networks/test.dat --template microphysics --indir templates/kokkos_ode --files custom.cpp --outdir output/

Language Support

JAFF supports automatic language detection from file extensions. If a file extension is unsupported, you will need to specify the --lang option, the code will crash otherwise

Supported Languages

Language	Aliases	File Extensions
C	`c`	`.c`, `.h`
C++	`cxx`, `cpp`, `c++`	`.cpp`, `.cxx`, `.hpp`
Fortran	`fortran`, `f90`	`.f90`, `.F90`
Python	`python`, `py`	`.py`
Rust	`rust`, `rs`	`.rs`
Julia	`julia`, `jl`	`.jl`

NOTE: The supported extensions are case independent

Specifying Language

jaffgen --network networks/test.dat --files template.txt --lang rust --outdir output/

Output

Generated files are written to the output directory with the same filename as the template:

jaffgen --network net.dat --files rates.cpp --outdir generated/
# Creates: generated/rates.cpp

Output Directory Behavior:

If --outdir is not specified, files are generated in jaff/generated/
The output directory is created if it doesn't exist
Existing files are overwritten without warning