GENOA

The GENerator of Optimized Atmospheric chemical mechanisms

GENOA is an open-source framework for scalable, accuracy-controlled reduction and analysis of highly detailed volatile organic compound (VOC) mechanisms.

Documentation and user guide: https://tool-genoa.github.io/genoa

Current version

This repository hosts GENOA v3, which advances scalability, modularity, and workflow design for the reduction of mechanisms containing up to millions of reactions, including those generated by GECKO-A, while preserving key indicators such as secondary organic aerosol formation (SOA) and gas-phase reactivity.

Earlier GENOA implementations, GENOA v1 and GENOA v2.0, coupled to SSH-aerosol, were released as the GENerator of Reduced Organic Aerosol Mechanisms.

Key capabilities

GENOA introduces a scalable, graph-aware framework that integrates two reduction processes:

Threshold-based reduction (TBR)

A fast, strategy-driven pruning process that reduces low-influence species and reactions using configurable thresholds.

Simulation-based reduction (SBR)

An iterative refinement process guided by box-model simulations and quantitative error metrics, enabling accuracy-controlled mechanism reduction.

Together, these processes allow users to explore reduction trade-offs across VOC classes and chemical evaluation targets within user-defined accuracy constraints.

Installation

GENOA can be run using Docker (recommended) or installed from source.

git clone https://github.com/tool-genoa/genoa.git
cd genoa
docker build -t genoa .
docker run -it genoa

For complete installation and configuration instructions, see the GENOA documentation.

Quick Start

Run GENOA with a configuration file:

genoa ./test_cases/config/1_build.ini

or from source:

python -m genoa ./test_cases/config/1_build.ini

For long jobs or HPC environments, use nohup or the provided runtime script:

./runtime/scripts/run_job.sh ./test_cases/config/1_build.ini ./output/logs/run.log

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Directory Layout

genoa/
├── data
│   ├── gecko-files
│   └── ssh-aerosol-files
├── Dockerfile
├── LICENSE
├── pyproject.toml
├── README.md
├── requirements.txt
├── runtime
│   ├── logs
│   └── scripts
│       └── run_job.sh
├── src
│   └── genoa
├── test_cases
│   ├── conditions
│   ├── config
│   ├── input
│   └── output
└── vendor
    ├── boxmodel4gecko-v-1-0-genoa
    └── UManSysProp_public-master

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Vendor Models

The vendor/ directory contains external models that have been adapted for integration with GENOA v3. Those coupled versions in vendor/ remain compatible with the standard distributions. When using these models with GENOA v3, ensure that their dependencies (e.g., compilers, NetCDF, Open Babel) are correctly configured and compiled on your system.

boxmodel4gecko-v-1-0-genoa

• Source code: GECKO-A box model

  Archived release v1.0

• Modifications: Many changes for integration with GENOA v3

UManSysProp_public-master

• Source code: UManSysProp

  Archived release v1.04

• Modifications: Fixed Python 3 import path for openbabel

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Test Cases

The test_cases/ directory provides representative examples demonstrating the full GENOA v3 workflow, including:

• mechanism conversion and preprocessing,
• box-model simulation and comparison,
• threshold-based and simulation-based reduction,
• evaluation and post-processing.

All test cases are based on a six-generation 1-hexene GECKO-A mechanism (U6), which provides a compact but realistic system for local or HPC runs. Each test case is configured via an .ini file and designed to be self-contained and reproducible.

Configuration files

Config File	Purpose
1_build.ini	Convert GECKO-A -> GENOA format
2_build_run.ini	Convert and run the mechanism
3_run.ini	Simulate a specific mechanism
4_run_compare.ini	Simulate and compare with a reference
5_threshold_reduction.ini	Perform threshold-based reduction
6_training.ini	Conduct simulation-based reduction (training)
6_training_parameters.csv	Stage-specific parameter definitions for training
7_testing.ini	Evaluate reduced mechanisms
8_reductions.ini	Execute sequential reductions and evaluation
9_postprocess.ini	Generate plots and perform post-processing
config_reference.ini	Reference for all configuration sections and options
parameter_reference.csv	Reference for parameters used in simulation-based reduction

A detailed description of configuration options and parameters is provided on the GENOA v3 documentation site.

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Citation

If you use GENOA v3, please cite:

(...)

Contact

Zhizhao Wang (zhizhaow@ucr.edu)