Skip to content

Basic Workflow

GENOA v3 are action-based, meaning each run is defined by the task(s) you want to perform, including:

  • Mechanism parsing and preparation
  • Threshold-based reduction
  • Simulation-based reduction (training)
  • 0-D box-model simulation
  • Post-processing and visualization

General workflow

The general workflow for using GENOA involves the following steps:

  1. Identify your workflow:

    Decide which action(s) you want GENOA to perform.

    Each action corresponds to a module activated in your configuration file (see Configuration Reference for details).

  2. Prepare files for your run:

    For the selected action(s), gather and prepare the necessary input files. Generally, you will need:

    • GENOA configuration file (.ini). This file specifies:

      • The action(s) to perform
      • Paths to input/output files
      • Parameters for the selected action(s)

    • Mechanism files for parsing, such as:

      • reaction and species lists
      • species directory with molecular structure in SMILES and properties
      • aerosol properties file

    • Box model inputs for simulations, such as:

      • initial concentrations
      • environmental conditions (temperature, humidity, etc.)
      • simulation namelist files (containing time steps, output frequency, etc.)
        • Note: some namelist parameters will be overridden by GENOA based on the configuration file
      • photolysis rate files (if applicable)

    • Any additional data/files required for specific actions, such as:

      • training parameter CSV file for simulation-based reduction

  3. Run GENOA:

    Execute GENOA with your configuration file.

    • From the GENOA root directory: 
      python3 -m genoa <your_config_file.ini>
    • If GENOA is installed as a package (see Installation Instructions), you can simply run: 
      genoa <your_config_file.ini>

    To run GENOA in the background and save logs to a file: 

    nohup genoa <your_config_file.ini> > <your_log_file.log> 2>&1 &
    This command uses nohup to run GENOA in the background, redirecting on-screen output to a file (<your_log_file.log>).

    It is the recommended method for long simulations or reduction tasks.

  4. Check outputs and postprocess

    After the run completes, review the output files generated by GENOA.

    A copy of the on-screen warning and error messages (according to the current logging level set in GENOA) is saved under runtime/logs/. If no errors or warnings occurred, this file will be empty.

    Other output files are written to the directories specified in your configuration file. These depend on the selected actions and may include:

    • For mechanism parsing and preparation:
      • parsed mechanism files with updated species and reaction lists,
      • GENOA species directory recording all species information required for subsequent actions,
      • Other properties files that may required for simulation runs.
    • For simulation:
      • namelist files used for the simulation,
      • model output files (e.g., time series of species concentrations),
      • log files recording on-screen outputs during the simulation.
    • For reductions:
      • reduction logs and summary files,
      • reduced mechanism files,
      • Checkpoint or restart files for continuing reductions,
      • other files generated/used during the reduction process.
    • For post-processing:
      • Visualization and analysis outputs (plots, CSVs, etc.)

Next Steps

Once you are familiar with the basic workflow, you can explore more detailed guidance for each action in the following sections: