Sargassum growth model

Repository for the interactive notebook and simulations for the article A Lagrangian framework to simulate Sargassum transport and growth by Elena Gianotten, Meike F. Bos, Darshika Manral, Fabio Nauer, Erik Zettler, Linda A. Amaral-Zettler, and Erik van Sebille

How to install

1. Install Pixi

• On Mac or Linux, run the following command in your terminal:

curl -fsSL https://pixi.sh/install.sh | sh

• On Windows, run the following command in PowerShell:

powershell -ExecutionPolicy Bypass -c "irm -useb https://pixi.sh/install.ps1 | iex"

2. Restart your terminal
3. Clone this repository

git clone --depth 1 https://github.com/Parcels-code/Sargassum_growth_model.git

4. Change into the repository directory

cd Sargassum_growth_model

5. Install the required dependencies

pixi install

6. Start JupyterLab

pixi run jupyter lab

7. The interactive_sargassum_notebook.ipynb opens automatically. Run the cells to see the simulations.

Content of this repository

• interactive_sargassum_notebook.ipynb: The interactive notebook to run the Sargassum growth simulations and visualize the results.
• src/: A directory containing the source code for the Sargassum growth model, including the transport and growth kernels in src/sargassum_kernels.py.
• satellite_simulation.py: The script that runs the simulation described in the manuscript with satellite-based initialisation.
• basin_simulation.py: The script that runs the simulation described in the manuscript with basin-wide initialisation.
• Manuscript_Figures/: A directory containing the notebooks used to create the figures for the manuscript.