This repository contains the model i.e. simulation output, the oceantracker model itself, and the script to produce the plots used in the publication ``` Title: Effects of coagulation processes on phytoplankton mortality in the Elbe estuary from a Lagrangian perspective Authors: Laurin Steidle, Johannes Pein, Adrian Burd, Ross Vennell Url: https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2025.1624762/abstract DOI: 10.3389/fmars.2025.1624762 ``` The repository was created by Laurin Steidle (laurin.steidle@uni-hamburg.de). Feel free to reach out. 1. If you would like to reproduce the plots you will need to download the "model_output_archive.tar.xy.part*", unpack it, and run the the "collapse_paper_plot.ipynb". To unpack the model output data (from a unix based machine) ``` # join the parts together cat model_output_archive.tar.xy.part* > model_output_archive.tar.xz # and unpack them tar -xJf model_output_archive.tar.xz ``` 2. If you would like to reproduce the output you will need to download "oceantracker.tar.xy". To install it take a look at the documentation (https://oceantracker.github.io/oceantracker/_build/html/index.html) The short version of it is: ``` mamba create --name oceantracker mamba activate oceantracker cd oceantracker pip install -e . ``` The model configuration used to produce the paper output is ```22_07_29_depth_losses_v57.py```. (You can also find it in oceantracker/experiments/collapse/) Sadly, I am not allowed to share the simulation input i.e. the hydrodynamics publicly. You can reach out to Johannes Pein (johannes.pein@hhereonereon.de) or me directly to me to get the hydrodynamics.
