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.
- 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
-
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.
{"references": ["10.3389/fmars.2025.1624762"]}
