Marine Ecosystem Toolkit for Optimization and Simulation in 3-D


Metos3D is a collection of simulation software, models and data intended to be used for simulation and optimization of marine ecosystem models. Metos3D is organized in separate git repositories. The current versions are:

main script, should be run as a shell command
main software, transport driver
marine biogeochemical/ecosystem models
geometry data, forcing data, transport matrices


To install the toolkit, just paste the following line into your terminal: (python and curl required):

python -c "$(curl -fsSL"

The code will be installed in a subdirectory called ".metos3d" of your home directory.


The main scientific document can be found at:

A technical report explaining the matrix command can be found at:

Additionally, each repository consists of a documentation folder named doc. Quick access:

Simulation package: metos3d-simpack.pdf
Model package: metos3d-model.pdf
Data package: metos3d-data.pdf


Metos3D needs the Portable, Extensible Toolkit for Scientific Computation (PETSc) to run. Here, version 3.7 is required.


Important changes that has been accomplished lately:

Diagnostic versions of the N, N-DOP, ..., NPZD-DOP models have been added.
The BGC API includes now diagnostic variables. See: metos3d-model.pdf
The matrix command has been added.
Metos3D works with PETSc 3.7 now.

Authors and Contributors

The software is written and mainted by Jaroslaw Piwonski ( The original data is provided by Samar Khatiwala ( as part of the Transport Matrix Method.

The homepage concept is copied from GitHub Pages and the homebrew project.

Support or Contact

Have trouble installing Metos3D? Contact Jaroslaw Piwonski, attach the output of the script and kindly ask for help.