CGEM (Coastal General Ecology Model) is a biogeochemical, lower trophic level ecosystem model that describes biogeochemical processes regulating carbon, oxygen, nutrients, phytoplankton, and zooplankton.
This repo is CGEM code** that is being reformatted into a SCHISM module. (Sorry, no actual SCHISM here!). It its current state, it can be used to run and visualize CGEM equations in a 1D water column with no boundary conditions.
** Original code base is what Cody emailed me December 7, 2022.
Right now:
- Temperature and salinity are fixed, set in grid.nml
- RAD calculated by solar zenith angle (lat/lon/time)
- Cloern is there but I didn't test it (need to check DailyRad_init)
- no fluxes implemented yet
- no sinking yet...(this used to be handled in the Adv3D routine)
And this will never have:
- transport. That's SCHISM's job.
This is not a production repo! The purpose is for testing code changes. The general workflow is to git commit locally and only do a push to GitHub when everything is working, then after the push, make necessary changes to the Python/Notebook. That narrows the OMG it's broken! window a bit, but not completely.
The Binder buttons below are attached to tagged releases. When using a tagged version, all Notebooks are expected to run with out errors. We hope that's the case.
- Clicking on the "launch binder" icon will start a Notebook
- Be patient, it might take some time. It is starting up a VM (little computer in the cloud), installing all the necessary Python packages, and loading the data...and all for free!
- Once you start one Notebook, you can click the folder icon on the left and access any other Notebook. You don't have to launch a new Binder.
A basic tour of CGEM Python interface: compiling and running code, changing the inputs, calculating stuff, and making plots.
Plots Phytoplankton growth at two different temperatures
This notebook prints each variable at each k layer
This notebook shows how to change parameters and makes plots of each phytoplankton group at layer k=1.
Using Binder, you can actually modify the code or makefile and recompile, change the namelists, add to the Python library or the Notebooks...
If you make changes, figure out some good parameters, or develop new Python code to look at stuff, SAVE your work locally! The Notebooks, nml files, cgem.py, everything new you created will disappear forever when Binder stops.
If you happen to be browsing and see something odd, please open an Issue and let us know.
Thanks!
This effort is funded by the National Oceanic and Atmospheric Administration's RESTORE Science Program under award NA19NOS4510194 to North Carolina State University.