Biogeochemical (BGC) models can be used within the Oceananigans biogeochemistry framework or as stand alone box models. All BGC models should be setup in the same way so that they can easily be substituted for each other. You can easily implement a different model (or a variation on a current model) by following the guide here.
For details of the BGC models currently implemented please see the following pages.
At the simplest level, all that is required to setup an existing OceanBioME BGC model is to pass it to the Oceananigans model setup:
model = NonhydrostaticModel(; grid, ..., biogeochemistry = MODEL_NAME(; grid))
MODEL_NAME is the name of the model. You may also need to pass additional parameters like:
MODEL_NAME(; grid, growth_rate = 10.0)
The above will set up the required tracers and auxiliary fields, and you may also set boundary conditions or additional forcing through the usual Oceananigans setup.
Models usually have a default light attenuation model specified, these may be substituted easily by passing different models as parameters as above.
Our models are implemented in an abstract framework
Biogeochemistry which contains
modifiers. This is automatically set up for existing BGC models, but may also be used to couple any BGC model with light attenuation and sediments. See the implementation page for some more information on how to couple other models.