How can I remove unnecessary processes from FABM-ERSEM?

[LinZhonghao1]

Hi all,
I am currently using FABM-ERSEM for my project. For my specific application, I only require some subsets of the biogeochemical processes included in the full ERSEM model.
I would like to ask: what is the recommended approach to remove or disable unnecessary processes from FABM-ERSEM? Should I manually modify the source code, or is there a better (e.g., configuration-based) way to achieve this?

My goal is to keep the model lightweight and focused only on the processes I need.
If there are any guidelines or examples for this kind of customization, I would appreciate it if you could point me to them.

Thank you very much for your help!

Best regards,
Lin

[glessin]

Dear Lin,

There are certainly previous examples of simplifying ERSEM configuration, most commonly running it with reduced number of phytoplankton and/or zooplankton functional groups.

Most of the modifications can be done from within the configuration file, thanks to the flexibility allowed by FABM: individual modules can be disabled by adding "use: false" statement (but you have to be mindful to take care of any unfulfilled dependencies it might create), and many processes disabled by e.g. specifying zero rates.

However, more concrete advice will depend on your specific needs. Which processes are you trying to isolate in the model?

Best wishes,
Gennadi

[LinZhonghao1]

Dear Gennadi,

Thank you very much for your helpful reply！

In my current work, I plan to use ERSEM primarily as a biogeochemical exchange module to supply essential nutrients and fluxes to a newly added seagrass model. As you mentioned, I would like to consolidate the plankton-related processes to make the model more computationally efficient. However, this does not seem easy, and I am concerned that removing these components might affect other processes.

So I think I will put this issue on hold for now. Meanwhile, if possible, I would like to ask for your advice on how to access the bottom layer value of parEIR. Since my seagrass model relies on light availability at the seabed, I need to use only the bottom layer value of parEIR in the calculations. What is the recommended way to extract this?

Thank you again for your help! I look forward to your reply.

Best regards,
Lin

[jornbr]

Hi Lin,

Regarding the seagrass: the typical way to handle this would be to implement the seagrass as a bottom-associated process, by implementing do_bottom in your seagrass module. Any pelagic dependency that you register (e.g., light, temperature) will automatically be set to the value in bottom layer when you are in do_bottom. Since ERSEM's parEIR is registered with identity downwelling_photosynthetic_radiative_flux, you can get the desired effect in your seagrass module with something like call self%register_dependency(self%id_parEIR,standard_variables%downwelling_photosynthetic_radiative_flux).

Cheers,

Jorn

BTW there is a seagrass example in FABM here: https://github.com/fabm-model/fabm/blob/master/src/models/csiro/seagrass.F90. It handles temperature as I describe above, but its light treatment is already slightly more complex as it deals with PAR above the canopy.

[LinZhonghao1]

Hi Jorn,

Thank you very much. The problems related to bottom-layer light has been resolved.

Best regards,
Lin