Hello Branden,
I only got 4 files from the provided link, in particular no BINARY ATMOSPHERIC DATA FILE or DROGUES INITIAL POSITIONING DATA FILE.
I am not a specialist of algae transport feature.
Anyway, I would recommend to proceed step by step:
- validate your hydrodynamic model without algae feature,
- add drogues to the pure hydro model to see if you also reproduce your issue,
- use a simpler algae model (1 algae class),
- do you have the same behaviour with another algae type?
Maybe try to use a coarser mesh to have quick results.
Try to start with parameters from canalalgae example.
When you write "drogues moving off the domain to 0, 0 location at certain times in the simulation", do you mean at certain time steps you do not have any algae in the area but it can appear again after?
Perhaps you have to enlarge the extent of your model.
Hope this helps,
Chi-Tuan