Tools for generating ATLANTIS flux data from ROMS output?

[m.hadfield]

ATLANTIS is a spatially compartmentalised ecosystem model (Link et al 2010; van Putten et al. 2013) that requires data on time-varying horizontal and vertical fluxes between the compartments from a hydrodynamic model like ROMS or HYCOM. The preparation of the fluxes is conceptually simple (provided you ignore the hyperdiffusion problems inherent in representing transport through large spatial compartments) but looks somewhat tricky. (I reckon a couple of days to write the code myself, potentially quite enjoyable days, but days I don't really have to spare.) So, can anyone point to code (in Matlab, I would expect) that takes ROMS averages-file output and calculates ATLANTIS fluxes?

References:

Link, J.S.; Fulton, E.A.; Gamble, R.J. (2010). The northeast US application of ATLANTIS: A full system model exploring marine ecosystem dynamics in a living marine resource management context. Progress in Oceanography 87(1–4): 214-234.

van Putten, I.E.; Gorton, R.J.; Fulton, E.A.; Thebaud, O. (2013). The role of behavioural flexibility in a whole of ecosystem model. ICES Journal of Marine Science: Journal du Conseil 70(1): 150-163. doi: 10.1093/icesjms/fss175