Padding out mixing
Given that ROMS and other hydrodynamic models don’t always resolve coastlines well you may find you have the odd small box that gets no fluxes. A very crude fix for this has been added to the physics.prm file of AtlantisDem. If this option is activated then if a box hasn’t had any flow in/out for a user specified number of days Atlantis forcibly does some mixing with the matching layer of the adjacent boxes (with the amount exchanged scaled on their relative areas).
This has meant adding a couple of extra parameters to the physics.prm file
If you do want to use this feature
fill_zero_exchange 1
flush_threshold n
where n is the number of days of no flow before it kicks in
and then you need to (i) set the existing parameter wc_kz (already in physics.prm from ancient Atlantis days but not really used much anymore) to a reasonable value (e.g. 1.48e-9 or something of that order, you can then tune this up/down to get reasonable flow rates based on observations) and (ii) set use_fill_horizmix (add this to physics.orm) to 1 if you want to use the same horizmix as in your bgm file (used to scale the transport vetcors read in from hydro files) or 0 to just have base dispersion.
If you don’t want to use it
fill_zero_exchange 0