bathymetry not represented in model output

[shendepp]

hi everyone,

I am running a model for Indian Ocean. For the IC file, I have filled the entire domain(till maximum depth and even land)("ic.png" shows a section along a latitude). The model output does not show bathymetry(output is a column) ("output.png" shows same section). how can i correct this?
(I am running in Z* mode but the problem is there for HYCOM1 too.)

 

[adcroft]

The MOM_IC.nc file is not masked. Only the diagnostic output in z-coordinates is masked. If you look at the thickness ("h"), it will have zeros or tiny values for the vanished layers overlaying topography.