Creating domain file from input bathymetry with DOMAINcfg

I use DOMAINcfg to create initial condidtions for NEMO, e.g. domain_cfg.nc file.
I expect Bathymetry field in bathy_meter.nc and domain_cfg.nc to be identical but actually they differ at some points.
Is it possible to make domain_cfg.nc with the same Bathymetry field as in bathy_meter.nc ?

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The bathymetry available in your domain_cfg.nc file is indeed different from your input bathymetry. The reason for this is that in case of partial bottom cells, there are additional constrains on your minimum thicknesses at the bottom. Stability reasons dictate this. Minimum bottom thicknesses are set by the minimum of rn_e3zps_min (in meters) and rn_e3zps_rat (the fraction of the ‚Äúreference‚ÄĚ vertical grid thicknesses), which are namelist variables. Setting one of these to zero, you should be able to recover your input bathymetry, but it is not recommended‚Ķ