Below is the format of processed HYCOM files expected by gen_hot_3Dth_from_hycom.f90:

netcdf TS_1 {
dimensions:
        time = 12 ;
        depth = 40 ;
        lat = 489 ;
        lon = 488 ;
variables:
        float salinity(time, depth, lat, lon) ;
        float water_temp(time, depth, lat, lon) ;
        float depth(depth) ;
}
(Note: depth() is positive downward)

netcdf SSH_1 {
dimensions:
        time = 12 ;
        lat = 489 ;
        lon = 501 ;
variables:
        float surf_el(time, lat, lon) ;
        float lat(lat) ;
        float lon(lon) ;
}

netcdf UV_1 {
dimensions:
        time = 12 ;
        depth = 40 ;
        lat = 489 ;
        lon = 488 ;
variables:
        float water_u(time, depth, lat, lon) ;
        float water_v(time, depth, lat, lon) ;
}