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Mixing NWP and RCM mode is always a bit tricky, since this has not been fully tested. As far as I know the GRIB API was newly introduced in INT2LM2.00 for the NWP . Therefore there may be still some bugs when combining it with the RCM setting lbdclim=.TRUE. For instance: the T_SO and W_SO in GRIB are read/write in the dimensions are different: 0:ke_soil_in+1 (T_SO) and 1:ke_soil_in+1 (W_SO). In netCDF the dimensions for the soil quantities have to be the same (both are 1:ke_soil_in+1). The “0” index of T_SO in netCDF is written to and from T_S. This means T_S exists only in the reading/writing process of netCDF. Maybe this was not taken into account for the GRIB API read to netCDF write in INT2LM2.00.
If INT2LM2.01 works for you, please go for that version.