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If you are interested in changing the inner-most nest, make the change in wrfinput_d0X (where 'X' is your inner-nest domain ID). When you run wrf.exe, you should use input_from_file = .true., .true., .true. so that the model uses data from the nest domain input. If you made changes in the geogrid files (geo_em.d0x.nc), set surface_input_source = 3 before running real.exe.