You read longitude_U in bathy.F90 routine.
Assign the variables :
name_in_longitude_u = 'longitude_U'
name_in_longitude_v = 'longitude_V'
name_in_longitude_f = 'longitude_F'
in your paramain.txt file, according to the fields present in the file of bathymetry that you read (file_bathy='../inputs/bathy_menor.nc)