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The traj_ warning is an error

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--- WARNING: traj_opt is zero, but num_traj is not zero; setting num_traj to zero

IF ( ( model_config_rec%traj_opt .EQ. 0 ) .AND. &
( model_config_rec%num_traj .NE. 0 ) ) THEN
wrf_err_message = '--- WARNING: traj_opt is zero, but num_traj is not zero; setting num_traj to zero.'
CALL wrf_debug ( 1, TRIM( wrf_err_message ) )
model_config_rec%num_traj = 0

by default, traj_opt is 0, default num_traj is 1000, so by default you have a warning?
It does seem silly, but unfortunately this was necessary to prevent other errors. The trajectory option is, by default, turned off (which makes sense). The developers of the trajectory code wanted the default value to be 1000 to give users a good starting point for the number of trajectories they should use. But the two default settings contradicted each other and caused problems.

This simple harmless message was an easy solution at the time of the correction. We have recently (in the past few versions) modified the code so that these warning messages will not print out unless a user specifically sets debug_level >= 1, which is not recommended. We also removed debug_level from the default namelist so that users will not intentionally use the option. This option was originally put in the namelist many years back for some specific testing purpose and should have been removed. It rarely provides any useful information, and actually just fills the rsl files with a lot of junk, making them nearly impossible to read through, and can sometimes even make the rsl files so large that they fill up disk space and cause the model to stop.