run_tower --ad flag not working correctly

[wwieder]

Brief summary of bug

following instructions in this NEON tutorial to create an AD NEON case my case only ran for 5 days. This makes me wonder if other user_mods or features of the run_tower command are also broken.

Note I was doing this in the cloud, for a tutorial, but I'd expect the same behavior on Derecho.

using ctsm5.3.043

[ekluzek]

There are some STOP_OPTION control in the default shell_commands for NEON and PLUMBER2 for example here:

https://github.com/ESCOMP/CTSM/blob/master/cime_config/usermods_dirs/clm/NEON/defaults/shell_commands#L26

Possibly this should be handled in run-tower?