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If I understand your question correctly, you are providing an outfall pipe to a wetlands, ditch, or other open system? When I encountered this I discussed with StormNET tech support and was told to provide a junction at the outlet end of the pipe (as you noted) and then provide a link from that junction to the outfall node. This last link the tech support had me create it as an arbitrary channel 20 feet wide and 40 feet long from the outlet pipe junction node to the outfall node. This channel is does not really exist.
I originally had the link modeled with the "Direct" option checked in the link properties, but was direct to use the overly wide channel (not sure why). I'm not answering your question for you, but that's how their tech support had me do it, so I'm interested in the StormNET response on this as well.
Brad Smith, PE
NCSU 1993
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