If the slope of a link is negative and the solution is dynamic wave then the following data will be switched in link.c in SWMM 5. All upstream data for the link is switched to the downstream end of the link and vice versa. The means that if the flow is from the original upstream node to the downstream node the flow will be negative in the output of SWMM 5.
Negative flow in SWMM 5 means:
1. The link has an adverse or negative slope,
2. The link has reverse flow if the link slope is positive.
