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no prob
negative velocities mean an opposing direction of flow from ur assumption while doing the model in epanet.exmple, u draw the pipe from left to right..epanet wil consider also left to right assumption of flow in that pipe ..however,upon running epanet will check flow..and give negative value of velocities for different flow direction.
with regards to ur emptying reservoir, try adding the head of the reservoir until it never empties.
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