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Creating New Hydrograph for segment of River

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I've been running a handful of sediment transport sims but am finding some of them are taking much longer than I have time for. If you look at the attached image there are two defined channels that feed into my area of interest ( the trenches further down stream). Is there a tool that could be used to create two new hydrographs at these two inputs based on the singular hydrograph that originally filled the entire domain (figure also included)  through these areas? My second question is then would this task in itself be worth the time? There is no specific tool I can see that may be of use here. My end goal  is to reduce the number of elements, and therefore the domain size and hopefully see a significant decrease in simulation time.

Domain Overview.JPG

Trenches Overveiw.JPG

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