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I think with Isabel the angle at which it hit the coast was significant. I also think Katrina was a good example of how powerful hurricanes can "bank up" water in addition to the predicted storm surge simply by prolonged high wind speed in the same direction as the coast. Of course, thats my observation...I'm no expert
I've done some work on wave models, specifically using Isabel data, that demonstrates that hurricanes can also produce enhanced wave heights and periods when they're moving at certain speeds and in a linear fashion, in a process called fetch-trapping. It's one of the reasons Isabel did so much coastal damage.
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Re: 12Z SHIPS output