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OK, that looks sensible. Have a look at angular velocity too - we're trying to identify the vortex core. 

From the above the cyclone is doing what it's supposed to. So, next step is to see where the particles are. Ie are they getting stuck in the vicous sublayer or in a bulk flow feature? Zoom in on the flow around the base of the cyclone: does the reverse flow in the core trap particles at the base of the cone?