Altering the mask function

I understand that as the mask function works now it blocks flow through all layers within the water column, I am trying to simulate the effects of something floating on top of the water, similar to a dock. Is there a way to modify the mask function to only block flow through the top layer or two of water or down to a specified depth? If so what files would I modify to make this possible?

This could be done but is not done currently as of release EE7. One way would be to modify would calpuv subroutine. However this is calculated on a depth averaged basis so it is clear how you would handle it as as a pressure condition, as your scenario would not be open channel flow.

A better and simpler solution would be that you apply the mask to block the flows, and then specify an hydraulic structure for which you define the discharge relationship. This would mean externally calculating the upstream and downstream pressure distribution in order to calculate flow. Effectively this is a calculation external to EFDC which is then put into EE as the rating curve for that structure. We hope this helps. Let us know how you get on.

I am trying to simulate the wave created by a device to push floating debris off to the side on a river. The device itself is moored to a buoy and floats, allowing the the flow to pass underneath is not exactly what i am looking for as the characteristics of the wake is what interests me. I am also using Version 5 if that changes anything.

If you are wanting to do a full 3D hydrodynamic near field analysis of the wake then EFDC cannot handle this. Details of wakes and reduced pressure regions behind wakes would require another model.

Do you have any recommendations, or know of a model that can handle this task?

Your analysis requires a full 3D hydrodynamic algorithm with wall boundary turbulent model. LES (Large Eddy Simulation) or several k-epsilon improved models have shown good performance with flow similar to yours. The selection of model also depends on your zone of interest and range of flow. CFX, Fluent, Star-CD are good commercial software and may be helpful.