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You're right. The sponge zones in this implementation use the standard diffusion, so diffusion has to be on for them to work. That's the case in example.inp but not the other input files here. The linked PR fixes the issue. Sorry for the confusion on this!
https://github.com/AMReX-Combustion/PeleC/blob/development/Exec/RegTests/EB-ConvergingNozzle/eb-converging-nozzle.inp
pelec.diffuse_vel = 0
prob.do_sponge_zones = 1
pelec.diffuse_vel should be 1 instead of 0 to make the sponge zone work.?
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