Hi George Chen,
In the current version of HydroDyn, wave stretching theory for extending wave kinematics above the still water level (SWL) is not included. Once implemented, wave stretching would be enabled by the user through the WaveStMod switch that exists after the WaveMod switch.* With WaveStMod = 0, wave kinematics are always computed up to the SWL regardless of whether the wave elevation is at a crest or trough.
This topic has been discussed on our forum before, e.g., see: model Validation - #23 by Jason.Jonkman.
Footnote
*NREL did have a project to add wave stretching into OpenFAST, but the project ran out of funding before a successful completion, and the solution was not numerically stable for structural flexible substructures; and we have not yet been funded to restart and finish the project.
Best regards,