The whipping scenes in episode 6 of Outlander were filmed at Blackness Castle which overlooks the River Forth west of Edinburgh.
Filming location was in the courtyard of the castle to the north east of the centrally placed keep.

The outside of Blackness Castle (with a bit of CGI) appeared in episode 8 of Outlander as Fort William

See Blackness Castle location page for information on it and the other movies filmed there.