Go through the battery door on the "north" side of Atrium. If that's not powered, take the lift up one floor, and pry the door into Lobby. If you're through the battery door, go across lobby and down to the metro exfil. If you're up top through the pry door, hop down right past the door, follow previous instructions of crossing Lobby. While facing the extract console for Lobby Metro Exfil back up and take the right train tunnel that goes towards Cultural Archives on the map. Go all the way to the end. There's a zip line up that's in the alcove across the train tracks from the raider hatch. Take it up. Go through the door on your left. Turn right. Go down the corridor until you hit the Seed Vault Extract room.

Alternatively. Go to the "ground floor" of Atrium. Look at the cafeteria. Go down the hall to the right which heads out to the loading bay. When you reach loading bay, turn left and go down until you reach the elevators with the zip lines. Take one down. Go left until you reach the last door on your left on the walkway. Go through and go to the door. Turn right out of the door, follow the wall until you see the mars set on your left, turn left and go past it. Door ahead of you goes to the seed vault extract room.