Are you sure that you need to run it completely flat? The technology inside the battery gets damaged when you run it flat. The normal battery gets callibrated by charging it to 100% pulling the battery out and then charge it again till 100%.
Lion battery's get damaged by 3 things:
- Discharging to 0%.
Samsung Galaxy S 4 I9505 | WanamLite v3.0
Samsung Galaxy S II I9100 : AOKP 4.2.1
HTC Touch Pro2 | ROM: Valkyrie 6.5.23115TR2.5
HTC HD2 | DarkStone1337 [FroyoStone Sense - V3.2]
HTC Desire : Oxygen v2.1.3