Fadeway comments on My simple hack for increased alertness and improved cognitive functioning: very bright light - Less Wrong
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At night F.Lux is usually great. Except when waking up or doing polyphasic (where you actually treat night and day as the same thing). I discovered the program a week after I started Uberman, and a shortly after installing it, I started having trouble staying up during the early morning hours between 3am-7am, where previously I had no issue at all. I am no longer doing polyphasic, so it's awesome - I never get blinded by my monitor etc. I only wish I could make it so that it uses the daylight setting if I turn the PC on at night - so it helps me wake up. As it stands, I get two hours of "you should be in bed" lighting before it finally gives up on sending me for a nap.
Use the 'disable for an hour' option, and repeat as needed.