How do you change the clock frequency that is used in the AVR Simulator? I've set it in Project|Options but that did not seem to change it in the Simulator.
When in debug mode go to Debug > AVR Simulator Options. The projects option select the chips frequency (crystal or internal). I guess the 2 should match but the simulator will be many times slower that the real chip, so....
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Just to note that on my "average" PC the cycle counter in Hapsim tells me that AVR Studio simulator averages about 120,000 simulated cycles per second.
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