Do not post a question in the tutorials section. This is designed for posting, guess what, tutorials. This is not a tutorial so I have moved it to a better place.
this looks like good entry level for what you are trying to do:
have a look at the " Setting an exact frequency" section.
also did some math and it you plan to use only one timer to run both PWMs then your timer period should be a multiple of (6 x target output frequency)
for example
sig1 sig2
t=0 HIGH LOW
t=T/6 HIGH HIGH
t = 2*(T/6) HIGH HIGH
t = 3*(T/6) LOW HIGH
t = 4*(T/6) LOW LOW
t = 5*(T/6) LOW LOW
t = 6*(T/6) HIGH LOW <------ or back to t=0 ;)
If it's that slow, you can generate the two output signals entirely in software. Have a cycle of 4 points in time to be calculated repeatedly, which will each generate an interrupt when its turn comes around. So you'd have A going high, then at 30 degrees B goes high, at 180 A goes low, at 210 degrees B goes low.
You do have to decide how much resolution in frequency you need, but I'm sure you won't want to share that. Or the minimum frequency either.
So in fact they are square waves 30* out of phase and variable frequency. If the duty cycle is always 50% then by definition they aren't "pulse width modulated"!
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Is CTC-12 Mode operation of TC1 a PWM-mode? If not, then we will not be able to change the duty cycle of the generated waveforms. The duty cycle will remain at 50% as the waveform toggles at every compare match event.