I want to make a digital clock project, but with my own PCB design. My question is, if I use a DS3231 IC, will it know already what to do, or I have upload something in order to make the AtMega32U4 operate with it?
Yes
Check the specs. Eventually You need to set the clock ones.
What do you mean by "need to set the clock ones"?
"Once"
(Just a guess)
No clock is fabricated being set to the current time and running from there.
I meant upload firmware or something like that to the IC itself, of course I have to set the clock once it is done
You do not need to upload anything to the RTC apart from setting the correct time
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Then "No". The circuit has all functions built in for setting, reading etc.
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Thanks to all of you
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