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I'm trying to select a 32kHz crystal and appropriate load capacitors for Atmega48A MCU.

Atmega48A specifies different capacitances for Xtal1 and Xtal2 pins:

18pF for Xtal1 8pF for Xtal2

The datasheet says: "The capacitance (Ce+Ci) needed at each TOSC pin can be calculated by using:C = 2 * CL – Cs" Where CL is load capacitance specified for the crystal and Cs is stray capacitance.

Can I assume that each pin has (18+8)/2=13pF of capacitance? Can I select a 8pF crystal and use it without external load caps assuming ~3pF of stray capacitance?

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The capacitance of the two pins in series is (18*8)/(18+8) = 5.5pF. So with a little stray capacitance (5pF per pin, approx. 2.5pF in series), that should match the 8pF crystal without additional capacitance.

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