Atmel Studio supports programming of Atmel AVR and Atmel SAM D20 ARM devices using the Atmel JTAGICE3. The programming dialog can be configured to use JTAG, aWire, SPI, PDI, or SWD modes, according to the target device selected.
When configuring the clock frequency, different rules apply for different interfaces and target families:
SPI programming makes use of the target clock. Configure the clock frequency to be lower than one fourth of the frequency at which the target device is currently running.
JTAG programming on Atmel megaAVR devices is clocked by the programmer. This means that the programming clock frequency is limited to the maximum operating frequency of the device itself. (Usually 16MHz.)
AVR XMEGA programming on both JTAG and PDI interfaces is clocked by the programmer. This means that the programming clock frequency is limited to the maximum operating frequency of the device itself. (Usually 32MHz.)
AVR UC3 programming on JTAG interface is clocked by the programmer. This means that the programming clock frequency is limited to the maximum operating frequency of the device itself. (Limited to 33MHz.)
AVR UC3 programming on aWire interface is clocked by the programmer. The optimal frequency is given by the SAB bus speed in the target device. The JTAGICE3 debugger will automatically tune the aWire baud rate to meet this criteria. Although it is usually not necessary, the user can limit the maximum baud rate if needed (e.g. in noisy environments).
SAM D20 ARM programming on SWD interface is clocked by the programmer. The maximum frequency supported by JTAGICE3 is 2MHz. The frequency should not exceed the target CPU frequency *10.