OCD and clocking
When the MCU enters stopped mode, the OCD clock is used as MCU clock. The OCD clock is either the JTAG TCK if the JTAG interface is being used, or the PDI_CLK if the PDI interface is being used.
The Atmel JTAGICE mkII does not offer a variable clock rate for Atmel AVR XMEGA targets.
SDRAM refresh in stopped mode
When the OCD is in stopped mode, the MCU is clocked by the PDI or JTAG clock, as described in the paragraph above. Since nothing is known of this frequency by the debugger or OCD, a low refresh period (0x10) is automatically used. This value can't be changed by the user.
I/O modules in stopped mode
Unlike most Atmel megaAVR devices, in XMEGA the I/O modules are stopped in stop mode. This means that USART transmissions will be interrupted, timers (and PWM) will be stopped.
Hardware breakpoints
There are four hardware breakpoint comparators - 2 address comparators and 2 value comparators.They have certain restrictions:
All breakpoints must be of the same type (program or data)
All data breakpoints must be in the same memory area (IO, SRAM or XRAM)
There can only be one breakpoint if address range is used
Here are the different combinations that can be set:
2 single data or program address breakpoints
1 data or program address range breakpoint
2 single data address breakpoints with single value compare
1 data breakpoint with address range, value range or both
Atmel Studio will tell you if the breakpoint can't be set, and why. Data breakpoints have priority over program breakpoints, if software breakpoints are available.
External reset and PDI physical
The PDI physical interface uses the reset line as clock. While debugging, the reset pullup should be 10 kΩ or higher, or be removed altogether. Any reset capacitors should be removed. Other external reset sources should be disconnected.