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If using the ChipWhisperer Capture Rev2 (CW1002), you do not have a glitch output port. Instead you need the VCC glitching add-on.
The VCC glitching add-on can be added to the AVR or SmartCard 6-pin headers, or connected to the XMEGA by a few additional jumper wires. An example of the connection is shown in the vccglitchhwsetup section.
The connection between the glitch input and FPGAOUT pin must be done via a jumper wire. This connects the glitch module output to the MOSFET input, such that whenever a glitch is requested the VCC on the target is shorted.