The "second function" you mentioned should refer to the peripheral module function. If you use the module, select "second function", and if you don't use the module, select "first function". You can select by setting the PxSEL register. Writing "0" to a certain bit is I/O; writing "1" is "second function". When using a comparator (on-chip peripheral module), set it to the second function. Of course, if you use an off-chip comparator and send its output high or low level (1 or 0) to MSP430, then select "first function".
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