Here is the piece:

Each workout is performed for the purpose of producing a stress that satisfies the immediate needs of the exerciser: burning some calories, getting hot, sweaty, and out of breath, pumping up the biceps, stretching – basically just punching the physical clock.

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    Punching the clock is a figurative expression that means to finish a day's work (or, less commonly, to start it). Here, by using the word physical, it implies that it's supposed to be taken literally. But I don't understand how that's possible, since it still has to be figurative in some sense. My best guess is it's an awkward way of drawing an analogy between the physical body and physical clocks. Jan 20 '19 at 9:44

To "punch the clock" refers literally to the timeclock, and figuratively (via metonymy) to a daily work routine, often monotonous.

Injecting the word physical there is a way of coopting the idiom for a specific purpose, namely, physical exercise: Basically, you are just putting in monotonous, repetitive, physical effort (to achieve your specific goal).

Along those lines, an astronomer bored with his job might say:

Oh well, I have to go punch the interstellar clock.

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