From help:
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Percent complete:

The % Complete field contains the current status of a task, expressed as the percentage of the task's duration that has been completed.

% Complete = (Actual Duration/Duration) * 100

Physical % Complete:
The Physical % Complete field shows an entered percent complete value that can be be used as an alternative for calculating budgeted cost of work performed (BCWP).
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The primary purpose of physical % complete is the different method of calculating earned value.