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I believe you only use the degeneracy equation when calculating the positional or residual entropy. So basically when you are dealing with calculating entropy in the molecular form, not with thermal entropy.
The equation W=2^n only refers to a specific model where the model is only in two microstates. In order to find the degeneracy of any molecule/atom the equation used is W=M^n where M= the number of states and n= number of molecules/atoms
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