I have a bunch of doubts and confusions on the concept of entropy which have been bothering me for a while now. The most important ones are of a more technical nature, arisen from the reading of this and Jaynes' paper "Gibbs vs Boltzmann entropies". Although they seem like great texts, they leave me confused when they argue that the Gibbs entropy remains constant and that this is precisely what one needs to prove in the Second Law. I quote, from the first link:
we return to the specific case of a gas of N particles, this time confined to one side of a box containing a removable partition. We suppose that the initial state is such that we can descnbe it using the canonical probability distribution. From our earlier discussion we can then say that the Gibbs entropy SG is maximized and equal to the experimental entropy SE.
We now suppose that the partition is opened and the atoms occupy the whole box. We wait until the state variables stop changing, so in that sense the system is in equilibrium and a new experimental entropy S'E can be defined. Also, all the motions of the gas molecules are Hamiltonian, so that the Gibbs entropy S'G has not changed: S'G = SG
The probability distribution of the N particles is no longer the canonical one, however, because of the (very subtle!) correlations it contains reflecting the fact that the molecules were originally on one side of the partition. This means that the Gibbs entropy S'G is now in general less than the maximum attainable for the new values of the state variables, which is in turn equal to the new experimental entropy. So
SE = SG = S'G ≤ S'E
Well, I can say they totally lost me here. After the expansion, the system reaches an equilibrium. We shouldn't care about how we reached that equilibrium, so I would think that maximizing $S_G= -K_B \int \rho \log \rho d \mu$ -with $\rho$ the joint probability distribution of the position and momentum of the $N$ particles and with the restriction that the average energy is, say, $U$- should give again the probability distribution $\rho$ in the new equilibrium. So, I defintely don't understand at all why they say that "The probability distribution of the N particles is no longer the canonical one," neither do I understand the statement "because of the (very subtle!) correlations it contains reflecting the fact that the molecules were originally on one side of the partition," since I believe it is not important at all how we reached the equilibrium! If this was the case, why could we prove that in the first case (when all the molecules are in one side of the box) the Gibbs entropy coincided with the "experimental" one (I, by the way, don't know exactly what they mean by "experimental" entropy; do they mean Clausius'?). Didn't Jaynes prove that Gibbs entropy coincide with Clausius'? (I got that from his paper, at least). But how can Gibbs entropy remain constant if the entropy "MUST" increase?
Jaynes, in his paper, writes things like $(S_G)_{2}-(S_G)_{1},$ so that changes in the Gibbs entropy must be something meaninful, despite being so clear that the hamiltonian evolution leaves $\rho$ the same.
Well, I guess it's being really hard to explain accurately the nature of my confusions, but hopefully someone around here has struggled with similar issues and can give an enligthening clarification.
Thank you very much in advance.
EXPANDING THE ORIGINAL QUESTION: Let me follow the notation from Jaynes' paper, which I linked above. If a let the gas go through a free adiabatic expansion, since the evolution is hamiltonian, it is clear that $\frac{dW_N}{dt}$ obeys Liouville equation, but since $\{ e^{-\beta H}, H \}=0,$ it is clear that the $W_N$ remains constant and thus so do the Gibbs entropy $S_G.$ However, at the end of section IV in Jaynes' paper, he states
If the time-developed distribution function $W_N(t^{\prime}$...
And then I don't know what's going on anymore..! Does the $W_N$ change in time or not?
And, if in a thermal equilibrium we do not use the Canonical Ensemble, which ensemble are we using instead? How is the distribution function? What is the mathematical expresion of the new macroscopic restrictions we should add when maximizing the entropy functional to derive that new probability distribution?