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For calculating ideal work: By applying entropy balance on a steady state flow process we get:- delta(S*mass flow rate) - (rate of heat transfer from system)/Tsurr = 0.

Thus according to this equation if the process is adiabatic then there can't be any net change in entropy of flow streams. But as in many cases like throttling and other adiabatic processes we see entropy of stream changes even though there is no heat transfer between system and surroundings.

So my question is what am I interpreting wrong here. Is the quantity (rate of heat transfer) in this equation is not rate of heat transfer between system and surrounding but something else.Or we just consider the heat transfer negligible in this processes but there is always some heat transfer if entropy of flow streams is changing.

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Your entropy balance equation includes entropy transfer between the surroundings and the system, but does not include entropy generation within the system as a result of irreversibilites associated with viscous dissipation and temperature gradients. In the case of throttling, for example, the entropy generation from viscous dissipation is very significant.

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