Hi all,
In regards to Wayne's original question about the 1D energy equation: The two terms in question are quite different. As noted, the first term is about diffusion: If you expand the derivative in the case of an ideal gas as dhk/dz = cpk dT/dz, you can see that this term is about the diffusion of sensible enthalpy in cases where species have different heat capacities. The second term is the reaction term, and deals with the enthalpy of reaction. So no, there is no double counting.
In regards to the reactor governing equations that Steven brought up: There is a distinction between the equations used for the generic reactor types like "ConstPressureReactor" which can handle any equation of state and the specializations for ideal gases like "IdealGasReactor". In the former case, the energy equation is written with the total enthalpy (or internal energy) as the state variable. In this case, chemical reactions do not contribute to a change in the total enthalpy, and so there is no reaction-related term in the energy equation. However, when setting the state based on that enthalpy with a changing composition, the temperature will also change.
In the case of the ideal gas reactors, the expression for dH/dt has been expanded so that the temperature appears, which also introduces terms for the rate of change of the species.
Regards,
Ray