You do not have to use the "free energies"(F=
logZ) in order to see the fact that the partition function
Zfull is composed of three parts although two of them we pack together sometimes and then we have two parts. I would probably write down the full partition function as
Zfull=Zclassical×Z1-loop×Zinstantons
and according to your notation
Zperturbative=Zclassical×Z1-loop. You ask what are the perturbative and what is the full part. The definition is tautological, the full partition function is a product of two pieces. The first piece, the perturbative, also sometimes called classical, is due to perturbation theory. We begin with some low energy effective action (mathematically a map from the space of "fields" to a field (no pun intended) usually
C. This contribution is obtained by expanding out the path integral in terms of divergent series, some sort of Taylor expansion, and each term corresponds to some Feynman diagrams. This is the usual process of perturbative quantum field theory which you can find in almost any quantum field theory textbook. To do this one and get reliable results has to have a small "coupling constant". The problem arises when this coupling constant is not small. The Seiberg-Witten theory, that is the
N=2 SU(2) or SO(3) (and in general U(N) theory with N>1) is an example of a confining theory (like real life QCD). This means that below some energy scale
Λ the coupling of the theory (the strength of the interactions of the particles if you wish) becomes so big that we cannot rely on perturbative expansion of the path integral. For most quantum field theories one has to rely to lattice simulations or AdS/CFT to learn something about them. What is special in SW theory is that one can determine a modular function called the pre-potential which fully controls the non-perturbative aspects of the theory. This is where the
Zinstanton part comes in. Seiberg and Witten gave a formula for the full solution of the path integral but it was only until Nekrasov (elaborating in older ideas he had with Shatashvili mainly but a few others too) came up with the solution in terms of the
Ω-background. I do not think that the instanton part is the genus zero free energy of the topological string. The free energy of the gauge theory is expanded in terms of the genus but you kind of get the whole answer. In specific you can write
logZ=(a,ϵ1,ϵ2;Λ)=∑n,g≥0(ϵ1+ϵ2)n(ϵ1ϵ2)g−1F(n/2,g)(a,Λ)
where
a is a coordinate of the Cartan torus of the gauge group modulo Weyl group and
Λ is the dynamically generated scale usually related to the instantons as
∑nΛ4n=∑nqn=∑c2qc2 since you want to sum over all c_2(E). Of course
E is the corresponding vector bundle over which you study the ASD equations. So, the (0,0) term of the above expansion would correspond to Seiberg-Witten prepotential and the rest of the terms, all given in terms of modular forms, would be higher order corrections corresponding to higher genus topological string amplitudes.
Finally, for a supersymmetric field theory there are various indices you can define one of them being the Hirzebruch
χy-genus but I know that this usually appears in the
N=4 Vafa-Witten theory. I am not sure if what you say is correct, I would have to check.Usually the exponents that appear in those formal variables in the indices are "charges" of various symmetries the theory has. You can consider mass as some kind of charge as well but, again, maybe you should say explicitly where in your reference is that thing for your second question so I can see exactly what is stated there.