In a time-dependent transport code, the flux of particles across a surface would be determined by solving the particle continuity equation, , where S is the local source rate. By SNAP's assumption of steady-state, . Applying the divergence theorem, , i.e., the rate at which particles are born inside a given region exactly balances the rate at which they cross the regions's surface.
From its beam and neutral calculations, SNAP has a complete calculation of the total source rate for electrons (from ionization of beam neutrals, wall neutrals, and halo neutrals) and ions (from ionization of wall neutrals and beam-ion thermalization). So it can compute the flux-surface-averaged flux of particles across any flux surface directly by volume integrating the particle source inside the region, and dividing by the flux-surface area.
SNAP has no models for impurity sources. It effectively assumes for all impurities.