GAMMA

I am trying to modify CE QUAL W2 (version 2) code to include light-induced decay of organic matter, and I could use some help understanding a few things. Right now, GAMMA is calculated in the algal subroutine as: GAMMA = EXH2O+EXSS*SS(K,I)+EXOM*(ALGAE(K,I)+LPOM(K,I)) for layers below the top layer. I have a few questions: First: since EXH2O should be calculated from secchi disk depth measurements, isn't light extinction due to particulate matter already accounted for? Should I try to use secchi depths from times with little algae and then let the program account for the blooms? Second: it doesn't seem like GAMMA allows for differences in light extinction in upper layers; if I am in a deep, 'clear' layer with large algae concentrations in uppers layers, doesn't calculating GAMMA in this way for the deep layer ignore algae in the upper layers? Thanks! Dan