… by using mole fractions instead of mass fractions, like cantera, which keeps the mixture molecular weight more bearable. As well as clipping mole fractions that were negative or over 1.

…he species conductivities. The formula used here is taken from "Chemically Reacting Flow" by Kee, Coltrin, and Glarborg, page 519.

…f the thermal conductivity

…l calculate perturbed mass fractions that can be used to calculate the transport, this will make it easier to implement a switch for perturbing the mass fractions. Also added a little more documentation, but can still use more here.