Ran a set on some code trying to break down the if statement for the substrate domain to only evolve concentrations in the substrate region (although I’m realizing that I messed this up as I visualize this towards the end and don’t have time to rerun the model for the fixed condition today – will do Tuesday).
Been looking into the core of the code again. Noticed that the free energy for domain two (particle) calculates only using the equilibrium concentration in the particle. Tried editing to include the eq concentration for the substrate but that resulted in a very much incorrect model. I think it was initially set to both particle and vapor equilibrium double well potentials. Probably was not supposed to alter this expression.