My side of the project mostly concerned the method we were using to manufacture the materials (I was experimenting with a technique called "Electrostatic Spray Reductive Precipitation"). When it came to analyzing what I had managed to make it mostly involved using SEM (with EDS mapping) and XRD. At the time it never crossed my mind to look into possibility of simulations it would have saved a lot of time as doing the analysis was very time consuming.
For the theoretical side I was guided by a postgrad student who used a physics software package to predict the intercalation of Li ions using Density of States calculations, most of what he was doing went way over my head but it involved him running code and then telling me "we should try to make something like this..." so I imagine this sort of package could help out a lot here as well.
I have to ask though, how many organizations are really designing their own cells for new products? And how much validation have these packages had? I know it's expensive and time-consuming to get a lot of battery discharge data. My experience may be overly coloring my thinking here - my idea of battery modeling involves a circuit simulator and only those effects that are not going to be drowned by the large tolerances in common batteries.
The one area where more detailed physical modeling would be interesting would be in long-term degradation and wear modeling for secondary cells. Is there a tutorial or example along those lines?