I am trying to find out where the differences are from the master to the dev version. Checking out.
I changed res to pa%phys_diam in the intensity call. I think this is correct.
I should have figured out the fix to the bug in fem_update. This version of the code has the fix commented out with another ouput saying Failure expected. I am going to run both the fixed and unfixed version tonight to test it. Uncomment the fix to fix the bug!