The error occurs when trying to plot the data.
a workaround is to modify the lines 49 and 50 of the mulliken-analysis.py script with:
axarr[0].plot(numpy.arange(len(c[0])),c[0]-net_charges[0][0])
axarr[1].plot(numpy.arange(len(c[0])),numpy.cumsum(c[0]-net_charges[0][0]))
or download the updated script (you may need to clean your browser's cache).
let me add some more details regarding this problem.
Starting from ATK 13.8.0 we changed some default parameters for spin.
In particular when you the atoms method in MullikenPopulation you need to specify the spin components you want, even if the calculation is non-polarized.
You can do that by using the spin keyword, cf. http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.mullikenpopulation.html (http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.mullikenpopulation.html),
and change the original script from:
mulliken_charges = [mulliken.atoms()-initial_population for mulliken in mulliken_list]
to:
mulliken_charges = [mulliken.atoms(spin=Spin.Sum)-initial_population for mulliken in mulliken_list]