Hi Simon and Mikkel,
Thanks for your insights. I am still a little confused about the documentation on 'Structure.Bisoequiv' still. I.e.,
>> Help on property:
Array of Debye-Waller isotropic thermal displacement or equivalent
values. Assignment updates the U attribute of all atoms.
And when I test this:
>> structure = loadStructure('test.xyz
>> array([[[0., 0., 0.],
[0., 0., 0.],
[0., 0., 0.]], ...
>> structure.Bisoequiv = 0.04
>> array([[[0.00050661, 0. , 0. ],
[0. , 0.00050661, 0. ],
[0. , 0. , 0.00050661]], ...
It certainly does appear that updating Bisoequiv for a structure object puts thermal parameters on all atoms in the structure object. Nevertheless, Mikkel, your solution addresses, somewhat, the odd behavior for the O-H correlations using the PDFCalculator.
However, I still do not understand, for example, the discrepancy between calculating the O-O correlations with the two methods. The partial PDF from the Debye calculator looks correct, but the real-space summation produces unphysical (and by the looks of it, undamped) oscillations in the PDF. Is there some reason the real-space calculator doesn't behave properly when using setTypeMask?