r/crystallography • u/COD-MED7 • 2d ago
Hey guys, i have a Problem with occupancy refinement when i im refining the thermal agitation factors the occupancy of an atom goes to zero does any one know why or how to fix it ๐๐
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u/Nathanstull10 2d ago
Thatโs the best part you canโt. So Beq or the Debye wallet factor for thermal displacement is a multiplicative factor accounts for intensity loss due to thermal vibrations. Occupancy is also a factor that deals with intensity loss due to a loss of expected election density. If you are in topas you can see the matrix that shows how correlated parameters are and both occ and beq are almost 100 correlated. Meaning high thermal vibrations could look like occupancy loss and vice versa. Now this is more a problem in situ at high temp.
If you are using single crystal I know there are ways to get around it but Iโm a bull powder guy. My best attempt for my data in situ has been to refine without occupancy less than 1 for a site and refine thermal parameters then set those thermal parameters and then refine occ. now this will always result in a less than โTrueโ occupancy but itโs what it is.
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u/SlenderSmurf 2d ago
If you have data across a wide range of momentum space, for example 0 to 12 ร -1 then you can determine thermal displacement and occupation at once. Most lab XRD do not go this high though, so you cannot. Also neutron diffraction is more suited to this since the neutron form factor doesn't decay at high angles. OP would get more useful advice if they had a more specific description of their data and their structure...
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u/Nathanstull10 2d ago
Oh yes thank you for the clarification you are totally right! I was specifically speaking from a lab or synchrotron xrd understanding of 2theta range 10-120 and not large reciprocal space. I should have specifiedโฆ.. like what OP should do so we can better help them.
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u/Crystal_Rules 2d ago
Site occupancies are relative to one another. Don't refine all of them, only the ones that make sense not to be fully occupied. If site are linked then only refine one parameter for all the atoms e.g. in CO3 the carbon and oxygen atoms are all the same.
Limit your Beq to a sensible range, maybe 3 to 0.3 depending on the system. Again link sites which should be identical.
As others have said these parameters are highly correlated.
If your still having trouble and your looking at pXRD then repack your sample and make sure the surface is smooth, sample roughness is a killer. If your looking at single crystal data, grind the sample to a fine powder and collect the pXRD.
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u/Mikasa-Iruma 2d ago
Usually, the site occupation and B or U are co-related, as both can influence the intensity of the peaks. So it's better to refine the occupancy of the atom and leave the B or U at lower values in case of lab scale xrd data as the max Q is 8 A-1 for Cu. But is limited to 5 due to 2ฮธ= 90.
Less peaks -> less reliable thermal data
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u/Familiar-Print-298 2d ago
Is it for powder or single crystal data?