e.g. in ABO3 oxides after Rietveld refinement of XRD pattern, can we have isotropy factor ( Debye-Waller) of A elements (rare-earth) with two different wyckoff positions, one of them negative?
You probably mean the isotropic atomic displacement parameter. The answer is NO, because this parameter is basically a variance. However, systematic errors in the structural model, in the couse of the measurement or improperly accounted details of the measurements (e.g. absorption) may be compensated by a negative atomic displacement parameter.
Thank you Andreas, However, at least for powder XRD, I did not count the absorption, is it usual to consider it for the powders with few microns size? I can see this option in Fullprof.
Absorption IS relevant, depends of course on geometry. Even in Bragg-Brentano reflection geometry (the most common), were absorption can usually be neglected for ideal specimens, absorption can become relevant due to 1. the effect of surface roughness and 2. in the case of specimen transparency.
be sure you considered all relevant corrections (as suggested also by Andreas)!. Positive (correct) thermal factors decrease the intensity at high angle whereas negative ones (unphysical) do the opposite. So in your case, as you need negative ones, you either have some correction who's killing too much the intensity (sometimes a wrong LP factor) or killing it in a wrong way (absorption), or you have wrong atom positioning (type or coordinates), that create a destructive interference..
Andreas suggests also possible problems with the measurement, but I would hope that problem was ruled out before even thinking of posting a question on this issue!
Thanks Andreas and Matteo. Most probably the difficulty rises due to the mentioned parameters ( let's say mostly instrumental). As I do microscopy, I can see high density of planar defects and nano-scale domains, which I hope, does not affect atomic displacement of ions in 3D space in XRD refinement. I know that Matteo did studies on this matter, but I'm not sure if it would be straightforward to assign the matter of atomic displacements to the large scale dislocations ( few ten nm) for that specific ion.