Dear Kamil and Dimitris,
I wonder what kind of scattering factors are mentioned below programs
using for Rietfveld refinement? Are these from IT for electron scattering?
Best,
Paulina
W dniu 12.11.2020 o 07:35, Dimitris Triandafillidis pisze:
Dear Kamil,
Since you have an initial model that is presumably close to what you
expect to find in your sample, then Rietveld refinement is the right
choice. In cases where no initial model is available, other types of
refinement are suitable, such as Pawley or Le Bail, which refine
lattice and peak shape parameters only.
Regarding the order in which parameters are introduced to a fit, a
good starting point would be:
- lattice parameters and zero shift
- peak shape parameters and scale factor
- background terms
- atomic positions
Depending on the quality of your data and the nature of your sample,
more parameters could be refined (i.e. atomic displacement parameters,
preferred orientation, absorption etc.).
My suggestion would be to get a better understanding of the effect of
each parameter to the fit, in order to troubleshoot your refinement
more effectively. For example, peak positions depend on lattice
parameters (and space group setting), therefore refining e.g. the
scale factor would not help much if expected peak positions are in the
wrong place. The following article might be helpful to you.
McCusker, L.B., Von Dreele, R.B., Cox, D.E., Louër, D., Scardi, P.,
1999. Rietveld refinement guidelines. Journal of Applied
Crystallography 32, 36–50. https://dx.doi.org/10.1107/S0021889898009856
As for the single peak not being explained by the fit, it could be due
to deviations in lattice parameters, but in that case more than one
peak would not match. If every other peak fits nicely and only one
does not, I would think that it is due to coexistance of a second,
trace, crystalline phase in the sample. In most refinement software
you have the option of excluding a peak from refinement. Refining
atomic positions would not help, as these change the relative peak
intensities, not peak positions. However, if you could share a few
images of the fit, it would really help to better understand what's
going on.
Finally, with regards to software, you could also try GSAS
<https://subversion.xray.aps.anl.gov/trac/pyGSAS>. It is one of the
most widely used software for powder diffraction and it is free. There
is also a mailing list
<https://mailman.aps.anl.gov/mailman/listinfo/gsas-ii>, consisting
mainly of powder diffractionists, and a handful collection of
tutorials
<https://subversion.xray.aps.anl.gov/pyGSAS/trunk/help/Tutorials.html>.
Best wishes,
Dimitris
On Thu, Nov 12, 2020 at 12:18 AM Kamil Krawczyk
<kamil.krawczyk7...@gmail.com <mailto:kamil.krawczyk7...@gmail.com>>
wrote:
Hello!
First, apologies if the scope of the question is beyond that of
the listserv - I was recommended this discussion page through a
colleague.
I am incredibly new to refinement, and have been trying to employ
the use of Rietveld refinement to better determine the crystal
structure of my lead sulfide (PbS) quantum dots. Data was acquired
as images on a home-built tabletop time-resolved electron
diffraction setup, and converted to diffractogram through a
combination of center finding and background subtraction. However,
since these are small (~ 5 nm), and we are certainly sampling the
ensemble average (as our focused beam is about 120 um in
diameter), our pattern is that of a polycrystalline sample.
>From what I've encountered in my research, Rietveld is best
suited for this case. I have taken an initial structure as
inferred from literature/the bulk and refined that (relatively
successfully to a Rwp value of ~2 - 6%). I do have a few questions
regarding this process as I believe I am not being as rigorous as
possible:
- is there a 'best practices' order of refinement operations? e.g.
refine the lattice parameters first, then peak profiles, etc.
- there is a single peak that is not matching (likely due to a
slight deviation in atomic positions from the expected simple
cubic structure) - is refinement capable of moving individual
atoms or clusters of atoms to better match a small, unaccounted
for reflection?
For what it's worth, I have been using Reflex in Materials Studio;
if there is a more appropriate software for this application, I
would be happy to hear!
If any additional clarification is need, I'll fill it in!
Best,
Kamil
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--
Prof. dr hab. Paulina M. Dominiak
Group Leader
Electron Density Modelling Group
Laboratory for Structural and Biochemical Research (LBSBio)
Biological and Chemical Research Centre
Department of Chemistry
University of Warsaw
ul. Zwirki i Wigury 101
02-089 Warszawa, Poland
Room: 3.125
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