Re: [External] Re: some uncertainties regarding the Rietveld refinement results in TOPAS
I agree with everything Dave said. I was a little terse in my response. Physically, altering a unit cell's contents is going to alter its size and the intensities. On Thu, 7 Nov 2024, 20:49 Bish, David L, wrote: > Matthew has given a nice summary for you, but I'd like to add one thing. > Whenever the site occupancies change, the unit-cell parameters will/should > change (unless the substituting ions have identical radii). You can > actually use the refined unit-cell parameters to estimate compositions in > many cases. You should always refine the uc parameters (with the exception > of a certified standard), and if your materials' compositions change, you > can expect the uc parameters to vary. Even if they change by only a small > amount, they can have a significant effect on the fit. I would not fix the > uc parameters in a refinement unless you are working with materials of a > known, fixed composition, e.g., synthetic, pure materials. Having said > this, if the substitutions are very minor, e.g., ppm level, you will likely > not see any effect. But, as you said, reflection positions and thus uc > parameters vary even for the same materials listed in the PDF and the COD. > > Also, keep in mind that the extent of the effect of site occupancy > variations on intensities will depend on the scattering factors of the > substituting ions. Si-Al substitutions, for example, in minerals such as > feldspars will have a negligible effect on intensities but a larger effect > on uc parameters. On the other hand, Mg-Fe substitution in the olivine > minerals will affect both intensities and uc parameters, and you can use > either or both of these to estimate composition. > > Best of luck with your refinements. > > Dave > -- > *From:* rietveld_l-requ...@ill.fr on behalf > of Matthew Rowles > *Sent:* Wednesday, November 6, 2024 11:03 PM > *To:* Łukasz Kruszewski > *Cc:* Rietveld > *Subject:* [External] Re: some uncertainties regarding the Rietveld > refinement results in TOPAS > > > This message was sent from a non-IU address. Please exercise caution when > clicking links or opening attachments from external sources. > > Great questions! > > > does the Absorption correction also influences microabsorption? > > No. The absorption correction in TOPAS is only a peak-shape correction to > account for the transparency of the specimen. There is no real way to > correct for microabsorption beyond grinding to a fine particle size, > changing your wavelength, or moving to neutrons. > > > > Is it worthy to use the parameter known as "Sample Thickness", > associated with the Absorption Correction in TOPAS? > > Generally, no. You only need to worry about it if the penetration depth of > your incident beam is larger than the thickness of the specimen. If that is > the case, then "Sample Thickness" and "Scale Intensity" is necessary to > correct for the change in peak shape due to the finite depth, and the > change in diffracting volume. > > > >Is there any difference, to be expected, in the calculated unit cell > parameters, between approximating a phase using (1) a chemically pure > STRUCTURE model, and (2) a STRUCTURE with Occupancy information updated > with the known content of impurities? > > Altering site occupancies should only affect peak intensities, and so unit > cell parameters should only be a second-order effect. (disregarding the > physicality of various unit cell contents vs dimension pairings) > > > > Is the negative intensity in the difference curve... > > It is showing that there is some mismatch between your model and the data. > The intensities could be off because the peaks positions are wrong, the > peak-shape is wrong, the atomic displacement parameters are wrong (don't > refine these from normal QPA data), the LP factor correction is wrong, the > site occupancies are wrong, the atomic scattering factors are wrong. Could > also be that you have forgotten to refine a parameter that you should be. > > > > We have been working using few computers with, supposedly the very same > version of the software > > That does seem concerning. There can be differences between different > versions of TOPAS. You would also need to verify that all the scattering > factors, wavelengths, MACs, and space group files are the same for all > installations, and that nothing has been incorrectly edited. Also that > TOPAS.inc hasn't been touched. > > > Hope this helps. > > > Matthew > > > > > > > > > > > On Wed, 6 Nov 2024 at 19:12, Łukasz Kruszewski > wrote: > > Dear Rietvelders, > > after some years of being a happy user of TOPAS & Rietveld method (after > working-out a good approach, thanks to a great help from users of this > mailing list for which I am really thanful, and having it checked by > attendance in Reynolds Cup) I was recently confronted with few questions > I couldn't answer. I thus have a kind request of a help here: > > - does the Absorption correction also influences microabsorpti
Re: some uncertainties regarding the Rietveld refinement results in TOPAS
Hi Daniel The peak shape variation comes from exponential absorption of the incident and directed X-rays due to their interaction below the specimen's surface. In the case of a finite thickness sample, this exponential gets truncated. I'm pretty sure I talk about this in Rowles & Buckley. Intensity is the main thing. Peak shape is going to be dominated by crystallite size/strain, but in its absence, youll see cut off in the peak trails due to finite thickness. Matthew On Thu, 7 Nov 2024, 16:39 Daniel Chateigner, wrote: > Dear All, > > Just to be sure on two of the Q&As: > Le 07/11/2024 à 05:03, Matthew Rowles a écrit : > > Great questions! > > > > Is it worthy to use the parameter known as "Sample Thickness", > associated with the Absorption Correction in TOPAS? > > Generally, no. You only need to worry about it if the penetration depth of > your incident beam is larger than the thickness (t) of the specimen. If > that is the case, then "Sample Thickness" and "Scale Intensity" is > necessary to correct for the change in peak shape due to the finite depth, > and the change in diffracting volume. > > - Seems from your answer Matthew, that diffracting volume changes (Vd) > through the scan in BB geometry gives rise to some peak shape variations (I > assume here that "shape" includes "width"). I agree that the diffracting > volume changes with theta, and with the sample thickness, but these two > effects should not contribute the same on the peak shape: > > -- For a given sample thickness, the diffracting volume varies with Theta, > but to me the main contribution to the peak shape is due to the irradiated > surface (beam track on the sample surface). Since deeper dVd will be more > absorbed than the ones closer to the surface. You can picture this > measuring a 2Theta scan at fixed incident angle, up to 2Theta=90°, the peak > width increases notably with 2Theta because of this. > > -- For the same theta on the diffraction diagram, varying the sample > thickness will probably not modify this much the shape of the peaks, but > intensities. For the same reasons on dVd. For instance, if measuring 2 > samples with a 100 nm and 200 nm thickness respectively, the peak shape > variation will probably not be visible using lab instruments, while the > intensities will differ significantly. > > - I do not like much the term "penetration depth" (p), since the depth > reached by x-rays is always infinite. For instance, if as usual p is > defined as 1/mu (mu = absorption coefficient of the sample, the one we > never fully know exactly), using a Theta-2Theta scan in BB on a t=infinity > sample, the measured diffracted intensity is larger than the one coming > from p only. And, on a thin specimen, both absorption and Vd are varying > during the scans, each of them bringing a contribution to the intensity. On > the contrary, for t=infinite specimen, they compensate each-other and their > contribution is the same on the diffracted intensity throughout the diagram > (but the intensity does not come from the same irradiated volume). I was > then wondering if Topas was simply corrected from volume variations or also > including the absorption variations in the case of "thin enough" samples ? > > > > > > Is the negative intensity in the difference curve... > > It is showing that there is some mismatch between your model and the data. > The intensities could be off because the peaks positions are wrong, the > peak-shape is wrong, the atomic displacement parameters are wrong (don't > refine these from normal QPA data), the LP factor correction is wrong, the > site occupancies are wrong, the atomic scattering factors are wrong. Could > also be that you have forgotten to refine a parameter that you should be. > > What about preferred orientations ? Anisotropic crystallite shapes and > microstrains ? Improperly defined film thickness can give rise to > variations of the ADPs also. > > > My 2€cts ! > > Daniel > > > > > > > > > > > > On Wed, 6 Nov 2024 at 19:12, Łukasz Kruszewski > wrote: > >> Dear Rietvelders, >> >> after some years of being a happy user of TOPAS & Rietveld method (after >> working-out a good approach, thanks to a great help from users of this >> mailing list for which I am really thanful, and having it checked by >> attendance in Reynolds Cup) I was recently confronted with few questions >> I couldn't answer. I thus have a kind request of a help here: >> >> - does the Absorption correction also influences microabsorption? This >> question arose due to somewhat lowered expected wt.% of pyrite (19 >> instead of 25), FeS2, even though all the used parameters (Absorption, >> CrySize, Strain - for all the sample components) were checked and proven >> to give value > error, i.e., being physically meaningful for the >> refinement model. I was wondering how this supposed non-precision for >> pyrite could be addressed... >> >> - Is it worthy to use the parameter known as "Sample Thickness", >> associated with the Absor
