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 <lkruszew...@twarda.pan.pl> 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 Absorption Correction in TOPAS? I was taught in a > 5-day course of TOPAS that it's not a good idea, especially with the > Bragg-Brentano geometry, but I'm not sure... > > - Is there any difference, to be expected, in the calculated unit cell > parameters, between approximating a phase using (1) a chemically pure > STRUCTURE model (i.e., taken directly from a database / CIF file), and > (2) a STRUCTURE with Occupancy information updated with the known > content of impurities? I always thought that it shouldn't matter, as the > software simply "iteratively" compares the sample' reflections with the > structural information contained in STRUCTURE models (?). I have > compared these two situations, and option "2" actually gave me worse > fit. I thus wondered: does it really matter that much which model > (approximation) of the structure - chemically pure or with added > impurity info - is used? For most substances, the reflection positions > vary even for different standards found in databases like PDF or COD... > > - Is the negative intensity in the difference curve only informing us of > underestimation of the content of a particular phase, suggesting to > replace the Structure model used with another one? > > We have been working using few computers with, supposedly the very same > version of the software. However, even though we've been using exactly > the same Structure models, results were varying depending on the > computer stand used. I was wondering if this could have to do with some > errors in the JAVA script, or maybe a non-identical installation > conditions, or something about the Windows system? > > I would be thankful for any tips. > > Best regards, > > -- > Łukasz Kruszewski, Ph.D., Associate Professor > Polish Academy of Sciences > Institute of Geological Sciences > Twarda 51/55 str. > 00-818 Warsaw > Poland > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > Please do NOT attach files to the whole list <alan.he...@neutronoptics.com > > > Send commands to <lists...@ill.fr> eg: HELP as the subject with no body > text > The Rietveld_L list archive is on > http://www.mail-archive.com/rietveld_l@ill.fr/ > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Please do NOT attach files to the whole list <alan.he...@neutronoptics.com> Send commands to <lists...@ill.fr> eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
