Site occupancies refinement
Dear Rietvelders, I was actually doing the site (occupancy) refinement using TOPAS 4.1 software.While studying the effect of doping on one crystallographic site. We normally refine the sites of interest employ the following methodology.Consider e.g., Pervoskite structure (ABO3) as an example.If we wish to dope the A site in ABO3,and to confirm whether doping was successful or not, we normally refinethe occupancies in the following way. For example.We refine occupancies like occupancy of original site A =beq1 occupancy of dopant site A` =1-beq1 If the refinemnent goes well, all the crystallogrhic occupancies should merge to a single constant value,those crystallographic sites which are fully occupied should give [occ=1] and those doped should yield net occupancies [occ (A + A`= 1]. Can anyone share or suggest,why the Beq (isotropic temperature factor) values are going to huge,??at the end of such a refinement. Which otherwise should be around [ Beq=Uiso*8pi^2]. Also if possible share .pro file (GUI mode or Launch mode) of such a refinemnet or some literature. Best regards,Dr. Naveed Zafar Ali ++ Please do NOT attach files to the whole list Send commands to 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/ ++
RE: Site occupancies refinement (Many Thanks)
Dear Dr Peter Stephens, Dr. Martin Fisch and Dr. Noberto Masciocchi, Many thanks for your reply and useful tips.In particularcomments from Dr. Noberto M. and for sparing time in rearranging my .INP file. Best regards, Dr Naveed Zafar Ali Subject: Re: Site occupancies refinement Date: Mon, 28 Apr 2014 08:00:50 -0400 From: peter.steph...@stonybrook.edu To: naveed...@hotmail.com CC: rietveld_l@ill.fr You seem to be confusing beq (thermal parameter) with site occupancy. At a start, I would think that the site would have the same thermal parameter for either atom, and refine occupancies that sum to unity. For example, site A1 occ Fe feocc .9 x 0 y 0 z Az .055 beq Abeq 2site A2 occ Ru =1-feocc; x 0 y 0 z =Az; beq =Abeq;will put Fe and Ru in the same site, refine the iron occupancy (feocc), common z coordinate (Az), and give them the same isotropic thermal parameter (Abeq). You could imagine that the lighter atom could have a larger thermal parameter, but it would be very hard to determine that from powder data because it would be strongly correlated with site occupancy, etc. **Peter W. StephensProfessor, Department of Physics and AstronomyAssociate Dean for Curriculum, College of Arts and Sciences Stony Brook University(631) 632-8156http://mini.physics.sunysb.edu/~pstephensPlease update your records to my new email: peter.steph...@stonybrook.edu On Mon, Apr 28, 2014 at 7:39 AM, NAVEED ZAFAR wrote: Dear Rietvelders, I was actually doing the site (occupancy) refinement using TOPAS 4.1 software.While studying the effect of doping on one crystallographic site. We normally refine the sites of interest employ the following methodology.Consider e.g., Pervoskite structure (ABO3) as an example.If we wish to dope the A site in ABO3, and to confirm whether doping was successful or not, we normally refinethe occupancies in the following way. For example.We refine occupancies like occupancy of original site A =beq1 occupancy of dopant site A` =1-beq1 If the refinemnent goes well, all the crystallogrhic occupancies should merge to a single constant value, those crystallographic sites which are fully occupied should give [occ=1] and those doped should yield net occupancies [occ (A + A`= 1]. Can anyone share or suggest,why the Beq (isotropic temperature factor) values are going to huge,?? at the end of such a refinement. Which otherwise should be around [ Beq=Uiso*8pi^2]. Also if possible share .pro file (GUI mode or Launch mode) of such a refinemnet or some literature. Best regards,Dr. Naveed Zafar Ali ++ Please do NOT attach files to the whole list Send commands to 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 Send commands to 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/ ++
TOPAS Macro Language (peak shape broadening macros)
Dear Rietveld Experts and Colleagues, For most of the rietveld refinements (both qualitative and quantitative_Launch .INP mode) of XRD powder data,I often use Topas Academic Macro Library, well manged and maintained by John Evans and colleagues.https://community.dur.ac.uk/john.evans/topas_academic/topas_macros.htm But currently for samples, that encounter preferred orientation (e.g. nanotubes etc), the strong preferred orientation somehow influence the intensity distribution within a profile and hamper structural solution efforts using rietveld refinement of powder data.Are there any macros (written by experts) that can assist in such a case.I already tried the " Stephens peak shape broadening macro" but found no change in Rwp value.Also, If there is complete data bank of such macro..s. Please share. Accept my apologies for being ignorant, so far. Best regards, Naveed_____Dr. Naveed Zafar Alihttps://scholar.google.com/citations?sortby=pubdate&hl=en&user=V4Hsus8J&view_op=list_works "Being ignorant is not so much a shame, as being unwilling to learn." .― Benjamin Franklin ++ Please do NOT attach files to the whole list Send commands to 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/ ++
RE: TOPAS Macro Language (peak shape broadening macros) / THANKS
Dear All,Many thanks for the useful TIPS and tricks about the factors effecting both peak shape broadening and peak intensities (PO).Am grateful to Jon Wright, Alan Hewat, and Luca Lutterotti for also shraing their views on the issue.Eva McCabe: Topas Wiki, really is awesome for users like me. Normally, I copy paste the relevant macro and found reasonabledecrease in Rwp value. But I would request the user to place an example file relevant to each contributed macro. That would be beneficial I presume. Moreover, I am also thankful to Peter Khalifah for writing in detail about the stuff, and for sharing the useful tutorial written by Arnt Kern and Pamela Whitfield (MMRRSA). As a novice user with basic experience in diffraction, I really wish to join such a useful workshop (MMRRSA) on Modern Methods in Rietveld Refinement and Structural Analysis, in future. Please also share such an event on this mailing list. With my best regards, Dr. Naveed Zafar Ali ___ > Subject: Re: TOPAS Macro Language (peak shape broadening macros) > Date: Wed, 24 Jun 2015 22:16:56 +0200 > From: wri...@esrf.fr > To: rietveld_l@ill.fr > > Hi Alan, > > In the limiting case of orienting all crystals in 3D you get a mosaic > single crystal (e.g. [1], or using an XFEL to measure 1 at a time). Then > the refined the crystal structure has somewhat better accuracy than with > a 1D Rietveld fit. Perhaps not the most popular idea for this mailing > list :-) > > The intermediate case of multiple patterns with properly modelled > texture should also be better even for refinement. Simplistically - you > can add information about overlaps like 511/333 cubic overlap if you > have a series of patterns. > > With only a single pattern you introduce extra texture parameters > without adding the extra information to pay for this (which is why > people tell us to get rid of it). With multiple patterns the story is > different, but the price is figuring out the texture properly. > > Cheers, > > Jon > === > > [1] Kimura et al, Langmuir, 2006, 22 (8), pp 3464–3466 > DOI: 10.1021/la053479n > http://pubs.acs.org/doi/abs/10.1021/la053479n > > > > > On 24/06/2015 19:46, Alan Hewat wrote: > > Both Peter and Luca are correct :-) Preferred orientation can indeed be > > used to help SOLVE (unknown) structures, but when you want to REFINE > > structures you should try to eliminate systematic errors such as > > preferred orientation, if possible by better sample preparation. That > > may not be possible with highly oriented crystallites such as nanotubes, > > and as Naveed found, modelling peak broadening will not help. Search the > > program manual for "texture" or "preferred orientation" modelling. > > Pax. Alan. > > > > On 24 June 2015 at 17:44, Khalifah, Peter > <mailto:kp...@bnl.gov>> wrote: > > > > Yes, that is of course a more precise and correct answer. I did not > > mean to imply that diffraction physics work differently, just that > > the data processing resulted in some badly wrong assumptions about > > the data being used for Rietveld refinement. > > > > __ __ > > > > I tried to give a quick answer to a basic question from a basic > > point of view. If it was an expert question, I would have left it > > to the experts like you :-) > > > > __ __ > > > > -Peter > > > > > > > > __ __ > > > > *From:*Luca Lutterotti [mailto:luca.luttero...@ing.unitn.it > > <mailto:luca.luttero...@ing.unitn.it>] > > *Sent:* Wednesday, June 24, 2015 3:52 AM > > *To:* Khalifah, Peter > > *Cc:* rietveld_l@ill.fr <mailto:rietveld_l@ill.fr> > > *Subject:* Re: TOPAS Macro Language (peak shape broadening macros) > > > > __ __ > > > > __ __ > > > > On 23 Jun 2015, at 22:22, Khalifah, Peter > <mailto:kp...@bnl.gov>> wrote: > > > > __ __ > > > > Preferred orientation results in the central assumption that the > > measured intensity is proportional to the reflection structure > > being violated, > > > > __ __ > > > > This is actually quite new to me as definition of preferred > > orientation or better texture. Until now I thought that in the case > > of preferred orientations the measured intensity is proportional to > > the volume fraction of grains oriented in
