RE: Negative Uiso in GSAS
Negative U's in Rietveld can arise from several causes, so that there is not one single answer. Some of the reasons are 1. The structural model is simply incorrect. 2. High absorption means that the low-angle data are weaker than they should be, or conversely that the high-angle data appear stronger than they should be. Abnormally strong high-angle data give rise to a decrease in U's, even making them appear negative 3. Correlation between the refinement parameters. For instance U's will tend to be highly correlated with site occupation parameters, often making it difficult to separate them. 4. In general, many of the errors that one encounters tend to end up in the refined U's, and this is why their precise values have to be treated with caution. Rietveld refinement (as opposed to single-crystal refinement) is in fact refinement of degraded data (it is one-dimensional instead of three-dimensional) and so the errors will be more significant. Mike Glazer -Original Message- From: carolina.zip...@fi.isc.cnr.it [mailto:carolina.zip...@fi.isc.cnr.it] Sent: 03 March 2010 16:08 To: rietveld_l@ill.fr Subject: Negative Uiso in GSAS Dear all, could someone explain to me the meaning of obtaining a negative Uiso in GSAS? I thought it was always positive...(p. 123 manual) thanks Carolina _-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_- Dr. Carolina Ziparo Istituto dei Sistemi Complessi - sezione di Firenze, C.N.R. - Consiglio Nazionale delle Ricerche via Madonna del Piano, 10 I-50019 Sesto Fiorentino Italy tel.: +39 055 5226693 fax:+39 055 5226683 e-mail: carolina.zip...@fi.isc.cnr.it
RE: Comparison of powder patterns recorded at different wavelengths
Kurt The standard method is to use a wavelength made from the weighted (2:1) average of the two components. So for CuKa the standard value is 1.5418 angstroms Mike Glazer -Original Message- From: Kurt Leinenweber [mailto:ku...@asu.edu] Sent: 15 January 2010 16:46 To: Franz Werner; rietveld_l@ill.fr Subject: RE: Comparison of powder patterns recorded at different wavelengths HI Franz, It seems to me that the best thing would be to use K alpha 1 wavelength (which is 66 percent of the total intensity) and then mentally ignore the K alpha 2 contribution. The other option is to strip the original data of K alpha 2, if your diffractometer's software has that option, but since stripping is a kind of data manipulation, I don't usually like doing it. - Kurt * Kurt Leinenweber Dept. of Chemistry and Biochemistry Arizona State University Tempe, AZ 85287-1604 phone (480)-965-8853 fax (480)-965-2747 *** -Original Message- From: Franz Werner [mailto:franzwer...@gmx.at] Sent: Friday, January 15, 2010 6:27 AM To: rietveld_l@ill.fr Subject: Comparison of powder patterns recorded at different wavelengths Hello Rietvelders I want to compare graphically powder patterns of a phase which were recorded at different wavelengths. Therefore I'd like to overlay the patterns using d-values, calculated from their corresponding 2theta values. In the case of monochromatic X-rays it's trivial. But which wavelength should one use in the case of Kalpha1-Kalpha2 radiation (lab instrument)? Thanks for your help. Regards Franz Werner Tallinn University of Technology Estonia -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
RE: UVW - how to avoid negative widths?
As I have said before countless time, one should not lose sight of the objective of Rietveld refinement, that it is to refine a sensible crystallographic structure. One can reduce R factors in all sorts of ways by playing with the peak shape functions (even by using lower symmetry and increasing the number of refinable parameters!) but in the end what matters is: does the structure make sense? My own experience is that by judicious use of methods like bond valence calculations, studies of the bond lengths etc one can rule out unlikely refinements better than by concentrating on R factors. Many times one can reduce R factors by playing with the diffraction geometry terms, but with little obvious improvement of the structural results. -Original Message- From: Alan Hewat [mailto:he...@ill.fr] Sent: 20 March 2009 07:13 To: rietveld_l@ill.fr Subject: RE: UVW - how to avoid negative widths? matthew.row...@csiro.au said: From what I've read of Cagliotti's paper, the V term should always be negative; or am I reading it wrong? That's right. If FWHM^2 = U.tan^2(T) + V.tan(T) + W then the W term is just the Full Width at Half-Maximum (FWHM) squared at zero scattering angle (2T). FWHM^2 is then assumed to decrease linearly with tan(T) so V is necessarily negative, but at higher angles a quadratic term (+ve W) produces a rapid increase with tan^2(T). Cagliotti's formula assumes a minimum in FWHM^2, but if that minimum is not well defined, U,V,W will be highly correlated and refinement may even give negative FWHM. In that case you can reasonably constrain V by assuming the minimum is at a certain angle 2Tm, which may be close to the monochromator angle for some geometries. So setting the differential of Cagliotti's equation with respect to tan(T) to zero at that minimum gives: 2U.tan(T) + V =0 at T=Tm or V = -2U.tan(Tm) this approximate constraint removes the correlation and allows refinement. Cagliotti's formula simply describes the purely geometrical divergence of a collimated white neutron beam hitting a monochromator, passing through a second collimator, then scattered by a powder sample into a collimated detector. It takes no account of other geometrical effects (eg vertical divergence) or sample line broadening etc. This geometry is appropriate for classical neutron powder diffractometers, but not really for X-ray and other geometries. Still, such a quadratic expression with a well defined minimum in FWHM, may be a good first approximation in many other cases, requiring only a few parameters, hence its success. There are many more ambitious descriptions of FWHM for various scattering geometries and sample line broadening, usually allowing more parameters to be refined to produce lower R-factors :-) Alan __ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE alan.he...@neutronoptics.com +33.476.98.41.68 http://www.NeutronOptics.com/hewat __
RE: PDF refinement pros and cons
Alan I think you are misunderstanding what the PDF method is used for. The idea is to fourier transform directly the whole range of scattering including peaks and background (after removing artifacts in the background due to the diffractometer, air scattering etc). In a highly ordered crystal structure most of the diffracted intensity resides in the peaks, and there is little background. In such a case normal structure factor refinement to get the crystal structure is the way to go. However in a disordered structure there is a contribution to the background and then the PDF method is useful to obtain local information about atoms (it is a bit like the results of NMR or EXAFS). Thus for instance if we have a structure in say a hexagonal symmetry with an atom displaced along [001], we can find this using the usual structure factor methods which gives the AVERAGE crystal structure. However in the example I am thinking of we also find a very large aniotropic displacement parameter for this atom suggesting that the atom is not actually displaced along [001] but at the unit cell level is slightly displaced off this direction. PDF methods then show that the distance between this atom and its nearest neighbours is consistent with the off-axis displacement rather than for the atom being actually along [001]. Sp the point is that the PDF method is useful for looking at local order whereas the structure factor method is for average structures. Note byt the way that there is no phase problem for the PDF method. The main problems with the PDF are 1. Being able to account properly for extraneous background so that the remaining background which we need truly represents the crystal 2. The need for very high Q in order to obtain suficient resolution. The use of copper radiation for example does not give sufficientky high Q and so one needs generally to use vedry short wavelengths from a synchrotron or use time of flight neutrons. Mike Glazer
RE: % Crystallinity
Determination of crystallinity can be a fraught subject, because it is usually assumed in such measurements that the background is from amorphous material while the sharp peaks are from crystalline material. So the standard way to do this would be to have a method for extracting the background and then comparing the total area of the background with the total area under the peaks. However, the background need not arise solely from amorphous material but from several other sources, such as short range order diffuse scattering, air scattering, scattering from slits etc etc. Furthermore, determinign the total area under the background needs some care as one needs to know where it begins and where it ends. The literature on crystallinity usually talks about 1 and 2 state models. A 2 state model is one which one has a mixture of crystals and amorphous material, and if one believes that this is what you have in your sample then the percentage crystallinity can be derived from the comparison of peaks to background, as mentioned above. A 1-state model is where one has crystalline materials with sufficient breakdown in long-range order to give a background due to diffuse scattering. Mike Glazer
RE: advice on new powder diffractometer
As I have said in reply to Leonid, I don't know why we have such a large difference in our experimental setup. It may be that our 0.02 slits are misaligned -- I will have to check this. The question of what is meant by signal to noise ratio in connection with powder diffraction is one which I have been trying to find out about. You see this term used quite often in papers and in general discussion, but I have still to discover how one works it out in a properly defined way with regards to powder diffraction. It is well defined in radio frequency signals. One could for example take, as you have said the peak height minus the background and divide by the background as one measure, a value which would tend to zero as the peak becomes smaller. This definition would also imply that increasing measurement time has no effect on signal to noise ratio, since both peak and background would simply scale up with time, in which case we might as well measure for negligible amount of time. Or else one could take the peak intensity divided by the square root of the background: this at least would improve with measurement time. For instance suppose we have a peak above background of 1 counts and a background of 1000 counts, this would give a signal to noise ratio of roughly 322. If we measure ten times longer, the peak intensity becomes 10 and the background becomes 1, giving a signal to noise ratio of 1000, an improvement! So my question remains: what is the definition of signal to noise ratio that is accepted for powder diffraction? Mike ** -Original Message- From: Van der Lee [mailto:[EMAIL PROTECTED] Sent: 19 February 2008 07:39 To: rietveld_l@ill.fr Subject: Re: advice on new powder diffractometer After having purchased the set of 0.02 soller slits in Dec. 03 I have done some comparison tests on the (111) silicon peak under identical conditions except for the change of the primary and secondary sollers: background Bpeak height PH 0.0295 8580 0.04 32018900 negliable change on the FWHM so not an intensity drop with a factor of 25, neither 4, but only slightly larger than 2. How do I define signal/background ratio? There is not much scientific in it, it serves only to compare qualitatively these kind of 'optical' elements; it should be something like (PH-B)/B or more generally Bragg scattering intensity to non-Bragg-scattering intensity. Arie Dear Mike, Normally, changing sollers must not influence the signal/background ratio. Wider sollers, however, make the primary beam wider and if the sample diameter is small then a parasitic scattering from the sample holder edges may appear. I am really surprised that moving from 0.04 Soller slits to 0.02 you got 25 times intensity reduction. When I change the primary soller from 0.04 to 0.02 the intensity drops ~2 times, so if you changed both the primary and the secondary sollers the intensity should decrease ~4 times, but not 25 times. Leonid Solovyov How do you define signal to noise in powder diffraction? I have seen this term used several times, but I have not found a definition so far with regard to powder diffraction per se. I have just done two runs on a Panalytical one with 0.04 soller slits and one with 0.02 (both with a CuKa1 premonochromator) both for about 9 hours. The strongest peak for the 0.02 case is 2700 counts, half width 0.08 degrees and a background of 25 counts. The same peak with the 0.04 slits has 7 counts, half width 0.11 degrees and a background of 700 counts. Mike Glazer __ __ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- *** A. van der Lee Institut Européen des Membranes CNRS - UMR 5635 Université de Montpellier II - Case Courrier 047 Place E. Bataillon 34095 MONTPELLIER Cedex 5 - FRANCE Tel : 33 (0) 4 67 14 91 35 Fax : 33 (0) 4 67 14 91 19 Website X-ray scattering facility ICG/IEM: http://www.iemm.univ-montp2.fr/xrayweb/main_uk.html
RE: advice on new powder diffractometer
Leonid I don't know why we have such a large difference, but for some reason we do. I will send you privately the two diagrams. Mike -Original Message- From: Leonid Solovyov [mailto:[EMAIL PROTECTED] Sent: 19 February 2008 03:56 To: rietveld_l@ill.fr Subject: RE: advice on new powder diffractometer Dear Mike, Normally, changing sollers must not influence the signal/background ratio. Wider sollers, however, make the primary beam wider and if the sample diameter is small then a parasitic scattering from the sample holder edges may appear. I am really surprised that moving from 0.04 Soller slits to 0.02 you got 25 times intensity reduction. When I change the primary soller from 0.04 to 0.02 the intensity drops ~2 times, so if you changed both the primary and the secondary sollers the intensity should decrease ~4 times, but not 25 times. Leonid Solovyov
RE: advice on new powder diffractometer
Alan I absolutely agree with you regarding Rietveld refinement. The same argument is true for adjusting peak shapes to get the best fit, playing around with different peak formulae. Often such tweaking, while it makes the observed and calculated fit look nicer, has little effect on the atomic positions, which in the end is what one is trying to derive. One should not lose sight of the model. But my question about defining SNR is more to do with the use of powder data in general, and especially as used in industry or forensics. For example distinguishing in a legal sense between two materials may depend on which of two powder patterns has the higher SNR. I keep seeing this term used in papers and books but never defined. Mike -Original Message- From: Alan Hewat [mailto:[EMAIL PROTECTED] Sent: 19 February 2008 10:10 To: rietveld_l@ill.fr Subject: RE: advice on new powder diffractometer So my question remains: what is the definition of signal to noise ratio that is accepted for powder diffraction? Why does it matter? A higher Bragg/Background ratio does not necessarily mean better data if counting statistics are poor. Exaggerating slightly :-) consider a single peak with a ratio of 100/1 compared to a peak with a ratio 1/1000. The second measurement will give the lowest error, not the first which has a much higher signal/noise. And you measure lots of points on a slowly varying background, so you have a much better estimate of background than the normal error of a single point. Please don't encourage people to simply maximise signal/noise. Similarly, low profile R-factor's can be obtained with low resolution data and high background. That does not mean that low resolution data produces smaller errors in structural parameters. I worry about people treating measurement and refinement as black boxes with simplified measures of quality such as R-factors, signal-to-noise etc. You have to look at the physical reality of the model and the estimated errors in its parameters, while not cheating by removing data that doesn't fit for unknown reasons, adding too much a priori information such as constraints, or throwing in extra garbage parameters to improve the R-factors. __ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE [EMAIL PROTECTED] +33.476.98.41.68 http://www.NeutronOptics.com/ __
RE: advice on new powder diffractometer
How do you define signal to noise in powder diffraction? I have seen this term used several times, but I have not found a definition so far with regard to powder diffraction per se. I have just done two runs on a Panalytical one with 0.04 soller slits and one with 0.02 (both with a CuKa1 premonochromator) both for about 9 hours. The strongest peak for the 0.02 case is 2700 counts, half width 0.08 degrees and a background of 25 counts. The same peak with the 0.04 slits has 7 counts, half width 0.11 degrees and a background of 700 counts. Mike Glazer -Original Message- From: Van der Lee [mailto:[EMAIL PROTECTED] Sent: 18 February 2008 16:36 To: rietveld_l@ill.fr Subject: Re: advice on new powder diffractometer Leonid Solovyov wrote the following on 18/02/2008 16:27: Yes it is mainly down to the Soller slits, there was a very large thread on soller slits somewhere in the Rietveld archives about this discussion. I think the down side of changing the soller slits is a move away from the optimum FWHM that can be obtained? Changing sollers from 0.04 rad to 0.02 or 0.01 reduces the asymmetry, the FWHM and the intensity, so the peak shape and the resolution become more optimal but the intensity is sacrificed. However, the signal to noise ratio becomes better with 0.02/0.01 rad sollers compared to 0.04 rad Arie -- *** A. van der Lee Institut Européen des Membranes CNRS - UMR 5635 Université de Montpellier II - Case Courrier 047 Place E. Bataillon 34095 MONTPELLIER Cedex 5 - FRANCE Tel : 33 (0) 4 67 14 91 35 Fax : 33 (0) 4 67 14 91 19 Website X-ray scattering facility ICG/IEM: http://www.iemm.univ-montp2.fr/xrayweb/main_uk.html
Topas
Yes it does. One way is to add the command adps at the end of the line site E.g. site Pb1x 0.23y 0.15 z 0.28 occ Pb 1 adps Mike Glazer -Original Message- From: Peter Tzvetkov [mailto:[EMAIL PROTECTED] Sent: 10 December 2007 18:28 To: rietveld_l@ill.fr Subject: Topas Dear all, Does anyone knows if Topas can refine anisotropic temperature factors? I couldn't find information about this in the technical reference. Maybe I've missed something? Best, Peter Tzvetkov Institute of General and Inorganic Chemistry Bulgarian Academy of Sciences
RE: Kapton capillaries
There is an old method that I used to use for capillaries that you may useful. Take a metal wire of appropriate diameter and dip it into collodion (nitrocellulose dissolved in acetone), allow it to dry. Then stretch the wire with pliers and slip off the cellulose capillary. This is cheap, quick, has very low scatter and of course you can make it to whatever size you want. Mike Glazer From: Andy Fitch [mailto:[EMAIL PROTECTED] Sent: 17 November 2007 07:29 To: rietveld_l@ill.fr Subject: Re: Kapton capillaries Goodfellows www.goodfellow.com http://www.goodfellow.com/ Cole-Parmer http://www.coleparmer.com/ See also A rapidly filled capillary mount for both dry powder and polycrystalline slurry samples. R. B. Von Dreele. J. Appl. Cryst. (2006). 39 , 124-126 Andy At 19:49 16/11/2007, you wrote: Could someone please suggest a source for purchasing kapton capillaries? A search on the internet drew a blank. Thanks. Dipo Omotoso
