RE: Negative Uiso in GSAS
Michael Glazer said: > 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. While I agree with Mike's list, I can't let him get away with such a sweeping statement implying that single crystal refinements necessarily give better structures, simply because "the data is three dimensional". Errors in crystal refinement arise from all kinds of effects apart from problems due to overlapping peaks. Extinction is a cause for error that is usually more serious for single crystals than for powders - especially with strain associated with a structural transition. Texture is a problem associated mainly with X-ray powder diffraction etc... With todays high resolution powder diffractometers and Rietveld refinement, I don't even believe that overlapping reflections from "one dimensional data" is the main cause of error. Its true that if peaks are strongly overlapping at high angles then refining the background may result in it being overestimated, leading to higher temperature factors. Refinement of absorption will also strongly correlate with temperature factors. That is why you should not keep adding more parameters such as background, absorption etc simply to obtain a lower R-factor and expect that to equate to a better structure determination. You should try to actually measure these other effects and correct for them, not simply refine them away. __ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE +33.476.98.41.68 http://www.NeutronOptics.com/hewat __
Re: Negative Uiso in GSAS
To add some more simple reasons for apparently overmuch high intensity at high angles causing meaningless negative temperature factors: - the low angle peak intensities are suppressed by beam overflow (typically fixed slit Bragg Brentano geometry) - one is using automatic slit data instead of fixed slit ones, and the program used is unable to account for that - if one has used converted ADS data to fixed slit data: The conversion failed because of any wrong background correction, or the primary ADS data are wrong because of misprogramming or misalignement of the ADS system. And one addition to Jon's important point 5 below: This is often related to physically meaningless peak shape models, running out of meaningful peak width values, just by becoming broader and broader and "taking intensity" from the background into the high angle peak intensities. One should use a physically based and more rigid peak shape model. Regards Reinhard Jon Wright schrieb: I can't resist adding one more to Mike's excellent list: 5. When peaks overlap strongly it becomes difficult to determine the background level. Negative Uiso is a consequence of the background refining to a value which is too low, especially where the peaks are most dense in the pattern (shorter d-spacings or higher angles). All the best, Jon Michael Glazer wrote: 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: Negative Uiso in GSAS
I can't resist adding one more to Mike's excellent list: 5. When peaks overlap strongly it becomes difficult to determine the background level. Negative Uiso is a consequence of the background refining to a value which is too low, especially where the peaks are most dense in the pattern (shorter d-spacings or higher angles). All the best, Jon Michael Glazer wrote: 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: 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: Negative Uiso in GSAS
Dear Carolina, I have the answer. It's about the electron cloud of your elements. I'll tell you further tomorrow because I'm at home right now. I speak about this feature in one of my publications. You will have the answer tomorrow, if nobody replies. Best regards. -- Dr. Jean-Gabriel ROQUEFERE Institut de Recherche sur l'Hydrogène Département Physique (1)-819-701-3603 www.irhcanada.com carolina.zip...@fi.isc.cnr.it a écrit : 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 - Courriel expédié via https://courriel.uqtr.ca
Re: Negative Uiso in GSAS
As mentioned recently, Their is no physical meaning to have negative thermal agitation factor. It means that at high angle the observed data at upon the calculated. It means that you should put more electron (if you are doing X-Ray diffraction) or more electron or nuclear density in your crystallographic model. One of the usual problem could be: - You have used some automatic variable slit !! and you try to refined such data without correction. - Check your crystallographic model But if you have done such last things it should come from some absorption problem : if you are using X-ray with high absorption compound in reflection geometry this problem come quite often. For example the simple crystallographic compound metal Platinum simple cubic Fm-3m (N°225) Pt in 0,0,0 The absorption is big for copper radiation 4300cm-1. I find -0.6ang2 with X'Pert HighScore Plus. Normally we can make some correction for such absorption see : /Référence/ /*20.- W. Pitschke, N. Mattern and H. Hermann, Powder Diffraction 8(4),*/ /* 223-228 (1993).*/ / (In this paper the authors refine simultaneously all occupation/ / numbers. This practice should be avoided. If the calculation were/ / exact that gives rise to a singular matrix when the scale factor/ / is also refined)/ / See also/ /* W. Pitschke, H. Hermann and N. Mattern, Powder Diffraction 8(2),*/ /* **74-83 (1993).*/ / / / Dans HighScore on trouve la reference :/ //H. HERMAN & M. ERMRICH///, Microabsorption of X-ray intensity in randomly packed powder specimens, Acta Cryst. (1987), *A43*, 401 -- 405./ But I did not find so easy to apply such correction at least with HighScore or Fullprof. The data of the platinum or the molybdenum could be found in : http://perso.univ-lemans.fr/~fgouten/RX_data Best Whishes François Goutenoire Le 03/03/2010 17:08, carolina.zip...@fi.isc.cnr.it a écrit : 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 -- Dr. François Goutenoire Laboratoire des Oxydes et Fluorures UMR6010 tel: 02.43.83.33.53
