Re: Cagliotti and Other Issues
> According to the ccp14 news site the wiki (I guess from apparent lack > of interest) was recently deactivated after a ccp14 web server upgrade. In practice, people use whatever is available in the refinement programs (sometimes blindly :-) The authors of those programs have already spent considerable effort in writing manuals, and users should be encouraged to read those as a first step :-) The Rietveld mailing list http://www.mail-archive.com/rietveld_l@ill.fr/ is also a useful source of different opinions on techniques. Often wikis are well done, but sometimes represent wacky opinions of a few individuals. Google itself is often a better source of information. And of course most refereed papers are now available on the WWW, and can readily be found with google. Alan BTW Mike Glazer is right that people should be more concerned with physical-chemical tests of their structure, rather than trying to get the lowest possible R-factor by refining more parameters. __ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE +33.476.98.41.68 http://www.NeutronOptics.com/hewat __
Re: Cagliotti and Other Issues
Hi, > I wonder if we should, as a community, put some of this stuff on > wikipedia, or another such place. In other words, distill the > community's collective knowledge in a single place that can be updated > in the future, and also curated for correctness also by the community. > What are people's thoughts on this? Rietveldipedia? Some time ago I told William Bisson (ccp14 secretary) that it would be great to have a CCP14 wiki - which he added quickly (see his message to the list on 2007/06/18). Unfortunately this did not get popular (to my great shame I must say I did not add any information to that wiki...). According to the ccp14 news site the wiki (I guess from apparent lack of interest) was recently deactivated after a ccp14 web server upgrade. But I guess if there is interest it would be good to have it started again ? CCP14 seems like a nice place to collect that information, especially as a wiki data can be easily duplicated and would not be lost over time. The ccp4 project has several wikis which seem to be working quite well: - user wiki @ http://strucbio.biologie.uni-konstanz.de/ccp4wiki/ - developper wiki @ http://ccp4wiki.org/ Vincent -- Vincent Favre-Nicolin CEA Grenoble/INAC/SP2M http://inac.cea.fr Univ. Joseph Fourier (Grenoble) http://www.ujf-grenoble.fr ObjCryst & Fox http://objcryst.sf.net/Fox
Re: Cagliotti and Other Issues
Dear Simon, I think it would be nice to have an open web-resource summarizing good practice of full-profile refinement, especially if it is supported by real diffraction data for, say, simple widely available standards (quartz, silicon, corundum etc.) measured at various diffractometers and fitted using different models. Comparing data and refinement results might help answering such "intimate" questions like: - How good is the program I use (or going to use)? - What kind of model and parameters are the best for this or that setup and sample? - Is my instrument efficient enough and well aligned? - Whether the instrument I plan buying or the beamline I think visiting is that good as the advertisement suggests? .. So, the benefits are evident and the "only" problem is to find a coordinator of the movement - is it you, Simon? ;-) Regards, Leonid Leonid A. Solovyov Institute of Chemistry and Chemical Technology 660049, K. Marx 42, Krasnoyarsk, Russia www.icct.ru/eng/content/persons/Sol_LA www.geocities.com/l_solovyov --- On Sun, 3/22/09, Simon Billinge wrote: > From: Simon Billinge > Subject: Cagliotti and Other Issues > To: "rietveld_l" > Date: Sunday, March 22, 2009, 8:50 PM > Dear Rietvelders > > What is the most complete and authoritative source for > issues such as > profile function definitions, what is their scientific > basis, and when > are they appropriate to use, etc.? I am guessing > there is not > one-stop-shop solution (Young's book? GSAS manual? Rietveld > list > archive?) but advice on this would be helpful. > > I wonder if we should, as a community, put some of this > stuff on > wikipedia, or another such place. In other words, > distill the > community's collective knowledge in a single place that can > be updated > in the future, and also curated for correctness also by the > community. > What are people's thoughts on this? Rietveldipedia? > > S >
RE: Cagliotti and Other Issues
Dear All: Indeed, despite some more advanced approaches to modeling diffraction line shapes, the good, old Cagliotti function is still in use probably for historical reasons (as it is the case with many other things in sciences). However, to be fair to (practically all major) Rietveld programs, the original Cagliotti function (Gaussian term) was a long time ago amended by a Lorentzian contribution (linear in FWHM as opposed to a quadratic Gaussian term). This term immensely helps to accurately model high-resolution measurements, both x-ray and neutron (see, for instance examples of ESRF and ISIS data in Size-Strain Line-Broadening Analysis of the Ceria Round-Robin Sample, Journal of Applied Crystallography 37 (2004) 911-924--article and data available at http://www.du.edu/~balzar/s-s_rr.htm). As discussed in this thread, the original Cagliotti function often gets into trouble because of the square root of a negative number. Bill David described a much better function. Thus, the general approach described by Bill and in the article cited above is to refine coefficient of a function used on a pattern obtained from a suitable "standard", such as LaB6, and then fix them (unfortunately, not always possible for all instruments, because some instrumental parameters depend on the angle in the same way as the strain term in the Bragg-Brentano geometry). Moreover, for high-resolution data it might be helpful to add a Lorentzian FWHM to that expression and then post it to Wikipedia or perhaps publish a paper... :-) Davor > -Original Message- > From: simon.billi...@gmail.com > [mailto:simon.billi...@gmail.com] On Behalf Of Simon Billinge > Sent: Sunday, March 22, 2009 2:50 PM > To: rietveld_l > Subject: Cagliotti and Other Issues > > Dear Rietvelders > > What is the most complete and authoritative source for issues such as > profile function definitions, what is their scientific basis, and when > are they appropriate to use, etc.? I am guessing there is not > one-stop-shop solution (Young's book? GSAS manual? Rietveld list > archive?) but advice on this would be helpful. > > I wonder if we should, as a community, put some of this stuff on > wikipedia, or another such place. In other words, distill the > community's collective knowledge in a single place that can be updated > in the future, and also curated for correctness also by the community. > What are people's thoughts on this? Rietveldipedia? > > S > > 2009/3/20 May, Frank : > > Back to basics and First Principles > > > > As Alan says, the [use of the Cagliotti function is > appropriate for the neutron case], "but not really for X-ray > and other geometries." > > > > My recollection is the Cagliotti function was adapted to > the x-ray case when we had low resolution x-ray instruments > and slow (or no) computers. Now that we have high resolution > instruments and fast computers, why does this inappropriate > function continue to be used? > > > > On another note, the world is venturing into the infinitely > small realm of "nano-particles." The classical rules for > crystallography work very well for ordered structures in the > macro-world (particles of the order of micron-sizes). However, as the particles become smaller, does one not need to > address the contribution of the "surface" of the particles? > The volume of the "surface" becomes much greater relative to > the volume of the "bulk" of the crystal. Models today > account for "stress" and "strain" in the macro-world. As the > relative fraction of the "bulk" becomes smaller, both the > physical structure as well as the mathematics used to > describe the bulk suffer from termination-of-series effect, > do they not? Does any of this make sense? Any thoughts? > > > > Frank May > > St. Louis, Missouri U.S.A. > > > > > > > > From: Alan Hewat [mailto:he...@ill.fr] > > Sent: Fri 3/20/2009 2:13 AM > > 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). > > > > Cag
RE: Cagliotti and Other Issues
-Original Message- From: May, Frank [mailto:frank.l@umsl.edu] >My recollection is the Cagliotti function was adapted to the x-ray case when >we had low resolution x-ray instruments and slow (or no) computers. Now that >we have high resolution instruments and fast computers, why does this >inappropriate function continue to be used? There's probably a great deal of "it's always been done this way" in why its used, in addtion to a lack of education in when it should be used, as well as "Let's tick this box and see what happens"... :( >On another note, the world is venturing into the infinitely small realm of >"nano-particles."... As the relative fraction of the "bulk" becomes smaller, >both the physical structure as well as the mathematics used to describe the >bulk suffer from termination-of-series effect, do they not? Does any of this >make sense? Any thoughts? This is talked about by Grey and Wilson*. They show that while you can refine diffraction data from nanosize titania particles, the numbers (cell params in this case...) that you get out might not represent what is actually there. Basically, the assumption that there is an infinite lattice breaks down. *Titanium vacancy defects in sol-gel prepared anatase Grey, I; Wilson, N JOURNAL OF SOLID STATE CHEMISTRY (0022-4596); Volume: 180; Issue: 2; Date: 2007; pg. 670-678 Cheers Matthew Matthew Rowles CSIRO Minerals Box 312 Clayton South, Victoria AUSTRALIA 3169 Ph: +61 3 9545 8892 Fax: +61 3 9562 8919 (site) Email: matthew.row...@csiro.au
Cagliotti and Other Issues
Dear Rietvelders What is the most complete and authoritative source for issues such as profile function definitions, what is their scientific basis, and when are they appropriate to use, etc.? I am guessing there is not one-stop-shop solution (Young's book? GSAS manual? Rietveld list archive?) but advice on this would be helpful. I wonder if we should, as a community, put some of this stuff on wikipedia, or another such place. In other words, distill the community's collective knowledge in a single place that can be updated in the future, and also curated for correctness also by the community. What are people's thoughts on this? Rietveldipedia? S 2009/3/20 May, Frank : > Back to basics and First Principles > > As Alan says, the [use of the Cagliotti function is appropriate for the > neutron case], "but not really for X-ray and other geometries." > > My recollection is the Cagliotti function was adapted to the x-ray case when > we had low resolution x-ray instruments and slow (or no) computers. Now that > we have high resolution instruments and fast computers, why does this > inappropriate function continue to be used? > > On another note, the world is venturing into the infinitely small realm of > "nano-particles." The classical rules for crystallography work very well for > ordered structures in the macro-world (particles of the order of > micron-sizes). However, as the particles become smaller, does one not need > to address the contribution of the "surface" of the particles? The volume of > the "surface" becomes much greater relative to the volume of the "bulk" of > the crystal. Models today account for "stress" and "strain" in the > macro-world. As the relative fraction of the "bulk" becomes smaller, both > the physical structure as well as the mathematics used to describe the bulk > suffer from termination-of-series effect, do they not? Does any of this make > sense? Any thoughts? > > Frank May > St. Louis, Missouri U.S.A. > > > > From: Alan Hewat [mailto:he...@ill.fr] > Sent: Fri 3/20/2009 2:13 AM > 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 > +33.476.98.41.68 > http://www.NeutronOptics.com/hewat > __ > > > > > -- Prof. Simon Billinge Applied Physics & Applied Mathematics Columbia University 500 West 120th Street Room 200 Mudd, MC 4701 New York, NY 10027 Tel: (212)-854-2918 (o) 851-7428 (lab) Condensed Matter and Materials Science Brookhaven National Laboratory P.O. Box 5000 Upton, NY 11973-5000 (631)-344-5387 email: sb2896 at columbia dot edu home: http://nirt.pa.msu.edu/
Cagliotti and Other Issues
Back to basics and First Principles As Alan says, the [use of the Cagliotti function is appropriate for the neutron case], "but not really for X-ray and other geometries." My recollection is the Cagliotti function was adapted to the x-ray case when we had low resolution x-ray instruments and slow (or no) computers. Now that we have high resolution instruments and fast computers, why does this inappropriate function continue to be used? On another note, the world is venturing into the infinitely small realm of "nano-particles." The classical rules for crystallography work very well for ordered structures in the macro-world (particles of the order of micron-sizes). However, as the particles become smaller, does one not need to address the contribution of the "surface" of the particles? The volume of the "surface" becomes much greater relative to the volume of the "bulk" of the crystal. Models today account for "stress" and "strain" in the macro-world. As the relative fraction of the "bulk" becomes smaller, both the physical structure as well as the mathematics used to describe the bulk suffer from termination-of-series effect, do they not? Does any of this make sense? Any thoughts? Frank May St. Louis, Missouri U.S.A. From: Alan Hewat [mailto:he...@ill.fr] Sent: Fri 3/20/2009 2:13 AM 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 +33.476.98.41.68 http://www.NeutronOptics.com/hewat __
