Deviations and internal standard
Dear all I would appreciate some statistical advice. We are measuring cell parameters variations in-situ of some structures using in-house diffractometers. Because the in-situ variations also causes sample displacement, we have been using an added internal standard (Si) and corrected the 2-theta axis so that the silicon lines are in correct positions. Because we wanted to be sure that our method is reproducible, we have repeated our experiments 5-10 times, and that has given us a standard deviation for the unit cell parameters. The standard deviation for the Si cell parameters is of course very small, in the order of 10^-5 Å, whereas for the samples it is in the order of 10^-2 Å. That is also the accuracy we can reasonably report our data at. I would like to know how to report a single statistical variation from our values. We have the deviation of the IS, deviation of the samples, and then the error of the refinement itself (multiplied by a number given in the output files). How to put it all together? Our software is FullProf 2k. Thank you in advance, Arto Ojuva Stockholm University ++ 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: Deviations and internal standard
Dear Leo and the rest Thank you for the rapid answer. The statistical analysis of diffraction data is indeed to my experience not much used - one usually performs one measurement and obtains a perfect result, every time! I should maybe clarify the Si correction procedure right away: we made a refinement of the two-component powder sample letting all parameters go free. Then we compared the observed Si lines with calculated ones, made a second-decree correction function, and manually modified the 2-theta of the data file so that the Si positions would hit the expected values. Then we made a new refinement, once again with all parameters free, and confirmed that the Si unit cell is indeed within 0.01 Å of the expected value. If not, we would make another correction. So all unit cell parameters are let free in the refinements. Indeed the Si uncertainty is three orders of magnitude lower than that of the sample and not contributing much to anything, but I am concerned that any reviewer would give me a hard time if I simply ignored it in the statistical analysis. Best regards, Arto On 2013-09-13 17:18, Leopoldo Suescun wrote: Dear Arto and rietvelders, This probably should not taken as a definitive answer to the question because I may have skipped something from my statistics clases, but I'd be tankful if someone comments if the procedure I suggest below is not a good option and why. I have found myself in situations like this when s.u. determination is important but hard to perform within statistically accepted procedures. If you have some 5- to 10 independent determination of your cell parameters at each temperature you can use the values as statistically independent observations and estimate the s.u. using conventional statistical analysis (average, variance and standard deviation using statistical tables to asses the confidence range for your number of observations). This will give you a valid s.u. value that will estimate the aleatory variation of your cell parameters within your procedure. Now, you know there is a sistematic component of uncertainty that is caused by correction of sample height with Si cell parameters and other systematic efects intrinsic to the Rietveld method, such as selection of profile function, etc.. Lets assume that FULLPROF estimates your cell parameters uncertainty in such a way that it takes into account all the s.u. of the parameters you use for the refinement (including Si cell parameter that I guess you fixed in the refinement to allow sample height to refine, but you included a s.u. for this fixed parameter).Then the s.u. that FULLPROF gives you could be 100% attributed to the procedure so you can combine your statistical s.u. obtained above with the uncertainty from FULLPROF, using also conventional combined uncertainty. It is very important that the s.u. of Si cell parameter, that is your callibration for temperature, includes a possible variation of cell parameter with temperature. For instance, if your temperature precision is 1 K, and Si cell parameter uncertainty is less than the linear thermal expansion of Si, then you have an uncertainty that is not considering that the temperature may be off by 1 K. One way to assess if the FULLPROF uncertainty is atributable to a systematic cause is to compare values from independent determinations. I mean if you have very different s.u. extracted from FULLPROF for the 5-10 determinations, then this uncertainty may be influenced by other factors that change within your independent determinations and make them not comparable so you don't really have such well defined procedure that determines the systematic uncertainty. Finally, to make sure the aleatory component of uncertainty is meaningful you have to make sure there is not a systematic evolution of the cell parameters within the 5-10 determinations (such as increase or decrease with time) that may imply that you have some systematic problem with your data collection, such as temperature variation in the surface of the sample, or sample reaction/decomposition/interaction with atmosphere or Si, or other kind of instability that will make all the procedure much harder to assess and meaningful uncertainty to be determined. In any case, if one of the two such uncertainties is much larger than the other one it will not make a big effect on the total uncertainty. I hope this helps or at least generates a useful discusion and correction to my proposition if wrong. Best regards, Leo 2013/9/13 arto ojuva mailto:arto.oj...@mmk.su.se>> Dear all I would appreciate some statistical advice. We are measuring cell parameters variations in-situ of some structures using in-house diffractometers. Because the in-situ variations also causes sample displacement, we have been using an added internal standard (Si) and corrected the 2-theta axis so that the silicon lines ar
Re: Uiso Beq etc. - calculation problems
Hi Just a general warning about using Excel with trigonometric functions: =sin(0) gives 0 =sin(90) gives 0.893997 =sin(180) gives -0.80115 In other words, I haven't gotten sine and cosine to work reliably with Excel. It might be a good idea to check the calculations using some other software, maybe just a good old hand calculator. That was my five cents. :) /Arto On 2014-02-11 10:13, "Łukasz Kruszewski" wrote: Ok - sorry, changed degrees into radians. But there is still a difference for sulphur in aluminite. Best regards, Luke K. OK, here it goes: Uiso = 1/3 * [U22 + 1/sin^2(beta)*(U11 + U33 + 2U13cos(beta)] = 1/3 * [0.01562 + (1/sin^2(110.18))*(0.01937 + 0.01277 + 2* (-0.00027)*cos(110.18)] = 1/3 * [0.01562 + (1/(0.9386)^2) * (0.03214 + (-0.00054)*(-0.345)] = 1/3 * [0.01562 + (1/0.88097) * 0.0323263] = 1/3 * [0.01562 + 1.135 * 0.0323263] = 1/3 * (0.01562 + 0.03669) = 1/3 * 0.05231 = 0.01726 The given Uiso for sulphur is, meanwhile, 0.01621. I have also been trying to calculate Uiso for melanophlogite, which is cubic, co the formula goes: Uiso = 1/3* (U11 + U22 + U33). Using this formula, I have obtained the value of 0.0339, which is exactly the same as the one given in the corresponding CIF file. However, calculating the Uiso using the GENERAL formula gives the value of 0.0287. Both values (0.0339 and 0.0287) were calculated using an EXCEL spread sheet. So how is such a difference possible? Best regards! Luke Kruszewski Dear Łukasz, There must be something wrong with your calculation. A quick examination shows that S must have a higher displacement parameter than Al and that Ueq must be approximately 0.016. I hope this helps. Bob Gould On 10/02/2014 21:50, "Łukasz Kruszewski" wrote: Dear Rietveld friends, I'm having some problems with calculating Uiso from the anisotropic parameters. Here is an example - I copy first two sites of aluminite (monoclinic): _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 S 0.01937 0.01562 0.01277 -0.00248 -0.00027 0.00954 Al1 0.01117 0.01169 0.01295 0.6 -0.00012 0.00789 Using the formula for Uiso for the monoclinic system, which is: 1/3 * [U22 + 1/sin^2(beta)*(U11 + U33 + 2U13cos(beta)] for the "S" site we obtain the value of 0,0054 for "Al": 0.01225 Meanwhile, the listed Uiso are: _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv S 0.70076 0.37376 0.93018 0.01621 Al1 0.65581 0.45332 0.47633 0.01229 While the author-given value for Al is close to the one calculated myself, the one for S is much different. By the way, 0.01621 * 1/3 = 0.0054. I could find it a simple mistake, I've found such a problem in case of many other structures. And here's my kind question: am I missing something? Best regards! -- Robert Gould Tel.UK: +44 (0)131 667 7230 or +44 (0)796 040 3872 Canada: +1 519 387 8223 --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com ++ 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: Quantitative phase analysis on FullProf
Hi Kotaro ATZ is the Z*Mw*f that you were calculating. You can find it described in the FullProf manual .pdf file around page 91 (or search for “ATZ”), and it is given for each phase in the line : !Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZNvk Npr More You can calculate it yourself, but the program also calculates a value for you for each phase, so if you are unsure and want to check, you can just take that value. Especially if you refine occupancies, the programs’ value can change from what you have entered. It will however take the values you enter, not the ones it calculates (unless there is a way to get it to accept the calculated values?) Sometimes I also find it useful to use the ATZ calculated for the framework of a structure, and not for example the ATZ including loosely bound water and exchanged cations. But that’s another story. I hope I understood the question and that this helps a bit. ☺ Regards, Arto From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of Kotaro SAITO Sent: den 24 februari 2015 11:53 To: Rietveld_l@ill.fr Subject: Quantitative phase analysis on FullProf Dear Rietvelders, Does anyone know how FullProf calculates weight fractions “Fract(%)” in a .sum file? or Is there any known bugs for calculating ATZ? According to the manual, it seems that ATZ is used for calculating the values... but no further information is written in the manual. I am also wondering, in my case, why different phases have the exact same value for ATZ. It should be different for different materials from the definition in the manual. Here are the related descriptions in my .out file. Phase 1 => The given value of ATZ is688.48 the program has calculated: 4345.96 Phase 2 => The given value of ATZ is688.48 the program has calculated: 576.91 I confirmed that 4345.96 and 576.91 seem to be Z*Mw I calculated the weight fractions using the values in the sum file and a equation Wp=S_p(ZMV)_p/ΣS_i(ZMV)_i (R. J. Hill and C. J. Howard, J Appl. Cryst., 20, 467-474), and ended up in getting quite different fractions from those in the .sum file. I got 97.3% and 2.7% with my calculation and the values in the .sum file are like this. Phase 1 => Bragg R-factor: 2.74 Vol: 941.374( 0.009) Fract(%): 82.46( 0.85) => Rf-factor= 1.81 ATZ: 688.475 Brindley: 1. Phase 2 => Bragg R-factor: 7.65 Vol: 137.093( 0.079) Fract(%): 17.54( 0.97) => Rf-factor= 5.35 ATZ: 688.475 Brindley: 1. When I ran an example pcr for quantitative phase analysis in Examples (si3n4r.pcr), I got ATZ and weight fractions below Si3N4 alpha => The given value of ATZ is560.00 the program has calculated: 561.14 Si3N4 beta => The given value of ATZ is280.00 the program has calculated: 280.57 => Phase: 1 Si3 N4 alpha => Bragg R-factor: 0.969 Vol: 292.623( 0.016) Fract(%): 92.88( 0.44) => Rf-factor= 0.600 ATZ: 560.000 Brindley: 1. => Phase: 2 Si3 N4 beta => Bragg R-factor: 2.26 Vol: 145.711( 0.027) Fract(%):7.12( 0.09) => Rf-factor= 1.09 ATZ: 280.000 Brindley: 1. and the these fractions are consistent with those derived from the equation Wp=S_p(ZMV)_p/ΣS_i(ZMV)_i. I would like to know which weight fractions I should trust for my case… Best regards, Kotaro ////// Kotaro SAITO High Energy Accelerator Research Organization Institute of Materials Structure Science 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan ////// ++ Please do NOT attach files to the whole list mailto:alan.he...@neutronoptics.com>> Send commands to mailto: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 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: regress in crystallographic good practices and knowledge
I too enjoy reading the discussions that emerge every now and then in this group, and I hope to see more of them in the future. Speaking of that, could you change my e-mail to arto.oj...@gmail.com? My employment ended and with it, the mail account will be gone soon as well. Regards, Arto From: rietveld_l-requ...@ill.fr [rietveld_l-requ...@ill.fr] on behalf of Kurt Leinenweber [ku...@asu.edu] Sent: Friday, May 08, 2015 6:16 PM To: Alan Hewat; Leopoldo Suescun Cc: rietveld_l@ill.fr Subject: RE: regress in crystallographic good practices and knowledge Hi Alan, I still like the Rietveld list and do read all the posts. Is it possible to block attachments so that people can’t attach files any more? - Kurt From: alan.he...@gmail.com [mailto:alan.he...@gmail.com] On Behalf Of Alan Hewat Sent: Friday, May 08, 2015 9:07 AM To: Leopoldo Suescun Cc: rietveld_l@ill.fr Subject: Re: regress in crystallographic good practices and knowledge I apologize in advance for attaching a file but I cannot share my astonishment without it. that´s why I worry more and more every day. And I worry that people are still attaching files to the whole list when they are explicitly asked not too. Most papers are on-line now, so just give a link to the paper. Or post your file to a free file sharing service - see: http://en.wikipedia.org/wiki/Comparison_of_file_hosting_services Anyone who still posts files to the whole list is automatically suspended for 1 week. Actually, I worry that the Rietveld list no longer serves a useful purpose. There are few interesting discussions, and apparently few people actually read the posts. Alan __ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE mailto:alan.he...@neutronoptics.com>> +33.476.98.41.68 http://www.NeutronOptics.com/hewat __ ++ 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: Powder diffraction w/Internal standard
Hi Josh Do you mean a standard for the peak positions, to correct for the sample shift? If so, then I'd say it depends on whether the mesh and sample are exactly on the same plane. And what type of in-situ? If it is temperature, then they should ideally have similar thermal expansion behavior as well. I would suggest you to add another sprinkle of a well-known powderous standard, such as silicon powder, to one measurement. Sure, you will have a three-phase refinement ahead of you, but silicon gives very distinct lines and its thermal expansion is well known. That'll tell you also how well the aluminum is behaving as a standard. Best, Arto On Fri, May 15, 2015 at 4:32 PM, Josh Kim wrote: > Dear Rietvelds, > > I’d appreciate some advice related to precision lattice parameter > calculation: I am currently performing in-situ measurements on a powder > sample which is deposited onto an aluminum mesh support. Due to the setup a > 3-axis stage is used to ‘align’ the sample in the diffractometer, however > my optimization of the sample alignment has simply been done to maximize my > signal to noise ratio. My question then becomes… is it feasible/reliable to > utilize the aluminum peaks (or even the beryllium peaks from my in-situ > cell window) from my support as an internal standard ?? (even though that > itself is not in the same plane as my sample) > > My initial thoughts would be that I am not able to do so without > introducing further error into my result, but am curious if anyone else has > had a similar experience. > > Thanks, > Josh > ++ > 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/ ++
