Date: Tue, 26 Feb 2002 16:17:40 +0100 To: rietveld_l@ill.fr From: Jonathan WRIGHT [wright@esrf.fr] Subject: RE: X'Cellerator and Proportional counter >1) Good resolution in 2theta (or equivalent measure of d*); > >2) A reasonably complete model that includes all the important >structural and instrumental variables (including peak shape); > >3) Good counting statistics. 4) Good q-range, extending to high angles or short d-spacings, to have the best possible structural "resolution". eg: a 1.0 angstrom structure with CuK_alpha radiation would mean data where peaks can still be seen as far as 100 degrees in two theta. This is clearly sample dependent, but I was slightly surprised to see that the data posted to the list had constant counting statistics across the two theta range. At least with x-rays, aren't people spending longer on the high angle data for Rietveld refinements? Cheers, Jon |
From: "L. Cranswick" [lzc@dl.ac.uk] Subject: Re: X'Cellerator and Proportional counter - VCT data To: rietveld_l@ill.fr Date: Tue, 26 Feb 2002 22:15:07 +0000 (GMT) > 4) Good q-range, extending to high angles or short d-spacings, to have the > best possible structural "resolution". eg: a 1.0 angstrom structure with > CuK_alpha radiation would mean data where peaks can still be seen as far as > 100 degrees in two theta. This is clearly sample dependent, but I was > slightly surprised to see that the data posted to the list had constant > counting statistics across the two theta range. At least with x-rays, > aren't people spending longer on the high angle data for Rietveld refinements? > > Cheers, > > Jon Which hardware vendor's software allows the collection of variable count time data and the merging into a single file with ESDs (or count time)? As far as I can tell - the answer is "None" (some vendors may say it is possible but in practise it is so kludgy and cumbersome to perform that it is almost impossible to do this effectively). Thus you may have Rolls Royce quality diffraction hardware - yet by not having modern data collection features in the control software - vendors would have you use their hardware as though you were riding a rusty bicycle. ------ However, rather than just doing ad-hoc increasing of count times, there is a Variable Count Time program available (VCT) (Fortran source and DOS executable) for collecting Madsen and Hill style VCT data. This also generates a command script for a Philips 1710 diffraction system (which you can then send down the serial control cable if you have the software for doing this). http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/variable-count-time/ References: "Collection and analysis of powder diffraction data with near-constant counting statistics", I. C. Madsen and R. J. Hill, J. Appl. Cryst. (1994). 27, 385-392, http://www.iucr.org/cgi-bin/paper?hz0014 I. C. Madsen and R. J. Hill, Adv. X-ray Anal. (1992), 35, 39-47 ---- Though there seems to be source code, executable or algorithms available based around the following abstract (?): W. I. F. David, Accuracy in Powder Diffraction, Abstract P2.6 NIST Special Publication No. 846, Page 210, (1992) National Institute of Standards and Technology, Gaithersburg, MD, USA. ------ Fullprof and Winplotr can read Madsen and Hill VCT data without any required conversion. (format 11 in the manual) For GSAS (and programs that use GSAS ESD format), there is a tutorial for converting Madsen and Hill Variable Count Time data into GSAS ESD format at: http://www.ccp14.ac.uk/solution/gsas/convert_vct_data_to_gsas.html This is using Mark Bowden's VCTCONV for DOS program. http://www.ceramics.irl.cri.nz/Convert.htm ----- If you are using the above Madsen and Hill code and have a Philips 1710 (and a way of sending the script down the serial control cable); you can use the Philips PW 1710 script it generates as a template to generate "custom" Variable Count Time data collection scripts. This can be useful for some refinements - e.g., collect intense subcell reflections and weak supercell reflections with similar counting statistics. The above webpage tutorial shows such an example. As mentioned in recent talk notes (using data collected by Jeremy Cockcroft as the example), Variable Count Time can also be very effective for phase ID, quantitative analysis, powder indexing and unit cell refinement - where you collect every minor to trace peak with the same counting statistics as the major peaks. (VCT can allow you to refine the structures of trace phases - assuming there is not excessive overlap with peaks of the major phases) Refer: (slides 17 to 29) http://www.ccp14.ac.uk/poster-talks/axaa2002/ Lachlan. -- ----------------------- Lachlan M. D. Cranswick 1st Feb to 8th Feb - then 18th Feb to 17th March 2002 CSIRO Division of Minerals PO Box 312, Clayton South, Melbourne, Victoria, Australia, 3169. Tel: (613) 9545-8802 Fax: (613) 9562 8919 Collaborative Computational Project No 14 (CCP14) for Single Crystal and Powder Diffraction Birkbeck University of London and Daresbury Laboratory Postal Address: CCP14 - School of Crystallography, Birkbeck College, Malet Street, Bloomsbury, WC1E 7HX, London, UK Tel: (+44) 020 7631 6850 Fax: (+44) 020 7631 6803 E-mail: l.m.d.cranswick@dl.ac.uk Room: B091 WWW: http://www.ccp14.ac.uk/ |
From: "Shankland, K (Kenneth) " [K.Shankland@rl.ac.uk] To: rietveld_l@ill.fr Subject: VCT Date: Wed, 27 Feb 2002 10:34:47 -0000 >Which hardware vendor's software allows the collection of >variable count time data and the merging into a single >file with ESDs (or count time)? It may not be able to be done 'routinely' but it's hardly 'almost impossible'. However, it's probably true to say that most people would use a VCT facility if it was an option, or better still, the default option. Ultimately, it all depends on how good you want your data to be. Most folks are simply wary of changing their tried and tested methods and are content with the results they normally get. *Every* data set for structure solution that we've collected on BM16 of the ESRF has been collected in a VCT fashion, and that's going back as far as experiments run in 1997. The benefits of VCT are clear for solution (both by direct methods and global opt) and refinement. It's so easy to apply and to do it "correctly" takes only a little more effort than to say "oh, I counted for twice as long at high angles".... Cheers, Kenneth |
Date: Wed, 27 Feb 2002 13:15:03 +0100 To: rietveld_l@ill.fr From: Armel Le Bail [alb@cristal.org] Subject: Re: VCT >The benefits of VCT are clear for solution (both by direct >methods and global opt) and refinement. It's so easy to >apply and to do it "correctly" takes only a little more >effort than to say "oh, I counted for twice as long at high >angles".... Using variable slits (VS) can be considered as a (bad) way to obtain data analogous to VCT data. However, few Rietveld programs allow the direct use of VS data, you have to correct them before refining the structure or extracting structure factor amplitudes. So, Rietveld programmers, please add the possibility to cope directly with VCT and VS data. And manufacturers, please make VCT measurements easy. (one can suppose that both programmers and manufacturers are listening, even if few are writing here ;-). Armel |
From: Reinhard Kleeberg [kleeberg@mineral.tu-freiberg.de] Date: Wed, 27 Feb 2002 13:52:21 +0000 To: rietveld_l@ill.fr Subject: Re: X'Cellerator and Proportional counter - VCT data Hi, some naive questions from a none-mathematician without experience in structure solution: At 22:15 26.02.02 +0000, Lachlan wrote: > >Which hardware vendor's software allows the collection of >variable count time data and the merging into a single >file with ESDs (or count times)? What about a simple manually dividing the pattern in 2Theta ranges with increasing counting time? This can be done with all diffractometers. Each range contains either the pure counts or the cps and the counting time. As I understand, the Rietveld programs should use these two types of information to get the ESDs or store the ESD information separately in the data file (see GSAS ESD format). As another example, BGMN derives the ESDs from the range headers to use this in its weighting method. Therefore, it is not recommended to use data with wrong statistic information (say, wrong counting time entries in converted files) or to falsify the statistics by background substraction (as Joerg Bergmann told me). In extreme cases, one could define manually a lot of measuring ranges (of course, a lot of work, but for structure refinement ...). Has anyone experience in using data with pre-selected counts (variable counting time for each step, until the pre-selected number of counts is reached)? Than the counting statistic is equal for each step. This can easily done by the most diffractometers, but I know nothing about the reaction of Rietveld programs (using different weigthing methods) if they have to use such data (and whether the programs are able to identify these data type automatically). On the other hand, for low background configuration/samples, such a measurement will need a lot of time, and it will seldom be practicable. Reinhard Dr. R. Kleeberg TU Bergakademie Freiberg Institut für Mineralogie Brennhausgasse 14 D-09596 Freiberg Germany Tel. +49 (0) 3731-39-3244 Fax. +49 (0) 3731-39-3129 |
Date: Wed, 27 Feb 2002 15:19:11 +0100 To: rietveld_l@ill.fr From: Jonathan WRIGHT [wright@esrf.fr] Subject: Re: VCT >So, Rietveld programmers, please add the possibility to cope >directly with VCT and VS data. For the VCT data at least, don't we just take counts=total_counts/total_time and esd=sqrt(total_counts+k)/total_time, where k=0, 0.5 or 1 according to taste, and then use an esd data format for the refinement? There doesn't seem to be anything a Rietveld programmer can do to help. Are there *any* modern Rietveld programs which don't support an esd data format and conventional least squares weights?? A nice extension might be to get the Rietveld program to write out the derivatives of various parameters of interest for each point in the pattern so you can work out which particular data points are most important for the refinement of each parameter. Then send the diffractometer off to concentrate on the points where the derivatives are largest. That kind of requires that you can solve the problem before you collect the data, or at least much faster than it takes to collect the full dataset, so I doubt if it'll take off ;-) >And manufacturers, please make VCT measurements easy. Given that most (all?) already let you program a series of scans there doesn't seem to be a great deal the manufacturers can do to help either. All that is needed is a trivial program to combine the data. I guess this doesn't exist because of the infinite variety of file formats it'd end up needing to support and possibly that no one would try to write up something you can do with excel. Cheers, Jon |
Date: Wed, 27 Feb 2002 16:04:28 +0100 To: rietveld_l@ill.fr From: Armel Le Bail [alb@cristal.org] Subject: Re: VCT >For the VCT data at least, don't we just take >counts=total_counts/total_time and esd=sqrt(total_counts+k)/total_time, >where k=0, 0.5 or 1 according to taste, and then use an esd data format for >the refinement? There doesn't seem to be anything a Rietveld programmer can >do to help. Are there *any* modern Rietveld programs which don't support an >esd data format and conventional least squares weights?? Sure, obviously, no help is needed from a Rietveld programmer if you transform your original data back into the classical form (just like if there was no VCT, no VS). But you may consider using the case where counts = counts ;-) In that case, VCT or VS data would allow to give more weight than usually at increasing diffracting angle, in a way that mimics neutron data. > >And manufacturers, please make VCT measurements easy. > >Given that most (all?) already let you program a series of scans there >doesn't seem to be a great deal the manufacturers can do to help either. Again, the idea is to use the data as they were registered (counts=counts) Rather than to program a series of scans (quite tedious) which would need to have several scales in your refinements (hypothesis counts=counts), you may consider that the manufacturer allows you to select (at a push of one button) between a few possibilities of simple laws giving counting times as a function of diffracting angles, and that the Rietveld program would also have these laws inside. So let me ask again (more clearly ?) : Rietveld programmers, please add the possibility to cope directly with VCT and VS data. And manufacturers, please make VCT measurements easy. And let me add : both of you, work together coherently. Armel PS - Anyway, you can continue to use Excel if you want. |
From: "Joerg Bergmann" [bergmann@rcs1.urz.tu-dresden.de] To: "rietveld_l@ill.fr" [rietveld_l@ill.fr] Date: Wed, 27 Feb 2002 16:26:12 +0100 (CET) Subject: Re: VCT Dear Jon, On Wed, 27 Feb 2002 15:19:11 +0100, Jonathan WRIGHT wrote: >A nice extension might be to get the Rietveld program to write out the >derivatives of various parameters of interest for each point in the pattern >so you can work out which particular data points are most important for the >refinement of each parameter. Then send the diffractometer off to >concentrate on the points where the derivatives are largest. That kind of >requires that you can solve the problem before you collect the data, or at >least much faster than it takes to collect the full dataset, so I doubt if >it'll take off ;-) > You are about to re-develop Optimal Experimental Design! This is a field of mathematics since many decades. For a background in mathematics, read for example: Fedorov, V.V. "Theorija optimal'novo eksperimenta" , Moscow 1971 (in russian, "The Theory of optimal experiments"). Of course, it is not such simple as you mean. You must optimize the error matrix, which follows from some inversion of the data given by the measurements. And, in most cases, the optimal designed experiment must have at least as many points as the number of parameters used in the Rietveld refinement. Otherwise, the calulation will diverge. Optimal experimental design in XRPD was the topic of my doctoral thesis 1983 (see http://www.jbergmann.de/thesis.pdf). And, Optimal Experimental Design was part of the BGMN Rietveld program from the beginning. I have just remanufactured it last weekend. I had not touched this code part for many years, so it was somewhat out of function. See http://www.bgmn.de. We hope to present new results of Optimal Experimental Design in near future. Joerg Bergmann, Dresden email@jbergmann.de |
Date: Wed, 27 Feb 2002 17:22:31 +0100 To: rietveld_l@ill.fr From: Armel Le Bail [alb@cristal.org] Subject: Re: VCT >between a few possibilities of simple laws giving counting >times as a function of diffracting angles, and that the Rietveld >program would also have these laws inside. One evident possible law could be one proportional to the inverse of the Lorentz-polarisation factor, which is known in advance. In that case, the Rietveld program would even be simplified and calculation times would be slightly shorter... "D'une pierre deux coups" (in French in the text). Remember that people refining structures from single crystal data work on |F]squared data, generally. We work on the same data, but they are modified by a number of multiplicative factors that give undue weights to some parts of the powder diffraction pattern. Removing the Lorentz-polarisation factor would be all benefit. No need to publish that in J. Appl. Cryst... Take the idea with a copyleft (unless it was already published maybe ;-). Armel |
Date: Wed, 27 Feb 2002 18:09:44 +0100 To: rietveld_l@ill.fr From: Jonathan WRIGHT [wright@esrf.fr] Subject: Re: VCT >Armel wrote: >But you may consider using the case where counts = counts ;-) After you've finished the esd format refinement, you could plot (y_obs/esd)**2 instead of normalised counts for y_obs and you have the same thing (the intention is to plot something such that the esd is the square root of what's on the y-axis, so you recover whatever the real counts were, just in case I got the sums wrong or it wasn't immediately obvious). >In that case, VCT or VS data would allow to give more weight >than usually at increasing diffracting angle, in a way that mimics >neutron data. I thought an esd format already gives more weight? For seeing that clearly you just need to modify your plot so that it represents the least squares problem. Either use a weighted difference curve, or scale y_calc according to y_obs above and then plot the straight difference. This will look strange if you slow down for superstructure peaks! VCT is equivalent to handling the changing incident intensity during a synchrotron experiment, which is why I still think the Rietveld programmers cannot be blamed for the method not catching on in the lab. Reading a scale factor with each data point might be more convenient, but the gain is only aesthetic. As Joerg has just pointed out, these ideas have been around for some time, which was the reason I bought it up after the LaB6 data was posted. For indexing and looking for superstructure peaks (and checking for a clean pattern) it may not be appropriate, but otherwise it seems like a fairly simple (and cheap) way to improve data quality? Cheers, Jon PS: Some time ago I heard it said that anyone who is not using VCT data with x-ray data for Rietveld refinement of structures should be shot. I guess the person who said this is not doing much refereeing. |
Date: Thu, 28 Feb 2002 11:57:29 +0100 To: rietveld_l@ill.fr From: Alan Hewat [hewat@ill.fr] Subject: Re: VCT > >Which hardware vendor's software allows the collection of > >variable count time data and the merging into a single > >file with ESDs (or counts)? I was hoping that some of the maintainers of the current Rietveld codes would answer this, but since they haven't I will comment :-) Ever since multiple detectors have been used on neutron machines ie ever since the early 70's :-) we have had an additional weighting factor for each point that took into account the number of detectors used to obtain the average count for that point (since different points were measured a different number of times by different detectors). I suppose that similar things are done for the ESRF machine to which Kenneth Shankland refers, since it also uses multiple detectors. Each point is then recorded with two numbers - the average count and the number of times it was measured. Both GSAS and Fullprof accept this kind of data. So it seems to me that it is commonly possible to refine data for which different regions of the pattern are collected with different counting times, and if that is all that is meant by "VCT" I am surprised to see so much discussion about it :-) The wisdom of trying to measure some parts of the pattern more precisely because they are thought a priori to be more "important" is another matter :-) And to allow users to choose their own weights seems even more dangerous. Alan. Dr Alan W. Hewat, Diffraction Group Leader. Institut Laue-Langevin, BP 156X Grenoble FRANCE 38042 fax (33)4.76.20.76.48 tel (33)4.76.20.72.13 (or .26 Mme Guillermet) [hewat@ill.fr] http://www.ill.fr/dif/AlanHewat.htm |
From: "Sean X. Ouyang" [ouyang@mail.chem.tamu.edu] To: [rietveld_l@ill.fr] Subject: Re: VCT Date: Thu, 28 Feb 2002 10:06:23 -0600 The EVA software come with Bruker D8 machine allow you to merge multiple data into a single one. You should configure your data collection with overlapping for scaling. (ie. 5-40 10s, 35-65, 20s, 60-80 30s etc. and you final collected data will have multiple sections). The overlap portions of your data will be used for scaling and the data will be merged into a single one. However, no esd provided. BTW, how many Rietveld packages can handle data with esd? Could some body point me to a data converting program which could import/export GSAS esd data? (not powder2/3, which rounds off and flatten my data!). Sean X. Ouyang Ph.D. Department of Chemistry Texas A&M University |
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