Re: Negative Uiso in GSAS

2010-03-03 Thread Jon Wright
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 (short

Re: [sdpd] Re: Are restraints as good as observations ?

2013-07-31 Thread Jon Wright
On 31/07/2013 20:19, Brian Toby wrote: To perform R-free with powder data, one must excise multiple complete peaks from the pattern, say a few sections making up 10-20% of pattern. Hi Brian, It is not so bad, you only need to throw in some peak intensities as variables (a partial Pawley). You

Re: Delta ferrite by xrd

2013-08-08 Thread Jon Wright
On 08/08/2013 18:04, led15 wrote: Is possible confirm the presence of delta ferrite in steel by xrd. Yes: http://dx.doi.org/10.1007/s11661-010-0371-7 ++ Please do NOT attach files to the whole list Send commands to eg: HELP as the su

Re: regress in crystallographic good practices and knowledge

2015-05-08 Thread Jon Wright
Dear Kurt, You can peaksearch the images with any number of packages and then look at the extracted spot positions. The stuff we wrote lives at http://sourceforge.net/projects/fable/ and it is normally used to fit grain-by-grain strain tensors. If you can isolate the spots you do indeed get a l

Re: TOPAS Macro Language (peak shape broadening macros)

2015-06-24 Thread Jon Wright
Hi Alan, In the limiting case of orienting all crystals in 3D you get a mosaic single crystal (e.g. [1], or using an XFEL to measure 1 at a time). Then the refined the crystal structure has somewhat better accuracy than with a 1D Rietveld fit. Perhaps not the most popular idea for this mailing

Re: Asymmetry peak shape difference between (pellet/powder)

2017-12-08 Thread Jon Wright
Hello, In the photo, the pellet is black and the powder is white. Why is that? Best Jon On December 8, 2017 3:35:20 PM GMT+01:00, "François Goutenoire" wrote: >Dear Rietveld users, > >We observe an unusual asymmetric peak shape on pellet and not when the >sample has been crushed in powder. >

Re: GSAS-II - indexing TOF data

2020-04-13 Thread Jon Wright
Hi Alex I think conograph does well for tof. Best Jon On April 13, 2020 8:24:55 PM GMT+02:00, Alexandros Lappas wrote: >Dear colleagues, > > > >We are working on some neutron time-of-flight (TOF) data and attempt to >index them within GSAS-II. > > > >As the low-angle detector banks contain i

Re: Comments on "Importance of matching software with hardware"

1999-03-26 Thread Jon Wright
hed up into some spikes. Horses for courses... shouldn't a fit show information which all has approximately equal weighting in the minimisation algorithm? In the same way that difference/esd is often more illuminating than just a plain difference curve. Jon Wri

Re: Graphics

1999-03-31 Thread Jon Wright
ld try MI/X. The URL to download MI/X from MicroImages' is http://www.microimages.com/ in the "Free Downloads" section. Hope this helps, Jon Wright On Tue, 30 Mar 1999, Hongwu Xu wrote: > Hi, Everyone, > > We have some neutron diffraction data collected and stored in t

Re: Errors in Rietveld refinement

1999-04-13 Thread Jon Wright
r intensity or position. This fix says that the systematic problems are really just random noise and effectively increases the weights on the y_obs accordingly, giving larger esd's. Hope this helps, Jon Wright PS: See also GSAS/fullprof manuals and "Rietveld refinement guidelines"

Re: Combined neutron/x-ray refinements

1999-05-11 Thread Jon Wright
lable as a beta version. It appears you can assign the statistical weight to each pattern, and in the example x-rays and neutrons are weighted equally. I'm wondering what the best choice is. Each observation comes with a statistical weight from the experiment? Isn'

Re: data format for GSAS using ISIS Polaris

1999-05-19 Thread Jon Wright
Renyang, Your best bet is to log into isis and read the data back into genie, then write it out using gsasgen. Something like the following will read your data in (check with the instrument scientist, it depends on you login.com file as to which commands you need and what works) : >> lo w1 myfil

Combined neutron/x-ray refinements

1999-05-25 Thread Jon Wright
oday. Incidentally does anyone have an example of a refinement where parameters are degraded by the combined fit *and* they agree with each other when two separate fits are carried out. Jon Wright PhD Student, Chemistry Dept, Cambridge Uni, UK. On 25 May 1999, Andrew Wills wrote: > Alan,

RE: Combined neutron/x-ray refinements

1999-05-25 Thread Jon Wright
ing combined fits anyway? Apologies to the list if I am displaying my ignorance, sometimes it's the quickest way to learn. Jon Wright PS: Sorry to pick at your comments Paolo, it's a shame I'm not at RAL at the moment. Could have discussed it out over a coffee...

RE: Combined neutron/x-ray refinements

1999-05-25 Thread Jon Wright
a neutron expert might look on this as an systematic error in the x-ray model :) Maybe not if one looks on the x-ray refinement as fitting of the electron density function, rather than the nuclear positions. For bonding studies it is the differences which are of interest! Jon Wright. PS: Any offers

Re: RIET: Are Spherical Harmonics for Preferred OrientationCorrection Evil?

1999-09-16 Thread Jon Wright
On Thu, 16 Sep 1999, Dr.Joerg Bergmann wrote: > (high systematic error, bad difference plot, but low e.s.d.'s) > (low systematic error, good difference plot, but high e.s.d.'s). Apologies for diving off onto the general case, but does this make sense? You improve your model and the quality of y

Re:

1999-09-20 Thread Jon Wright
There are two programs which spring to mind. GSAS and Fullprof both allow you to simulate neutron data. GSAS only does commensuate magnetic structures. See www.ccp14.ac.uk for link to the programs. Jon Dept. of

Re: RIET: TOF Neutron Web based programming resources?

1999-09-20 Thread Jon Wright
Lachlan, You can get hold of the freely available CCSL code from your site and compile programs tf112m etc for doing TOF neutron Reitveld fits with magnetism too! Compiles with the free g77 compiler after some minor changes. All code is there, I have compiled and run it on a PC and presented the

Re: Bond length and angle ESDs

1999-09-23 Thread Jon Wright
> On Thu, 23 Sep 1999, Ed Cussen wrote: > > We're forced to use CCSL for the superior peak shape description and > > so simply changing refinement program is not an option. I'm sure > > that this problem must have been encountered before and I'm suprised that > > there's not a 'standard' solutio

RE: As sent to the neutron mailing list

1999-09-27 Thread Jon Wright
> ... not at all for magnetism, ... Ahem, magnetism - resolution is very useful, in certain (rare) cases. I guess that magnetic structures are not Armel's primary interest but in at least one case resolution was essential. (FeAsO4 from IRIS (TOF neutron) dataset, J.Phys:Condens.Matter 11 (1999) 1

Non standard space group settings.

1999-11-12 Thread Jon Wright
generators. Is this possible with fullprof or would I run out of matrices there too? Thanks for any hints, Jon Wright -- >From international tables Fd-3m has a subgroup F 1 -3 2/m, which is a non standard setting of R-3m. I get the following output from expedt: Enter space group symbol

Cell constraints question

1999-12-02 Thread Jon Wright
st squares matrix rather than the real space unit cell parameters? I haven't picked up yet on why the derivatives cannot be converted from w.r.t A* etc to w.r.t a etc. Is it just a time saving? Thanks Jon Wright

Re: Understatement of the year..so far

2000-01-10 Thread Jon Wright
On Fri, 7 Jan 2000, Armel Le Bail wrote: > 15mn for checking a crystallography set is about my > performance too. Just out of interest, how long does it take people to pick up the error in entry number 17280, attached below. It's just a cell transformation from the cubic spinel [a->(a+b)/2, b->

Re: Understatement of the year..so far

2000-01-10 Thread Jon Wright
On Mon, 10 Jan 2000, Armel Le Bail wrote: > The number of papers published in crystallography which > have incorrect space group or cell choice are quite numerous. > Databases should show exactly the same number (5-10% > or even more ??). But isn't one of the values of a database that it should

Re: Understatement of the year..so far

2000-01-10 Thread Jon Wright
On Mon, 10 Jan 2000, Jaime Alamo wrote: > >PS: Has anyone found the error in that Fe3O4 entry yet? > > I think, It lacks the sqrt symbol, so ... > > [a->(a+b)/sqrt(2), b->(a-b)/sqrt(2)), c->2c] > > Also, it yields a negative setting that is less important. ?? I'm thinking of vector a b c,

Re: Absorption GSAS and TOF Instruments

2000-02-04 Thread Jon Wright
me out right when absorbtion is taken into account. So absorbtion is only a problem when the peaks disappear. Hope this helps, Jon Wright PS: Can anyone tell me if sigma_abs goes as 1/v for Gd? Dept. of Chem

Re: Asymmetry

2000-03-07 Thread Jon Wright
Asymmetry is discussed in: J.Appl.Cryst (1984) 17, p.47 - van Laar & Yelon (+ ref's therein) The above method is implemented in: J.Appl.Cryst (1994) 27, p.892 - Finger, Cox & Jephcoat. and source code for this peakshape is available. (They also talk about secondary monochromators). Hope th

Fitting lorentzian tails in GSAS

2000-03-21 Thread Jon Wright
e (with an low angle asymmetry correction) would be also be appreciated. Thanks in advance, Jon Wright Dept. of Chemistry, Lensfield Road, Cambridge, CB2 1EW Phone-Office 01223 (3)36396; Lab 01223 (3)36305; Home 01223 462024

Re: GSAS and CYCLIC refeinements ?

2000-06-02 Thread Jon Wright
Alex, There's something below which might help you. You'd need to set up a refinement with a .exp file and a .raw file with the same root name (eg fit.raw and fit.exp). The batch file then takes two arguments, the data file name (eg run1.raw) and the root of name of the .exp file (eg. fit for fit

Getting background subtracted r-factors from GSAS?

2000-06-21 Thread Jon Wright
Hi all, Does anyone know if there is a quick way of getting at a background subtracted r-factor within GSAS? (Without wishing to start a discussion about why I might want one) Thus far the only idea I've had is to calculate it by hand from hstdump, but that appears to be listing the background as

Re: Lp correction in GSAS

2000-07-11 Thread Jon Wright
being applied to data before presenting it for refinement, which sounds ugly. Fullprof has a flag for transmission geometry, hence my question. Thanks in advance, Jon Wright PS : If someone could refer me to simple derivatio

Re: Powplot problems with NT

2000-08-08 Thread Jon Wright
On Tue, 8 Aug 2000, Brian H. Toby wrote: > Brian Mitchell wrote: > > > > I have recently installed Windows NT on my laptop and find that the GSAS > > graphics plot takes an excessive amount of time to appear. I did not have > > this problem with Win 98. > > > > Any help/advice appreciated. > >

RE: Riet_L: Scale factor in Rietveld (with a question for Bob and Juan)

2000-09-15 Thread Jon Wright
Paolo, On Fri, 15 Sep 2000, Radaelli, PG (Paolo) wrote: . > Finally, here is a question for Bob and Juan. To me, it would be much more > natural to remove Vo from the scale factor, that is to redefine a new S' so > that > > Y=S'*L*A*E*|F|^2/Vo^2 and S'=K*Ltot*f > > This way, the scale fa

Re: Bragg R and GSAS

2004-02-26 Thread Jon Wright
In comparing refinements with different powder datasets there is no "number of observations" in common usage and no 10:1 rule of thumb. Broadly, this means "crappy" data with a chemically unreasonable model can sometimes give much better figures of merit than a good structure with "good" data.

Re: Is it really preferred orientation problem?

2004-03-05 Thread Jon Wright
> Like Rp, Rwp, Chi2, RB are respectively from 3.96, 5.33, 2.68, 5.80 > to 3.35, 4.42, 1.85, 3.07. This should pass a test of statistical significance. That does not mean it really is preferred orientation, but if it is not preferred orientation, then you

Re: CIF to powder pattern

2004-03-08 Thread Jon Wright
With all the file converters floating around, what are the chances that we are going to proliferate files with corrupted formats? I have gotten some files already that were supposed to be "GSAS files" but didn't have 80 columns, had blank lines, etc., and I assume they were made by file converter

Re: Magnetic Form Factor of Ru+4

2004-03-09 Thread Jon Wright
Ozhan Unverdi wrote: Could someone give me the magnetic scattering factors of Ru+4 please? www.google.com searching for "Ru4+ magnetic form factor" gives 17 results. One of them is Sidis et al, "Evidence for Incommensurate Spin Fluctuations in Sr2RuO4", Phys. Rev. Lett (1999) 83, 3320. In

Re: Is it really preferred orientation problem?

2004-03-15 Thread Jon Wright
zhijian fan wrote: *> Like Rp, Rwp, Chi2, RB are respectively from 3.96, 5.33, 2.68, 5.80 > to 3.35, 4.42, 1.85, 3.07. This should pass a test of statistical significance. * I made a hypothesis testing. H0: It needs not PO correction. The model with PO correction: G1=sum[wi

Choosing origins

2004-03-31 Thread Jon Wright
I am amazed by the flow of miss information that flows on this list whenever an apparent problem with a space group comes up. I asked a related question on sci.techniques.xtallography a few weeks ago, but have yet to hear anything, misinformation or otherwise. If anyone here can give me some

Re: GSAS informations

2004-04-13 Thread Jon Wright
Nicolae Popa wrote: the condition to not violate some elementary principles, in particular, here, the invariance to symmetry. Dear Prof Popa, I had been meaning to implement the quartic form for peak width in a refinement program for some time, but did not figure out how to generate the const

Re: GSAS informations

2004-04-14 Thread Jon Wright
Not violating symmetry restrictions you may either have the sphere with the terms 11=22=33 and 12=13=23=0 or something else allowing the 12=13=23 terms to be equal but different from 0. These two possibilities are all you can do in cubic symmetry with h,k,l permutable. If I am not wrong. The (111)

Re: GSAS informations

2004-04-26 Thread Jon Wright
>... to answer to your (too) long questions. May be later, OK? Going back to this quartics versus ellipsoids peak broadening stuff, maybe I can summarise: Why should the distribution of lattice parameters (=strain) in a sample match the crystallographic symmetry? If the sample has random, isolat

Re: fundamental parameters approach

2004-06-04 Thread Jon Wright
Is the fundamental parameter approach better than mathematical approach used in most of the Rietveld refinement programs? Perhaps someone is about to explain the difference is between "fundamental parameters" and anything else? I used to think it might mean convoluting something which was actu

Re: gnuplot, powder pattern

2004-08-19 Thread Jon Wright
Freidrich, Assuming you can use gsas2cif (or reflist or something) plus a text editor to get an ascii file containing a column of peak positions then in gnuplot I use: top=0 bottom=-100 set bar 0.0 plot "hklfile.dat" u (n):(bottom):(bottom):(top):(top) with financebars where n is the column in y

Re: Rietveld refinement and PDF refinement ?

2004-08-22 Thread Jon Wright
Well, that is an old chestnut that Cooper and Rollet used to oppose to Rietveld refinement. I think Rollet eventually agreed that Rietveld was the better method. Has Bill really gone back on that ? The difference between the two approaches are just an interchange of the order of summations wit

Re: Rietveld refinement and PDF refinement ?

2004-08-23 Thread Jon Wright
Bob, This exactly what is needed when the sample is a mixture of amorphous and crystalline components. But what happens when the material is a single crystalline phase with some coherent defects? Don't the defect <-> average structure correlations start to dominate, and separating components is

Re: TOPAS-Academic

2004-09-24 Thread Jon Wright
Alan, The "planned plugin architecture" sounds interesting. How concrete are the plans? I'm interested in auto-generation of restraints for proteins and fourier mapping at the moment... Regards, Jon alan coelho wrote: Dear all, An academic version of BRUKER-AXS TOPAS is now available to degree-g

Re:

2004-11-24 Thread Jon Wright
Alberto, Check you have the right polarisation correction. Synchrotron ~ 1, laboratory typically 0.5 with no mono... HTH, Jon Alberto Martinelli wrote: Dear all, I've got a problem with the Rietveld refinements of synchrotron data. I'm using Fullprof and the problem is that the overall B, and t

Re: Google Scholar

2004-11-26 Thread Jon Wright
Alan wrote: BTW, Google.com ranks ILL WWW pages 3rd worldwide, in both Condensed Matter and Crystallography, ahead of IUCr. To see what this means in practice, try a Google search on inorganic structure :-) http://rankwhere.com/google-page-rank.php?url=www.ill.fr www.ill.fr has Google PageRank 7

Rwp versus R(F^2)

2005-01-21 Thread Jon Wright
Hello everyone, Has anyone else noticed that sometimes when comparing two models Rwp is better for one and R(F^2) is better for the other? The case I am looking at is spacegroups P3 versus P-3, with the non-centrosymmetric structure having more degrees of freedom and therefore very slightly bett

Re: K alpha-2 stripping

2005-03-29 Thread Jon Wright
Gerard, If you "strip" the K-alpha-2 using a monochromator, then you might get better data. If you don't have that option, then fitting the data as they come is probably a better approach, as you don't run the risk of introducing artifacts. Jon Gerard, Garcia S wrote: Dear everybody, How impo

Re: Change format

2005-03-31 Thread Jon Wright
Brian Toby wrote: If the numbers are real values then they are not counts. They may be counts per second or something else. One needs to have uncertainty estimates for these intensities before one can do a meaningful Rietveld refinement (with any code). Following the above procedure, by multipl

Re: Questions about the asymmetry correction

2005-03-31 Thread Jon Wright
Xianqin, How did you calibrate the sample detector distance? For reliable absolute cell parameters it is very difficult to get good data with an area detector. One approach is to mix a standard material into the sample. As a gross approximation for small angles (in radians): sin(theta) ~ theta

Re: Level of Preferred Orientation

2005-04-01 Thread Jon Wright
Dear Bhuv > pattern and I have corrected possible graininess with spherical [...] > The data I have collected is on a image plate (only one frame). Not sure I understand? If you have a 2D image showing powder rings then you should have some very good ideas about the level of granularity or textur

Re: Mean vs. Median to reduce bias in grainy intensities (was Re:

2005-04-04 Thread Jon Wright
Alex, While I can understand the general rationale for the idea (minimize the weight of the very strong reflections to the final integrated intensity for the reflection), could you expand further on your level of success and any analysis you have carried out on this plan? The massive random spike

Re: fundamental parameters approach & X'celerator

2005-05-03 Thread Jon Wright
I did some tests on the profile of the first diffraction peak of LaB6, where I added a secondary soller angle, since I used secondary soller slits, and I added also the parameter for the horizontal divergence in the equitorial plane. Finally I added a crystallite-size parameter CS_L. I did the

Re: fundamental parameters approach & X'celerator

2005-05-03 Thread Jon Wright
Its best to use the terms axial plane and horizontal plane to avoid confusion. Alan, I'm confused! What do you mean by those terms? I thought "axial divergence" was "beam hits different points along the two theta axis" - is that a misconception? Last point, what do you mean by vertical diver

Re: How to prepare intensity and hkl files needed by SHELXTL-97

2006-05-31 Thread Jon Wright
I've attached a python script below which will convert a gsas rfl file into shelx hklf 4 format - it assumes there is no peak overlap at all, so it is *not* hklf 5 format and *not* suitable for refinement! After installing python from www.python.org and copying the script into your working directo

Re: How to prepare intensity and hkl files needed by SHELXTL-97

2006-05-31 Thread Jon Wright
Bob, Shelx's (3I4,2F8.2) for h,k,l,FoSq,sig is straightforward to do in fortran but needs a custom number format in excel? Some people are able to type: awk "{printf(\"%4d%4d%4d%8.2f%8.2f\n\",$1,$2,$3,$8/100,$9/100)}" < test.rfl > test.hkl ...and then delete the first and last line from th

Re: GSAS ESD/STD conversion

2006-06-29 Thread Jon Wright
Brian H. Toby wrote: I am trying to convert a GSAS ESD file to a GSAS STD file BTW, I would be surprised if FullProf does not have a way to input intensities with uncertainties rather than assuming intensities are counts. Indeed it does! INSTRM=10 is x, y, sigma format for fullprof where it

Re: Uiso constraints

2006-07-03 Thread Jon Wright
I would like to know whether GSAS is able to constraint the Uiso value so that it will be always bigger than zero. As others have indicated - GSAS does not do that (topas gives you the option, doubtless amongst others). Shelx does do that (with single crystal data) and you can't turn it off

Re: crystal structure of SUCROSE

2006-07-04 Thread Jon Wright
Sudhish, See: J. Appl. Cryst. (1991). 24, 352-354 "Sucrose, a convenient test crystal for absolute structures" R. C. Hynes and Y. Le Page P2(1), a = 10.8631(9) , b = 8.7044(6) , c = 7.7624(7) Å, [beta] = 102.938(7)° at 300(1) K Despite being great for availability, sugar crystals are freq

Re: GSAS: interpretation of strain broadening

2006-10-25 Thread Jon Wright
Let's say one gets a value of 0.1% strain. => width of the distribution of cell parameters in the sample But on the other hand there are also the unit cell sigmas. => error bar on the average value of the cell parameters How can one visualise this? There is a distribution of cell para

Re: Powder Diffraction In Q-Space

2007-02-22 Thread Jon Wright
Jacco, I/sigma_I is a good idea in principle. It just looks ugly if you get the sigmas right for certain instruments - there are meaningless steps all over the place. All of these problems of "what to plot" would go away if we all submitted powderCIF files for our refinements. The "plot" cou

[Fwd: [ccp4bb] Nature policy update regarding source code]

2007-03-23 Thread Jon Wright
Hi Everyone; Just in case you don't follow ccp4bb or nature methods: http://www.nature.com/nmeth/journal/v4/n3/full/nmeth0307-189.html I thought that some of you might be interested that the journal Nature has clarified the publication requirements regarding source code accessibility. It is li

Re: [Fwd: [ccp4bb] Nature policy update regarding source code]

2007-03-23 Thread Jon Wright
AlanCoelho wrote: Not sure what to make of all this Jon Don't shoot the messenger, I was surprised enough by it to forward it to the list. I guess they imply if you want to keep all implementation details secret you should be patenting instead of publishing? (Patents seems to be free online,

Re: peaks splitting

2007-05-22 Thread Jon Wright
Hi everyone, Three responses saying it might be a lower spacegroup? I wonder if the emperors have their clothes on today? (006) reflections can't split in R-3c as they only have a multiplicity of 2 in the first place (0,0,6 and 0,0,-6). You were lucky enough to split (00l) which rules out an

Re: gnuplot help regarding

2007-07-16 Thread Jon Wright
Easiest is to click on the top corner of the plot window and select options "copy to clipboard". Or directly write to gif via: gnuplot> set terminal gif Terminal type set to 'gif' Options are 'small size 640,480 ' gnuplot> set output "test.gif" gnuplot> plot sin(x) gnuplot> set terminal win Term

The magic of the algorithm

2007-08-14 Thread Jon Wright
Is there not some significant prior art in iterative phase refinement by an "FFT then flip" algorithm? See for example: Acta Cryst. (1996). D52, 30-42[ doi:10.1107/S0907444995008754 ] "Methods used in the structure determination of bovine mitochondrial F1 ATPase" J. P. Abrahams and A. G. W

Re: Absolute structure from powder data?

2007-11-14 Thread Jon Wright
Did anyone look into the effects of using circularly polarised x-rays? Just wondering... Jon Larry Finger wrote: Franz Werner wrote: Dear Rietvelders Is it in principle impossible to determine the absolute structure from powder data due to reflection overlap or is there a way via multiple w

Re: X-ray scattering contrast Fe/Cu

2007-11-19 Thread Jon Wright
Just a quick plug for a program called "chooch" which does a very nice job of calculating f' and f" from an edge scan, see: http://www.gwyndafevans.co.uk/chooch.html For Fe/Cu then neutrons may help. Cheers, Jon [...] Each edge to be used is recorded, this allow to calculate using Kramers-

Re: Hyper Lorentzian peak shape

2007-11-22 Thread Jon Wright
If you can fit via a sum of a broader lorentzian and a narrower one it may indicate the sample is a "mixture". Are you sure the sample is microscopically homogenous? Best, Jon Francois Goutenoire schrieb: Dear Rietveld users, I am currently working on Williamson-Hall graph in order to c

Open Access Articles: 60 years of Acta Crystallographica and the IUCr

2007-12-21 Thread Jon Wright
Hello Everyone, Some reviews have just come out in the first 2008 issue of Acta A: 60 years of Acta Crystallographica and the IUCr: http://journals.iucr.org/a/issues/2008/01/00/issconts.html Start citing now for a nicely skewed impact factor in a few years time :-) Happy Christmas, Jon

Re: Automated phase matching?

2008-02-04 Thread Jon Wright
Yetta Porter wrote: Hello all, I am interested in finding software that can convert 2D diffraction rings into 1D diffraction patterns AND allow phase/pattern matching using the ICDD's PDF database. Currently, I am using Fit2D to convert my rings to patterns and then Match! to phase match my pat

Re: GSAS total beginner questions

2008-02-13 Thread Jon Wright
Works for me. Just fill out a BANK line with FXY or FXYE as described in the manual :-) Cheers, Jon [EMAIL PROTECTED] wrote: Isn't GSAS able to handle XY data?? Cheers Matthew Matthew Rowles CSIRO Minerals Box 312 Clayton South, Victoria AUSTRALIA 3169 Ph: +61 3 954

Re: advice on new powder diffractometer

2008-02-15 Thread Jon Wright
Kurt Leinenweber wrote: ... with wRp of 25% and crystallographic R also near 25% .. Maybe the background is too low :-? Jon

Re: advice on new powder diffractometer

2008-02-18 Thread Jon Wright
Alan Hewat wrote: Many theoretical arguments about signal/noise forget that the experimentalist has a finite time to collect his data :-) The finite time to analyse and publish can also be rate limiting! In this respect a high background is a fine addition to any instrument; it gives a much l

Re: advice on new powder diffractometer

2008-02-18 Thread Jon Wright
Alan Hewat wrote: Even if you have a low profile R-factor (due to a high background and a low resolution pattern) the calculated standard deviations in parameters can still be large, which gives me confidence in Rietveld refinement :-) I hoped the values of esds come out similar to the ones put

Re: Fullprof setup Linux

2008-03-02 Thread Jon Wright
William, The "ELF" usually means it is the equivalent of a .exe file? Try: chmod a+x setup_fullprof_suite ; ./setup_fullprof_suite Something came up on the list a while ago about a upx issue. You previously needed something like: $ sudo apt-get install upx-ucl $ upx -d fp2k But perhaps thi

Re: WARNING: Posting large attachments on the Rietveld list

2008-03-17 Thread Jon Wright
We have also limited the size of Rietveld list messages to 0.5 Kbytes 0.5 KBytes is only 512 characters? I would h8 2 c text message style language as a consequence :-) Best, Jon

Re: interstitial hole size

2008-07-21 Thread Jon Wright
Won't you always be able to put a slightly larger atom if you let the atom move up or down out of the trigonal plane? Anyway, it sounds like you are asking for the largest circle which fits in the hole between three circles who are touching (this is a 2D problem?). Try a google for "Descartes C

Re: [sdpd] Re: Background Subtractions / 2D image plate

2008-08-11 Thread Jon Wright
radiated. Any suggestions or comments are welcomed. Thanks, Yetta P.S. Let me know if you can't access the files (its in Bckgrnd Subtr.zip), I'll send then to you directly. --- In [EMAIL PROTECTED] <mailto:sdpd%40yahoogroups.com>, Jon Wright <[EMAIL PROTECTED]> wrote:

Re: Portable XRD

2008-09-03 Thread Jon Wright
Hi, If you have the usual environment variables set : GSAS=c:\gsas PATH=...;c:\gsas\exe PGPLOT_FONT=c:\gsas\pgl\grfont.dat then it should all run from a dos prompt (run -> cmd or command.com). Or at least, you can type "expedt", "powpref" and "genles" etc and the programs run and even deal wi

Re: calculating f' and f''

2008-09-09 Thread Jon Wright
Try this: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/source/chooch-5.0.2-src.tar.gz Best, Jon Jean-Marc Joubert wrote: Hello, I am looking for a program able to calculate f' and f'' from absorption data for a resonnant diffraction experiment. I know that CHOOCH program was able to do that. This progra

Re: Beginer problems, difficulty charecterizing our diffractometer...

2008-09-17 Thread Jon Wright
Dear Blaise, A chi^2 of 500 means that on average your model is off by 500 sigma, or 500*500=25 counts. This usually means some technical detail has gone wrong in file formats or weights. If you don't manage to figure out the problem then if you can post your refinement somewhere I am su

Re: Bragg-Brentano vs. parallel beam

2009-01-23 Thread Jon Wright
Markus Valkeapää wrote: Any comments on these two different geometries here on Rietveld list? It depends on the sample? Reflection geometry helps when there is a lot of absorbtion. Jon

TotalCryst workshop, Grenoble, 1-3 April 2009

2009-02-25 Thread Jon Wright
You are warmly invited to attend a 3-day Workshop in Grenoble, which aims at explaining the TotalCryst methods and demonstrating the FABLE software package. http://www.esrf.fr/events/conferences/TotalCryst/TotalCryst/ Please bring this to the attention of your colleagues. Registration is open

Re: scattering factor for B+3

2009-02-27 Thread Jon Wright
Out of curiousity, I'm wondering, do many people use ionic scattering factors instead atomic ones for Rietveld refinement? Cheers, Jon Lubomir Smrcok wrote: Just one question : have you asked your supervisor before sending such a mail ? Though I understand your position it seems that you are

Re: cRs

2009-03-04 Thread Jon Wright
Dear Olga, As you've noticed, the Rietveld R-factors tell you how well you fit the pattern, but don't tell you how well you fit the peaks. There is a correlated intensities R-factor which follows from the methods outlined in: J. Appl. Cryst. (2004). 37, 621-628[ doi:10.1107/S0021889804013

Re: cRs

2009-03-06 Thread Jon Wright
Olga Smirnova wrote: Did anyone try to calculate simple mean deviance and compare with popular R factors? OS For "simple mean deviance" do you mean like in: http://en.wikipedia.org/wiki/Deviance_(statistics) Seems we normally call that "chi^2". If that's what you meant, then yes, people do

Re: How to determine the crystalline system

2009-03-09 Thread Jon Wright
Alan Hewat wrote: ... your name appears as ½¨²¨Áº The problem is your mail reader, thunderbird displays some chinese characters. Liang's mail correctly uses a MIME encoded word as the ascii string: =?GB2312?B?vaiyqMG6?= Which means character set "GB2312" (chinese), "B"ase64 encoding, and

Re: UVW - how to avoid negative widths?

2009-03-19 Thread Jon Wright
According to Caglioti relation, the dimensions of U,V,W are as (angle)^2. Quick question - does anyone have a trick to stop the Cagliotti formula going negative? Prodd currently has a habit of bugging out on a sqrt(negative) and I'm wondering how other folks worked around that, or if I've go

Re: UVW - how to avoid negative widths?

2009-03-19 Thread Jon Wright
Alan Hewat wrote: Jon Wright said: Quick question - does anyone have a trick to stop the Cagliotti formula going negative? This can happen if the resolution is relatively flat, so that there is no well defined minimum. Seems to be the problem - also rather close to zero anyway. if

Re: LP factor in the Rietveld refinement

2009-07-22 Thread Jon Wright
Sounds like the parameter is the monochromator angle you would need to use to convert an unpolarised beam into a beam with the polarisation state you have (eg, 90 degrees gives 100% polarised). Don't confuse this with the actual monochromator angle at the synchrotron, as the bean is usually pol

Re: Refinement of spiral magnetic structure from neutron powder diffraction

2009-07-23 Thread Jon Wright
Dear Alexander, This is theoretically one of the few things that can be done with PRODD, which is a refinement program based on the CCSL subroutine library. Some multibank spiral structure refinements were done with the program when I was doing my thesis. 1) How do I decide on the space gro

Re: Refinement of spiral magnetic structure from neutron powder diffraction

2009-07-24 Thread Jon Wright
Hi Andrew, A word on GSAS vs Fullprof: GSAS can only handle a magnetic structure that can be defined by a unit cell. So, your incommensurate structure would need to be close to a lock-in value to work, i.e. (0 0 0.32) is close to (0 0 1/3). While it is a lot easier to use a super cell, the

Re: Mask for Fit2d

2009-08-29 Thread Jon Wright
Just use mask polygon and draw a little triangle inside the pixel you want to mask. It helps to zoom in first. (Usually it is easier to find the hot pixels with a threshold mask anyway). Best, Jon Yang, Ling wrote: Hi, Does anyone know how to mask single pixel in Fit2d? I found it neces