Re: Rietveld ESD calc fortran code typo?

[Jonathan WRIGHT]

Dear Matthew

That fortran snippet was corrected in Appendix 1 of Andreev's paper here:

https://doi.org/10.1107/S002188989300891X

It is a shame that implicit none was not part of fortran 77. The google search 
resul leading me to that was:


https://www.researchgate.net/publication/359342753_Program_RietESD_for_correction_of_estimated_standard_deviations_obtained_in_Rietveld-refinement_programs

https://www.iucr.org/resources/other-directories/software/rietesd

Presumably similar things are computed as SCOR in fullprof output list files 
(Serial CORelation). There is some discussion in Hill and Madsen:


https://doi.org/10.1107/S0021889886090076

... who give the citations for Pawley 1980 and Scott 1983 to locate the origins 
of those estimates.


Best regards,

Jon



On 14/05/2024 10:56, Matthew Rowles wrote:

Hi all

Just been reading Berar & Lelann (J Appl Cryst 24:1-5).

In the paper's appendix, there is some Fortran code implementing their ESD 
multiplier calculation.

This code was added to the end of the CHISQ subroutine in DBW3.2

I'm interested in line 10:
    COREL = (DEL**2/Y(I)) + CD

Should CD be XD? Is this a typo?

If not, does anyone know what CD represents?

image.png


Thanks


Matthew


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Re: Misconduct

[Jonathan WRIGHT]

On 17/01/2024 09:40, Reinhard Kleeberg wrote:
> "Automated mineralogy"

Dear Colleagues,

It sounds like there crisis for this community? I didn't see anyone mention the 
AI story that was also in the news:


https://www.chemistryworld.com/news/new-analysis-raises-doubts-over-autonomous-labs-materials-discoveries/4018791.article

https://chemrxiv.org/engage/chemrxiv/article-details/65957d349138d231611ad8f7

Perhaps there is still a lot of interesting work to be done on methods?

With best regards,

Jon
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FPSM : (was Re: [EXT] [External] Re: Step-like basline)

[Jonathan WRIGHT]

Hi Luca,

Thanks for sharing the links to your method - I hope we can try it the next time 
we get stuck on identification.


It is a shame to hear you were delayed for so long by J.Appl.Cryst. Did they ask 
 you to cite some work from the Glasgow group as the commercial competitor? I 
have in mind that they were looking at measured profiles too 
(https://doi.org/10.1107/S002188980400038X, 
https://doi.org/10.1107/S0021889804011847).


Indeed I had overlooked your paper, so perhaps this list is still one of the 
better ways to reach some parts of the powder diffraction community!


With best regards,

Jon



On 06/09/2023 18:52, Luca Lutterotti wrote:
I am glad you find FPSM an inspiring idea, me and my co-workers will be quite 
happy if this will results in some citations. The FPSM publication back in 2019 
was a troubled submission. It took us more than 3 years as initially was just 
rejected (for economical reasons, as it would be unfair against the traditional 
search-match software developed by companies; you read it right, that was the 
reason for rejection by the reviewer and the editor accepted it even if the 
other reviewer was for accepting it as it is). We had some discussion, but no 
way. Then we tried to change journal (www were hesitant as it would have had 
much less visibility on the powder diffraction community) but finally Daniel 
discussed with another editor of the same journal and we re-submitted and got 
some fair reviewers. But it was long and the first rejection a bit shocking. I 
thought before you have to reject for scientific reasons…….


Now I am learning that not only at the academic level, but also some companies 
selling search-match software are including what they call WPF search-match, but 
no one cite the origin of the idea. I hope I don’t get a second 
Loopstra-Rietveld case….. ;-) Well in my case I wrote the software before 
publishing the idea.
That software was re-written from scratch to optimise for the speed and the 
method. That’s why we can work with several thousand structures at the same 
speed the other softwares work on less than hundreds. I did not use Maud for 
that in fact.


But I want you to know that the last version I developed on a recent EU project 
(not the one online), works also with turbostratic and modulated clay structures 
using your model (the Ufer et al.) to simulate them in the Rietveld. It is a 
fantastic trick that I use for texture analysis but also quantification and now 
in FPSM. Having a quick Rietveld help to search-match samples containing clays 
using data even at high angles (more than 60 degs). I indeed don’t pre-calculate 
and store structures because when you work with many of them it takes more time 
to load all the precalculations from a database (even the speedy ones) than to 
re-calculate everything.


So I am glad we both made use of each other models/ideas!

Best regards,

Luca


logo_unitrento_firma.png

*
Luca Lutterotti*
Dipartimento di Ingegneria Industriale
Università di Trento
via Sommarive, 9 - 38123 Trento (Italy)
tel. +39 0461 2824-14 (Office), -34 (X-Ray lab)


ico_fb_32x32.pngico_twitter_32x32.pngico_insta_32x32.pngico_linkedin_32x32.pngico_youtube_32x32.png

Maud: http://maud.radiographema.com 



On 5 Sep 2023, at 13:49, Reinhard Kleeberg  
wrote:


Dear Luca,
I completely agree and will be very happy to have a 1D detector with 
sufficient energy resolution to resolve a "pure" Cu Kalpha1/2 doublet from W 
Lalpha1. This would make routine work much easier. IMHO, the biggest 
improvements in XRPD instrumentation within the last decades came solely from 
the detector side, should be continued.


Regarding search-match by Rietveld: Your FSPM method is a very inspiring idea. 
Nicola Doebelin has incorporated a simplified approach in PROFEX, too:
https://www.youtube.com/watch?v=Oqj71TiifeI 



I'm routinely applying a run of ~500 structures/minerals what we are commonly 
using (+- the former QPA database of Seifert AUTOQUAN or from the BGMN 
webpage) for a phase screening of unknown samples, needs ~ 5 min without 
interaction. Than running QPA refinement with the best matching structures, 
clicking on remaining peaks in the difference plot for getting a proposal of 
best matching main line positions in the database, and adding these 
structure(s) to the refinement, running again... This is a typical workflow in 
our lab, no need for peak search, background treatment, thinking about 
artifact peaks...


Best regards

Reinhard

Zitat von Luca Lutterotti >:



Dear Reinhard and Rietvelders,

It is always a compromise. Ideally we would like the fastest instrument with 
a lot of intensity (so, 1D or 2D detectors) but no lines outside the Kalpha 
or even just the Kapha1 like the one of James Cline. But this means a 
monochromator on the incident beam and you get fluorescence background. Now I 

Re: scattering factor for O2- ?

[Jonathan WRIGHT]

Hi Matthew,

About the form factors : there is an active community doing "Quantum 
Crystallography" or charge density analysis with the IUCr. Some of them have 
been running a nice series of online lectures recently:


https://qcrwebinar.chem.uw.edu.pl/

You can find many experts there, and there are also recordings on youtube. For 
Al2O3 there should be several charge density studies in the literature. 
Extinction is usually discussed, as well as f' and f" values. More accurate data 
is a continuing need for that kind of work, so perhaps a combined refinement of 
powder and single crystal data can be interesting.


For Al2O3: this paper (https://doi.org/10.1107/S0567739482001478) gives Al:1.32+ 
and O:0.88-. You can probably find other numbers in the literature.


Best,

Jon




On 22/02/2023 04:14, Matthew Rowles wrote:

Warning, anecdote ahead! (and this wasn't the point of my original post...)

I get better (flatter difference plot) fits with SRM676A using charged atoms 
(Al+3, O-2) than I do with neutral. (Co Ka, lab BB diffractometer)
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Re: NIST SRM656 Analysis

[Jonathan WRIGHT]

Maybe a silly question: are you assuming you have the data on an absolute scale 
in order to do these calculations? Do things like surface roughness somehow not 
matter?


Best

Jon




On 13/04/2022 11:56, Matthew Rowles wrote:

Thanks Tony

When I add the absorption edge correction to the silicon nitride model (and add 
beta-silicon nitride), it becomes -2.8 wt% amorphous; up a little due to the 
added correction and down a little due to the extra phase.


If I change your al-SN thermals from 1 to those given in ICSD 77811, I get +4.8 
wt% amorphous. Your atoms were already neutral, so I left them as-is.


If I make all the Si-nitride phases' thermal parameters == 0, then I can get up 
to 8.5 wt% amorphous.


In all of this, corundum is staying as charged atoms, with Al and O beqs fixed 
at 0.334 and 0.278.


I'll have to have a go at applying the absorption edge correction; I always 
forget which parameter is which thing and have to rederive my understanding of 
it everytime...



Thanks

Matthew

On Wed, 13 Apr 2022 at 13:58, iangie mailto:ian...@126.com>> 
wrote:

Dear Matthew,

I tried your data and get ~-1% amorphous. My .pro is in below link.

https://www.dropbox.com/s/xuw13c91l9gq5m5/ROW.pro?dl=0


I normally do not refine Beq, which I believe gives biggest source of error
in QPA...


Cheers!

--

*Dr. Xiaodong (Tony) Wang*
*Senior Research Infrastructure Specialist (XRD)*
Central Analytical Research Facility (CARF)   |  Queensland University of
Technology
*Address:* Level 6, P Block, Gardens Point campus, 2 George St Brisbane QLD 
4000
*Tel:*+61 7 3138 1904  | *Mob:*0452 571 680
*Email:* tony .
w...@qut.edu.au
   | *Web:* www.qut.edu.au/ife/carf



At 2022-04-13 13:00:44, "Matthew Rowles" mailto:rowle...@gmail.com>> wrote:

Hi all

Thanks to those that have replied off-list.

I've managed to jiggle things around and get various answers. If you
want an answer between -14 and +6 wt% amorphous, I can make it happen. I
can either use charged atoms or not, or use thermal parameters or not.
Combining those between the corundum and Si3N4, you get the following:


image.png
This is using the scattering factors defined with 11 gaussians.

If you use the ones defined by 9 gaussians, you get
image.png

The structures I used are below. In the certificate for 656, the
structures are referenced, but those structures have no thermal
parameters. Does anyone know what was used in the NIST determination?



phase_name "Aluminium_oxide_alpha_10425_icsd"
Hexagonal( 4.759355, 12.99231)
space_group "R -3 c H"
site Al1 num_posns  12x 0      y 0 z 0.14772 occ Al+3 1. beq  0.318
site O1  num_posns  18x 0.3064 y 0 z 0.25    occ O-2  1. beq  0.334

phase_name "ALPHA_Marchand_ICSD_26191"
Hexagonal( 7.75411, 5.62034)
space_group "P31c" 'atom positions from Marchand. Thermals from ICSD 
77811
site Si1 num_posns  6x 0.0806 y 0.5095 z 0.3020 occ Si+4 1   beq 0.25
site Si2 num_posns  6x 0.1675 y 0.2560 z 0.0070 occ Si+4 1   beq 0.29
site N1  num_posns  2x 0      y 0      z 0      occ N    1.  beq 0.88
site N2  num_posns  2x =1/3;  y =2/3;  z 0.3500 occ N    1.  beq 0.46
site N3  num_posns  6x 0.0390 y 0.3860 z 0.0310 occ N    1.  beq 1.06
site N4  num_posns  6x 0.3190 y 0.3210 z 0.2660 occ N    1.  beq 0.17

phase_name "BETA_Billy_ICSD_35566"
Hexagonal( 7.60633, 2.90778)
space_group "P 63/m" ' structure from Billy, thermals from ICSD 170004
site Si1 num_posns  6x 0.2323 y 0.4096 z 0.25 occ Si+4   1  beq 0.231
site N1  num_posns  2x =1/3;  y =2/3;  z 0.25 occ N      1  beq 0.326
site N2  num_posns  6x 0.3337 y 0.0323 z 0.25 occ N      1  beq 0.314






On Tue, 12 Apr 2022 at 17:13, Matthew Rowles mailto:rowle...@gmail.com>> wrote:

Hi all

I've collected some more data, and am still getting spurious
results, and by spurious, I mean -5 wt% amorphous in SRM-alpha-656
when quantified by the external method against SRM 676a.

We had some SRM-656alpha (couldn't find any of the beta) stored in a
drying oven, and some SRM676a stored in a cupboard. I collected some
data using a D8 with Ni-filtered Cu and a lynx-eye detector (0.25°
fixed divergence, 250 mm radius, 2x2.5° sollers). The patterns were
collected consecutively (using the same program), with a single peak
from SRM1976 (b, I think), acting as an intensity calibrant (the
intensity didn't appreciably change), 

Re: Computing code for hkl generation

[Jonathan WRIGHT]

Dear Martin,

In addition to the other replies:


I am currently looking for a Python


xfab does this, see:

https://github.com/FABLE-3DXRD/xfab/blob/fd3015dbd4145daf6a471765887c3aa139eb8bab/xfab/tools.py#L1039


  or C/C++ module


sginfo (https://github.com/rwgk/sginfo) offers a "simple_hkllist" option.

Best,

Jon


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Re: Software re-binned PD data

[Jonathan WRIGHT]

If this rule is broken, such as the mode in 
FIT2D that smooths patterns by pixel-splitting) then one introduces 
correlation between points in the pattern 


Hi Brian, your comment has triggered me it seems :-)

For SAXS and PDF it could be better to under-sample the data (see end), 
but for profile fitting I find this story is causing more headaches than 
it solves. Splitting pixels was (and still is?) a pragmatic way to 
address the following:


- To fit peak positions and widths for strain you need >3 points within 
the FWHM. Output bins may be required as smaller than pixel sizes.


- Detector pixels may fall halfway between two output bins, so which 
output bin should they go into? If a bunch of pixels "jump" from one bin 
to another suddenly, so do your results. Your colleague, with a tiny 
change in calibration, might get wildly different answers to you.


Fitting the (raw) 2D images also overcomes that but runs into other 
problems: what are the weights for pixels with zero counts? Binning 
makes it is easier to look at a fit with ~5 points within a FWHM 
compared to 5000. Note that pixel splitting convolutes the pixel (or 
bin) shapes into the final peak shape, so you come out with broader and 
smoother peaks that tend to be more robust to numerical issues.


Serial correlation in the final fit remains a problem whether you split 
pixels or not, from a long time ago, e.g.:


Berar and Lelann: J. Appl. Cryst. (1991). 24, 1-5
https://doi.org/10.1107/S0021889890008391

Note that pixels from some detectors do not arrive as statistically 
independent quantities anyway. When spatial corrections have been done 
for you the patterns are obvious, but less so when a single X-ray photon 
is spread over several CCD pixels.


Is someone aware of a Rietveld example where "not splitting is better" 
while keeping the same bin size? I see the point for statistical 
analysis of the noise in SAXS and PDF data, but I do not get it when 
fitting strong peaks where the signal is greater than the noise level 
anyway. The reality for a lot of 2D detector data is that you counted 
way too many photons. Systematic errors in the fit are much larger than 
the statistical noise anyway.


Best,

Jon
===

PS: The SAXS argument against splitting pixels is here:
"Correlation Map, a goodness-of-fit test for one-dimensional X-ray 
scattering spectra"

Daniel Franke, Cy M Jeffries & Dmitri I Svergun
Nature Methods 12, 419–422 (2015)
https://doi.org/10.1038/nmeth.3358

The PDF case is here:
"On the estimation of statistical uncertainties on powder diffraction 
and small-angle scattering data from two-dimensional X-ray detectors"

X. Yang, P. Juhás and S. J. L. Billinge
J. Appl. Cryst. (2014). 47, 1273-1283
https://doi.org/10.1107/S1600576714010516

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Re: Literature on Rietveld limitations in nano materials

[Jonathan WRIGHT]

Hello,

I think it would be nice if I could cite some critical discussion, or 


There are a couple of comments in the current issue of J.Appl.Cryst that 
might be interesting for you:


https://doi.org/10.1107/S1600576719006575

Best,

Jon

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Something to read...

[Jonathan Wright]

Probably of interest to several readers here, a new paper on 
methodology:


"Use of Bayesian Inference in Crystallographic Structure Refinement via 
Full Diffraction Profile Analysis"
Chris M. Fancher, Zhen Han, Igor Levin, Katharine Page, Brian J. Reich, 
Ralph C. Smith, Alyson G. Wilson & Jacob L. Jones

Sci. Rep. 6, 31625
http://www.nature.com/articles/srep31625



Best,

Jon




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3D whole pattern fits for SFX data

[Jonathan WRIGHT]

3D whole pattern fitting has arrived:

http://dx.doi.org/10.1107/S2052252516001238

... and the samples are powders!



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Re: R: Re: synchrotron beamline info

[Jonathan WRIGHT]

Dear Natale

A good quality powder pattern starts with a good quality powder. Using a 
2D area detector is probably easier than trying to align a small sample 
on a Gandolfi spinner, to increase grain statistics. Also a lower 
resolution instrument will have fewer problems for grain averaging. With 
a 0.1x0.1x0.1 mm sample volume it can be very difficult to find the 
sample again after crushing it, assuming it has not transformed during 
crushing.


The following paper has nice examples when the sample was not crushed:

Application of synchrotron through-the-substrate microdiffraction to 
crystals in polished thin sections. J. Rius, O. Vallcorba, C. Frontera, 
I. Peral, A. Crespi and C. Miravitlles

IUCrJ (2015) 2, 452-463
http://dx.doi.org/10.1107/S2052252515007794

It was done in ALBA at the MSPD beamline.

We have some practice with the 3DXRD technique at the ID11 beamline at 
the ESRF, see:


Sørensen, H. O., Schmidt, S., Wright, J. P., Vaughan, G. B. M., Techert, 
S., Garman, E. F., Oddershede, J., Davaasambuu, J., Paithankar, K. S., 
Gundlach, C.  Poulsen, H. F. (2012). Z. Kristallogr. 227, 63–78.

http://dx.doi.org/10.1524/zkri.2012.1438

This approach might be useful to characterize your sample, but it is not 
the Rietveld method. Another approach would be diffraction tomography 
(XRD-CT), which has a Rietveld based variant:


J. Appl. Cryst. (2011). 44, -1119[ doi:10.1107/S0021889811024423 ]
Hard X-ray diffraction scanning tomography with sub-micrometre spatial 
resolution: application to an annealed [gamma]-U0.85Mo0.15 particle

H. Palancher, R. Tucoulou, P. Bleuet, A. Bonnin, E. Welcomme and P. Cloetens

... or a crystal indexing based variant:

Impurity precipitation in atomized particles evidenced by nano x-ray 
diffraction computed tomography ,  Anne Bonnin, Jonathan P. Wright, Rémi 
Tucoulou and Hervé Palancher

Appl. Phys. Lett. 105, 084103 (2014); http://dx.doi.org/10.1063/1.4894009

Obviously I am picking the citations closest to home. Most of these 
approaches should be available in most of the x-ray synchrotrons in 
Europe. For ESRF the next applications deadline is the 10th September. 
Plenty of time to try to measure it on Simon's 4-circle before then :-)


Best,

Jon




On 29/07/2015 14:10, Natale Perchiazzi wrote:

Hola Miguel,
A Gandolfi like setup would be definitely easier. I guess you suggest 
alternatevely to crush and dilute the material in a matrix? !

Cheers Natale

Inviato da Yahoo Mail su Android 
https://overview.mail.yahoo.com/mobile/?.src=Android



*Da*:GREGORKIEWITZ MICHAEL michael.gregorkiew...@unisi.it
*Data*:Mer, 29 Lug, 2015 alle 12:16
*Oggetto*:Re: synchrotron beamline info

Dear Natale,

do you think about a Gandolfi like setup? Or can the fragments be
crushed?

best

Miguel


---
michele gregorkiewitz
Dip Scienze Fisiche, della Terra e dell'Ambiente
Università di Siena
via Laterina 8, I-53100 Siena
gre...@unisi.it javascript:return, +39'0577'233810


Il 2015-07-29 11:33 Natale Perchiazzi ha scritto:
 Dear All,
 I would need to get good quality powder pattern, suitable for Rietveld
 analysys, working on mineral microcrystalline fragments with
 dimensions around 0.1-0.2 mm. From your experience, which could be an
 European synchrotron beamline with a suitable experimental setup to
 get these data?
 best regards Natale Perchiazzi



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Re: source of diamond powder for internal standard

[Jonathan WRIGHT]

Hello

In the reference below they say they purchased 2-4 micron grain size 
from Nilaco (perhaps it was:
http://nilaco.jp/en/order.php?DIR=CHEMIMENU=15CODE=FROM=14ITEM1=Diamond_PowderITEM2=Powder). 



/J. Synchrotron Rad./(2014).*21*, 
119-126[doi:10.1107/S1600577513028269 
http://dx.doi.org/10.1107/S1600577513028269]



 Model-independent structure factors from powder X-ray diffraction:
 a novel approach


 T. Straasø
 
http://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Straas%26oslash;,%20T.,A.-C.
 Dippel
 
http://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Dippel,%20A.-C.,J.
 Becker
 
http://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Becker,%20J.andJ.
 Als-Nielsen
 
http://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Als-Nielsen,%20J.

*Abstract:*Under the experimental condition that all Bragg peaks in a 
powder X-ray diffraction (PXRD) pattern have the same shape, one can 
readily obtain the Bragg intensities without fitting any parameters. 
This condition is fulfilled at the P02.1 beamline at PETRA III using the 
seventh harmonic from a 23 mm-period undulator (60 keV) at a distance of 
65 m. For grain sizes of the order of 1 µm, the Bragg peak shape in the 
PXRD is entirely determined by the diameter of the capillary containing 
the powder sample and the pixel size of the image plate detector, and 
consequently it is independent of the scattering angle. As an example, a 
diamond powder has been chosen and structure factors derived which are 
in accordance with those calculated from density functional theory 
methods of the/WIEN2k/package to within an accuracy that allows a 
detailed electron density analysis.



Best,

Jon


On 19/06/2015 09:10, Tony Raftery wrote:


Anyone,

Can someone tell me where to source diamond for use as internal standard.

It needs to be ‘ideal’ – small particle size ( 1um would be good), 
narrow particle size distribution, elementally pure (which precludes 
most ‘natural’ diamond),  fully crystalline (or near so).


Please contact me directly though there are others who may be interested.

regards,

Tony Raftery

*Tony Raftery*|  Laboratory Manager – X-ray  Particles Laboratory
*Central Analytical Research Facility (IFE)**| Queensland University 
of Technology*


P Block Podium, Level 6, Room P-628, Gardens Point Campus
*ph* 3138 5122 | *fax* 3138 4438 | *mobile* 0481 008 595 *email* 
a.raft...@qut.edu.au mailto:a.raft...@qut.edu.au

CRICOS No 00213J



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Re: Anomalous scattering factor and Dispersion coefficients

[Jonathan WRIGHT]

Dear Xiaodong, Jeremy,

Isn't it equation 3 here?
http://www.nist.gov/srd/upload/jpcrd488.pdf
f1/f2 are dispersion numbers and f'/f are the anomalous ones. The 
relativisitic correction number for iron then shows up on page 221.


Best,

Jon
===

On 11/06/2015 17:27, Jeremy Karl Cockcroft wrote:

Hi Xiaodong,
I think that the numbers quoted for f' in the second case have had 26e 
(atomic no.) added to them, i.e. it refers to the total dispersion 
value for the real component (as opposed to the imaginary component). 
Given that the numbers quoted are close to an absorption edge, then 
the remaining differences are not unexpected depending on source and 
precise energy quoted. If graphs of the data are plotted with Z 
subtracted, then they look very similar apart from the precise value 
of the minimum of f' at the absorption edge itself.

Just my thoughts on it...
Jeremy Karl.
***
Dr Jeremy Karl Cockcroft
Department of Chemistry
(University College London)
Christopher Ingold Laboratories
20 Gordon Street
London WC1H 0AJ
United Kingdom
+44 (0) 20 7679 1004 (laboratory)
j.k.cockcr...@ucl.ac.uk mailto:j.k.cockcr...@ucl.ac.uk or 
jeremyk...@gmail.com mailto:jeremyk...@gmail.com

http://img.chem.ucl.ac.uk/www/cockcroft/homepage.htm
***


On 11 June 2015 at 15:33, iangie ian...@126.com 
mailto:ian...@126.com wrote:


Dear Rietvelders,

I am little confused about the term Anomalous scattering factor
and Dispersion coefficients.
Anomalous scattering factor can be found here
http://skuld.bmsc.washington.edu/scatter/AS_form.html
Dispersion coefficients can be found here
http://www.cxro.lbl.gov/optical_constants/asf.html

Their numbers are quite different: e.g. Fe @ CrKα: f0=18.474,
Δf'=-1.6 Δf=0.9 ; however, the corresponding dispersion
coefficients are f' ~24.6808 and f ~0.759346
Can anyone explain their relationship?

Thanks!
--
Yours Sincerely,
Dr. Xiaodong(Tony) Wang
XRD Application Scientist
Bruker Singapore Pte. Ltd.

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++

Re: Powder Diffraction Discussion Group on Facebook

[Jonathan WRIGHT]

Thanks Davide for this useful initiative, I have joined. I don't doubt 
the value of the Rietveld list but pictures are also useful.


It was recently bought to my attention that funding may be related to 
public perceptions of research and for this reason we should pay 
attention to things like twitter. CERN have made a nice campaign 
recently with #RestartLHC and #13TeV. If you want to, you can read 
tweets about powder diffraction already:


 http://twitter.com/icddicdd/status/607995709426647040

... or find a nice job:

http://twitter.com/JobborseDE/status/603031335234576384

The signal to noise ratio on twitter can be surprisingly good when 
following people like @MikeGlazer1 or @HelliwellJohn. If you don't want 
to read those things then that is fine too, at least none of it comes 
into your inbox.


Cheers,

Jon

( @jonwright76 )


On 08/06/2015 09:24, davide levy wrote:


Good Morning
I created the Powder Diffraction Discussion Group on Facebook, to 
speak about powder diffraction, Rietveld etc..  open for all use 
powder diffraction.

https://www.facebook.com/groups/1087352967946225/
Davide



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++

bookmarks: Re: Powder Diffraction Discussion Group on Facebook

[Jonathan WRIGHT]

   Powder Diffraction Discussion Group on facebook
   http://www.facebook.com/groups/1087352967946225/


 So from what I gather we have:

http://www.xrayforum.co.uk
http://www.reddit.com/r/crystallography
http://www.researchgate.net/topic/x-ray_diffraction


There are many other places where crystallographers can gather:

Various LinkedIn groups:
http://www.linkedin.com/grp/home?gid=6966339
http://www.linkedin.com/grp/home?gid=3614857
http://www.linkedin.com/grp/home?gid=927967
http://www.linkedin.com/grp/home?gid=2683600
http://www.linkedin.com/grp/home?gid=4210959
http://www.linkedin.com/grp/home?gid=4324676
http://www.linkedin.com/grp/home?gid=4599287

usenet sci.techniques.xtallography (mostly abandoned)
http://groups.google.com/forum/#!forum/sci.techniques.xtallography

ccp4 list (high traffic, mostly protein crystallography):
http://www.ccp4.ac.uk/ccp4bb.php

(private) Rigaku Oxford Diffraction Forum, good for small molecule 
single crystal stuff:

http://www.rigakuxrayforum.com/index.php

(login needed) Topas Forum:
http://topas.dur.ac.uk/topaswiki/doku.php

GSAS-II list:
http://mailman.aps.anl.gov/mailman/listinfo/GSAS-II

Did the sdpd list die off from yahoo groups or did I unsubscribe? It 
seems to have evaporated. Anyway, the 140 character limit from twitter 
might not be a bad thing.


Jon

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++

3D powder averaging...

[Jonathan Wright]

On 2015-05-10 17:36, Alan Hewat wrote:

Jon... nicely illustrated... by posting an interesting link...


Thanks! Obviously I think these serial methods are a fantastic 
opportunity for this community. An IUCrJ commentary by me is here:


Serial crystallography for the masses: 
http://journals.iucr.org/m/issues/2015/01/00/hi0136/index.html


...which is all about a paper showing that unbelievably weak and noisy 
data can be merged into a 3D dataset.


An open question is: will the new community of people developing these 
3D methods ever show up on this list? In principle Rietveld methods and 
powder experts should have a lot to offer, but until now it seems to be 
mostly protein crystallographers who are getting the beamtime at the 
FEL.


Would point-by-point Rietveld refinement extend to scaling and fitting 
all the snapshots? The profile function comes in as where you think each 
intensity was on the rocking curve.



Actually I think Jon was being a little snarky himself. ...


Not entirely*, if I wanted to 'wind you up' I'd have linked something 
from electron microscopy :-) This one just came out:


http://news.sciencemag.org/biology/2015/05/electron-microscopes-close-imaging-individual-atoms

Obviously powder diffraction has a rich and exciting future, especially 
when it is used as an imaging method. Google finds this one for Rietveld 
tomography:


J. Appl. Cryst. (2011). 44, -1119[ doi:10.1107/S0021889811024423 
] Hard X-ray diffraction scanning tomography with sub-micrometre 
spatial resolution: application to an annealed [gamma]-U0.85Mo0.15 
particle H. Palancher, R. Tucoulou, P. Bleuet, A. Bonnin, E. Welcomme 
and P. Cloetens


There are always exciting future directions. Doubtless others will 
respond with what is new and exciting with neutrons and PDF's, etc. 
(yes, that is a challenge).


Choosing to single out individual publications for public abuse on a 
mailing list is a bit of a shame. If you write a comment on the 
authors get a fair chance to respond (and privately tear you apart if 
you're wrong). If your comment survives then future readers of the paper 
will be informed, which does not happen when something is posted here. 
Highlighting things which _are_ worth reading is something I always 
appreciated from Armel's contributions to the list over the years.


All the best,

Jon
===

* 
http://www.buzzfeed.com/lukelewis/what-british-people-say-versus-what-they-mean


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++

Re: Intensity issue with synchrotron data

[Jonathan WRIGHT]

On 15/01/2015 12:15, Norberto Masciocchi wrote:

Il 15/01/2015 11:46, Fauth Francois ha scritto:


1- the  data format of the input file your are using for your 
refinement does not allow counts more than 10^6, This is typically 
the case  with GSAS  input file format
Here at ALBA, as you suggested, we divide all the intensities by 
factor 10

and..what you do with the errors for weighing the observations?


At some point you can stop caring about the counting statistics error: 
with 1e7 counts it is around 0.03 %. This is far beyond the precision of 
a crystallographic model containing spherical atoms. The remaining 
misfit should be mostly due to systematic errors :-)


Best,

Jon
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++

Re: Statistics on semi-quantitative XRD data

[Jonathan WRIGHT]

Dear James,

I'm not sure these are quite what you are after, but I'm suggesting them 
anyway. There were several papers from Gordon Barr about non-parametric 
methods:



SNAP-1D: a computer program for qualitative and quantitative powder 
diffraction pattern analysis using the full pattern profile

Barr, G., Gilmore, C. J., Paisley, J., J. Appl. Cryst. (2004). 37, 665–668

A longer reading list is here: 
http://www2.chem.gla.ac.uk/snap/PolySNAP_index.html


You can find similar functionality in the panalytical software:

The HighScore suite Thomas Degen, Mustapha Sadki, Egbert Bron, Uwe 
König and Gwilherm Nénert. Powder Diffraction, 
http://dx.doi.org/10.1017/S0885715614000840


A related development would be XRD-CT. This is computed tomography via 
powder diffraction by raster scanning a small beam across a large 
sample (and rotating).


J. Appl. Cryst. (2014). 47, 1107-1117[ doi:10.1107/S1600576714008218 ]
XRDUA: crystalline phase distribution maps by two-dimensional scanning 
and tomographic (micro) X-ray powder diffraction

W. De Nolf, F. Vanmeert and K. Janssens

It seems that the colours in resulting pictures are semi-quantitative, 
but perhaps not in the sense you had in mind.


All the best,

Jon


On 13/11/2014 18:53, James Talbot wrote:

Hello All,

I had the following request from a client:

I am looking for examples of statistics used on semi-quantitative 
data, i.e. comparing XRD results of multiple samples.  Do you have any 
recommendations or know of any papers that clearly explain their 
statistical methods?  In so many papers, it is glossed over.  I have a 
pretty good handle on my stats, but would prefer to see what other 
have done with XRD datasets.


Can anyone help with this.?  I do not know of any of the top of my head.

Thanks in advance,
James Talbot


K-T GeoServices, Inc.
970-641-1235 (office)
940-597-9076 (mobile)
219 North Iowa Street, Unit J
Gunnison  CO  81230-2479
www.ktgeo.com


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++

Re: Stacking faults and antiphase boundary

[Jonathan WRIGHT]

On 06/04/2014 08:06, Leonid Solovyov wrote:

The faulting model in DDM gives nearly perfect agreement with the experiment:
http://sites.google.com/site/ddmsuite/home/Copper-DDM.png



It looks a little bit reminiscent of this pattern for ice:

http://www.science24.com/paper/15441

...but the little step at about 40.5 degrees doesn't seem to be in the 
model? Isn't that coming from some sort of defects or diffuse 
scattering? Not that I would attempt to model something like that, but a 
1D rod in 3D reciprocal space (coming from 2D defects) gives step-like 
profiles in a 1D powder pattern. Although you generally only know that 
if you've also got data from a single crystal :-)


Cheers,

Jon

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++

Re: Polarization factor por Ge (111) monochromator

[Jonathan WRIGHT]

Jools,

To get the value more directly I think you can also measure the 
scattering at two theta of 90 degrees in the horizontal versus vertical 
plane. We did this last week at the synchrotron in the course of making 
some detector correction files and there was a nice hole in the 
diffraction patterns in the horizontal due to the polarisation. If you 
set up the right experiment it should be very obvious what the 
polarisation is and not at all mysterious.


Cheers,

Jon





On 07/04/2014 22:48, Julian R Tolchard wrote:

I seem to have opened up a can of worms here. Sorry about that.

So in summary:

1. Easiest option is to use a value of 0 and accept that thermal
parameters will be a bit wrong 2. Second easiest option is to measure
a well characterized standard and refine the polarization. 3. Harder
option is to hire a clever physicist to model the system and
calculate a value via ray-tracing?

It strikes me as a little surprising that we are all buying these,
but the associated corrections are not well documented...


jools


 From: Whitfield, Pamela S.
[whitfiel...@ornl.gov] Sent: 07 April 2014 21:31 To: Artem Babaryk
Cc: Julian R Tolchard; rietveld_l@ill.fr Subject: RE: Re[4]:
Polarization factor por Ge (111) monochromator

If you want some REALLY ancient history try this one...

http://www.mail-archive.com/rietveld_l%40ill.fr/msg01654.html

The email from Nicolae is perfectly correct and I don't think anyone
would argue with it for monochromators. The formulae themselves
should be just as applicable to mirrors and summing all the effects
from differing diffracting angles of the mirror should give a decent
average but there are some devils in the details. Consider a flat
plate experiment with a parallel mirror. Different parts of the
sample will be hit by X-rays that have been diffracted by different
angles off the mirror due to the construction. If the diffracted beam
isn't 'averaged'/collapsed by using a secondary optic/0D detector
does it make a difference? Makes for an interesting puzzle?

Pam


-Original Message- From: Artem Babaryk
[mailto:baba...@bigmir.net] Sent: Monday, 07 April, 2014 3:14 PM To:
Whitfield, Pamela S. Cc: Julian R Tolchard; rietveld_l@ill.fr
Subject: Re[4]: Polarization factor por Ge (111) monochromator

Hi everybody,

Nobody is trying to be prickly (at all)!

The topic has been started with particular case for Panalytical
machines, and, again, a 'minute quote' from archive: This is obtain
from the help of X'Pert HighScore Plus... As the first instance
question is so the same kind of answer is coming...

And I would never made a feedback if I was not curious to the topic
too. I remember following branch clearly:
http://www.mail-archive.com/rietveld_l%40ill.fr/msg04948.html And to
be really pricky and boring=), see
http://www.mail-archive.com/rietveld_l%40ill.fr/msg04979.html

That makes me think again that there is nothing new under the sun...

Between, I like to send postcards=)

Cheers, Artem


07.04.2014 19:00, Whitfield, Pamela S.whitfiel...@ornl.gov

Now, now no need to be prickly

To be fair to Julian he didn't ask what the polarization was - he
asked how it was calculated. Given that Goebel mirrors are graded
multilayers (i.e. not a fixed diffracting angle) it's a fair
question and one I asked myself in 2001. As the 'minute quote'
demonstrates with the lack of d-spacing, etc, the value of 0.999
seems to have been picked from thin air

The experimental (as opposed to theoretical) methodology for
determining polarization was posted on the CCP14 website many
moons ago by Bob Von Dreele
http://www.ccp14.ac.uk/solution/gsas/graphite_monochromator_and_gsas.h



tml


I also used the same sort of methodology for a focusing mirror.
That requires a little bit of lateral thinking to cancel out the
effect of capillary absorption - answers on a postcard!

Pam

-Original Message- From: rietveld_l-requ...@ill.fr
[mailto:rietveld_l-requ...@ill.fr] On Behalf Of Artem Babaryk Sent:
Sunday, 06 April, 2014 4:21 PM To: Julian R Tolchard Cc:
rietveld_l@ill.fr Subject: Re[2]: Polarization factor por Ge (111)
monochromator

Dear Julian,

Here is a minute quote following the link to the excerpt from the
Rielveld Mailing list archive I've posted below:

Monochromator Wavelength [Å] Material Reflection /d/-spacing [Å]
2/θ/_m [°] POL ... All mirrors All wavelengths - - - - 0.999  Just
be attentive...

Cheers, Artem

06.04.2014 23:00, Julian R Tolchardjulian.r.tolch...@ntnu.no

Whilst we are on the topic - is the polarization factor from a
Göbel mirror calculated the same way as for a mono?


 From:
rietveld_l-requ...@ill.fr [rietveld_l-requ...@ill.fr] on behalf
of Artem Babaryk [baba...@bigmir.net] Sent: 06 April 2014 20:56
To: Josu Friedrich Cc: rietveld_l@ill.fr Subject: Re:
Polarization factor por Ge (111) monochromator

Dear Josu,

Somethimes browsing the Rietveld list archive I'm strengthening

Re: Dollase Paper

[Jonathan WRIGHT]

On 21/03/2014 10:59, Norberto Masciocchi wrote:
...
 So, the question is:
 Is there any way do get around this problem (without resorting to
 spherical hamonics or to grind the specimen in a WC, SiC or BN mill)?


High energy X-rays or neutrons in transmission geometry would seem to help?

Best,

Jon

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++

Re: X-ray diffraction laboratory manager position

[Jonathan WRIGHT]

Did I click on the right link? The second point says:

Develop new experimental approaches and measurement routines as
required by a growing user base.

It doesn't sound so bad, unless the candidate can't think of any novel 
experimental techniques to invent.


Jon


On 05/12/2013 19:02, Cline, James Dr. wrote:

Here is a position that looks a lot like what could be described as a
lab technician (no science anyway) and yet they require a PhD???

How could anyone recommend a specialization in the powder diffraction
technique if this is all that is available?

I find this very disconcerting.

Jim


James P. Cline Materials Measurement Science Division National
Institute of Standards and Technology 100 Bureau Dr. stop 8520 [ B113
/ Bldg 217 ] Gaithersburg, MD 20899-8523USA jcl...@nist.gov (301)
975 5793 FAX (301) 975 5334

-Original Message- From: rietveld_l-requ...@ill.fr
[mailto:rietveld_l-requ...@ill.fr] On Behalf Of Suchomel, Matthew R.
Sent: Tuesday, December 03, 2013 7:56 PM To: rietveld_l@ill.fr
Subject: Fwd: X-ray diffraction laboratory manager position

Dear Colleagues

On behalf of Prof. Jacob Jones, I am passing along the link below for
an open position of X-ray diffraction laboratory manager position at
North Carolina State University which may be of interest to someone
in our community.

. X-ray diffraction laboratory manager:
https://jobs.ncsu.edu/postings/30892



On Nov 27, 2013, at 14:46 , Jacob Jones jljon...@ncsu.edu wrote:

The Analytical Instrumentation Facility (AIF) at North Carolina State
University  is now seeking to fill multiple staff and postdoctoral
positions in the areas of electron microscopy and X-ray diffraction.
Positions are detailed in the links provided below. We are looking to
hire as soon as possible, but our first priority is finding the best
candidates to fill these positions. Please forward this information
to those who may have an interest in applying.

. X-ray diffraction laboratory manager:
https://jobs.ncsu.edu/postings/30892

Regards,

Jacob L. Jones Associate Professor, Department of Materials Science
and Engineering Director, Analytical Instrumentation Facility North
Carolina State University Raleigh, NC Email: jacobjo...@ncsu.edu
Phone: 919-515-4557

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++

Re: rocking curve

[Jonathan WRIGHT]

With a 2D detector you see spots for grains and smooth peaks for 
texture. You can also observe a collection of grains which exhibit 
texture giving a non uniform spot density. Usually by grains people 
expect randomised changes in intensity with small orientation changes. 
For texture there is a smooth variation of intensity with orientation 
change.


Which is which depends on your beamsize and instrument resolution in 
comparison to your grain size, and also what is the rocking width of an 
individual grain.


Best,

Jon

On 25/10/2013 11:33, Angel L. Ortiz wrote:

Dear Collages:

I can understand  the difference in the form of the rocking curve for
the cases of textured and un-textured materials. However, I would like
to know if there is any way to discriminate between the possible cases
of texture or graininess using the rocking curve or a set of rocking
curves. Is any difference expected in both cases (texture and graininess)?

Regards

--

Angel L. Ortiz, PhD

Associate Professor (Reader)

Materials Science and Engineering

Department of Mechanical, Energy and Materials Engineering

University of Extremadura, Badajoz 06006, Spain

(34) 924289600 Ext:86726 (Phone)

(34) 924289601 (Fax)

http://materiales.unex.es/miembros/personal/al-ortiz/index.html

---

*De:*rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] *En
nombre de *Mikko Heikkilä
*Enviado el:* viernes, 25 de octubre de 2013 10:56
*Para:* 'Angel L. Ortiz'; Rietveld_l@ill.fr
*Asunto:* RE: rocking curve

Dear Prof. Ortiz and other colleagues,

that is a good question, I suppose I need to think that a bit more, but
here’s my quick feelings about that. Since I measure with point detector
I measure just a “slice” from the full diffractogram I would see with a
2D detector, so I will get wrong intensities or even miss some
reflections if the sample is textured or very grainy. If I see a
reflection, set two theta to that angle and do a rocking curve (or equal
omega scan), I will have a probability with respect to surface normal of
finding crystallites with that lattice spacing. If I get a peak, then I
have an oriented film. If it’s just constant background, I’d say the
crystallites causing that reflection are evenly distributed and there’s
no orientation, like in this case of mine. If I have a veeery low amount
of crystallites, well, I’m not sure what would happen. Since that
rocking curve is in any case a sum of intensities of reflecting
crystallites, I suppose very small amount of crystallites would cause
the rocking to fluctuate in some manner (although I don’t think I’ll
ever have that small amount of crystallites). Then again even for small
amount but oriented crystallites it would give a peak, if all are
oriented to same direction.

That’s my thoughts, please correct me if I’m totally mistaken with this.

BR,

Mikko

*From:*Angel L. Ortiz [mailto:alor...@unex.es]
*Sent:* 25. lokakuuta 2013 11:19
*To:* 'Mikko Heikkilä'; Rietveld_l@ill.fr mailto:Rietveld_l@ill.fr
*Subject:* rocking curve

Dear colleagues

How can one distinguish between texture and graininess using the rocking
curve?. Which would be the expected difference in the rocking curve in
each case? I am not clear on this.

Regards

--

Angel L. Ortiz, PhD

Associate Professor (Reader)

Materials Science and Engineering

Department of Mechanical, Energy and Materials Engineering

University of Extremadura, Badajoz 06006, Spain

(34) 924289600 Ext:86726 (Phone)

(34) 924289601 (Fax)

http://materiales.unex.es/miembros/personal/al-ortiz/index.html

---

*De:*rietveld_l-requ...@ill.fr mailto:rietveld_l-requ...@ill.fr
[mailto:rietveld_l-requ...@ill.fr] *En nombre de *Mikko Heikkilä
*Enviado el:* viernes, 25 de octubre de 2013 9:32
*Para:* Rietveld_l@ill.fr mailto:Rietveld_l@ill.fr
*Asunto:* phase id for Friday refreshment

Dear Rietvelders,

I decided to completely embarrass myself and ask you a simple phase
identification question. I’ve had some trouble in trying to figure out
what’s going on with one measurement done in our lab. The sample is a
~30nm film heat treated in air at 500C, composition is Ce:Sn in close to
1:1 ratio plus oxygen in addition to those. I can’t tell if there’s any
very light elements as we only have EDX data at the moment, and the
actual amount of O is still unclear due to 3-4nm of native SiO2 under
the sample and I don’t have any XPS/RBS/SIMS profile data yet. I can’t
find anything from our databases that would fit even remotely close to
the measured data. (we have ages old PDF2 but I’ve imported every CeOx,
SnOx and CexSnyOz structure I could find from latest ICSD). Indexing is
a bit frustrating as well since I can’t be sure if it’s a single phase,
and I don’t have too much experience with unknowns anyway.

The 

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

[Jonathan WRIGHT]

On 31/07/2013 03:07, Leonid Solovyov wrote:

...  There is a
widely scattered belief that restraints always improve not only the
restrained values, but also the “unrestrained” part of structure such as
intermolecular distances, orientations, planarity etc.


Apart from your word always, I certainly believe restraints can and 
should improve the unrestrained output from Rietveld refinements. A 
couple of points:


1) You should be checking whether the restraint target value is 
consistent with the experimental data by looking at whether it comes 
back at the end of the refinement. For example:


input restraint: C(sp3) to C(sp3) distance ~ 1.54
output distance: 1.54 - OK
output distance: 1.4x - Could it be sp2-sp2 or a wrong atom assignment?

An outlier in the fit to your restraints is just as much as a problem as 
an outlier in the fit to your data. You should be looking at the 
difference/esd, where the esd was also input.


2) If you are terribly worried what restraints are doing then you might 
like to look into Rfree statistics. It would be cool for them to make 
it into some mainstream Rietveld software 
(doi:10.1524/zkri.219.12.791.55857, or doi:10.1038/nature12070).


So, assuming your restraints are correct for your sample then you are 
adding information into your refinement. This causes the rest of the 
results to improve as you reduce the noise in the output.



...  The general
practice, however, consists in applying restraints in the cases of
highly biased reflection intensities and peak shape misfits when the
residuals are strongly correlated. In such cases restraints compensate
the influence of misfits on the restrained values at the expense of
their increased influence on the “unrestrained” part.


The restraints should improve the model, if they don't, see above. 
Getting one part of a model right makes it easier to find out what is 
missing to get the whole thing (about) right. If there are serious 
misfits this means there is some problem to be resolved. Likelihood 
methods can be useful at that point: again, it would be cool for those 
to be more widely available.


Structure refinement is not likely to work out if you can't fit the peak 
shape or have unidentified impurities or unfitted texture texture etc. 
The Rietveld video game is about solving those problems to get to learn 
something you didn't already know. It does not make sense to have the 
atomic positions soaking up systematic problems.


The problem of having jammed the wrong molecule into a unit cell can be 
identified by restraints which are violated. With rigid bodies it is 
more difficult to find out what the data are trying to tell you. Is this 
wrong molecule issue the problem you fear?


TL;DR: Garbage in garbage out. OK. What has that got to do with restraints?

Jon

++
Please do NOT attach files to the whole list alan.he...@neutronoptics.com
Send commands to lists...@ill.fr eg: HELP as the subject with no body text
++

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

[Jonathan WRIGHT]

On 31/07/2013 17:25, Leonid Solovyov wrote:

One can make everything OK simply by choosing an appropriate weight
of restraints. The uncertainty in the restraint's weight appropriateness
makes every restrained refinement a know how.


Likelihood and/or the free R-factor offer routes to choose restraint 
weights, see eg:


http://www-structmed.cimr.cam.ac.uk/Course/Likelihood/likelihood.html#restraints
http://people.cryst.bbk.ac.uk/~tickle/rfree/paper.html

Regardless of the weighting chosen, the weighted difference which comes 
back (per restraint) tells you what the data think about the restraint 
target value. This information could be deposited along with the fit to 
the powder data for all to see.


I'm not against constraints, but how do you go about validating somebody 
else's choice of rigid definition?


Cheers,

Jon

++
Please do NOT attach files to the whole list alan.he...@neutronoptics.com
Send commands to 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/
++

Re: PDF refinement pros and cons

[Jonathan Wright]

Hi Alan,

I also find it hard to understand the rationale behind this approach. 
G(r) can suffer from fourier truncation artifacts due to the finite q 
range of the data, but there seems to be no such limitation in a model. 
Isn't there a risk of fitting to truncation ripples with G(r)?


As for computational costs, Bricogne has explained this somewhat better 
than I can in section 1.3.4.4.4 (.5 and .7) of International Tables 
Volume B (reciprocal space). To paraphrase; when N.Nhkl is huge an FFT 
helps. The reciprocal space R factors (and gradients) can be found via 
an FFT of an electron density map with cost savings for large problems.


Not having a unit cell for liquids and amorphous materials does present 
a conceptual problem, which seems to need the Debye formula, see eg:


http://srs.dl.ac.uk/arch/dalai/Formula.html

It seems that function is mainly used for small angle scattering, where 
the q range is too small to make a pdf. The distance histogram method 
mentioned there also looks interesting for computational speeds.


Looking forwards to hearing some more opinions...

All the best,

Jon



AlanCoelho wrote:


HI all

Looking at the Pair Distribution Function and refinement I come away 
with the following:


Fitting in real space (directly to G(r)) should be equivalent to 
fitting to reciprocal space except for a difference in the cost 
function. Is this difference beneficial in any way. In other words 
does the radius of convergence increase or decrease.


The computational effort required to generate G(r) is proportional to 
N^2 where N is the number of atoms within the unit cell. The 
computational effort for generating F^2 scales by N.Nhkl where Nhkl is 
the number of observed reflections. Is there a speed benefit in 
generating G(r) - my guess is that it’s about the same. Note, 
generating G(r) by first calculating F and then performing a Fourier 
transform is not considered.


In generating the observed PDF there’s an attempt to remove 
instrumental and background effects. In reciprocal space these 
unwanted effects are implicitly considered. This seems a plus for the 
F^2 refinement.


From my simple understanding of the process, there seems to be good 
qualitative information in a G(r) pattern but can someone help in 
explaining the benefit of actually refining directly to G(r).


Cheers

Alan

Re: Goodness of fit criterion

[Jonathan Wright]

There can be some value in comparing S values for different models with 
the same data (eg ranking at least). A value much less than 1 (eg 1E-3) 
indicates that you lost an esd column (or scaling factor) somewhere in 
your data processing, and you should really try to find it again. Having 
S2 means the model could somehow be improved, but not necessarily 
during your lifetime, and perhaps without changing your conclusions 
significantly.


Are you having trouble with a referee? Putting the data and model in a 
powder CIF file for submission with the article might be better than 
worrying about fit statistics. Having access to the refinement gives a 
reviewer an opportunity to help...


Best,

Jon

Lubomir Smrcok wrote:

Hi,
S is, strictly speaking a valid criterion only under special 
conditions which are not fulfilled in Rietveld. My advice is to 
forget about the value of S and think of physics, i.e. bond distances, 
angles, occupancies and in favorite cases, also of displacement 
parameters.

Lubo


On Tue, 3 Jun 2008, Franz Werner wrote:


Dear Rietvelders

I've a basic question on the Rietveld agreement index S (goodness of 
fit) . In The Rietveld Method (ed. R.A. Young) it says in chapter 
1.4 An S value of 1.3 or less is usually considered to be quite 
satisfactory. An S value of 1.7, for example, probably is a warning 
that you should look further into the reasons and question the 
adequacy of your model. In the literature, however, papers are 
published quite frequently with considerably larger S values (I'm 
just looking at an Acta Cryst. B paper with S values between 6 and 8.5).


The question is now how strict has the 1.3 limit to be applied, what 
is the largest acceptable S value? How does one assess S1.7 and 
justify it to referees?


I should add that I'm not a follower of the R-value cult but think 
that the most important criterion is chemical and physical plausibility.


Thanks for your advice.

Franz Werner
--
Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen!
Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

Re: atomic displacement parameters (ADPs)?

[Jonathan Wright]

sisir ray wrote:
How does the atomic displacement parameters (ADPs) works in TOPAS 
Academic?
Typically adp is anisotropic displacement parameter, and describes 
the rugby ball shapes atoms get in ortep pictures.
Are / there any litrature on unn /atomic displacement parameters ? 
Thank you for your help.

I'd guess these are the Uij matrix elements. There is rich literature, eg:

http://crystal.tau.ac.il/xtal/finrep/index.html

http://crystal.tau.ac.il/xtal/finrep/node8.html


Best,

Jon

Re: Preferred orientation?

[Jonathan Wright]

Martin wrote:

PS For anyone interested in an explanation of texture vs. PO, see:
 
http://pd.chem.ucl.ac.uk/pdnn/inst1/texture1.htm

http://pd.chem.ucl.ac.uk/pdnn/inst1/texture2.htm


I disagree! The web page has confused texture with granularity. See:

http://en.wikipedia.org/wiki/Texture_(crystalline)

If you need a way to separate students in an exam, you could pretend to 
believe that texture refers to solid samples, but preferred orientation 
is for free flowing powders. eg: texture is a static property of some 
object, preferred orientation is what you got once with a particular 
sample holder.


All the best,

Jon

Re: Neutron or X-ray?

[Jonathan Wright]

Davide,

Did you check for extinction and preferred orientation? Otherwise what 
does a combined fit give? The difference of about 10 sigma suggests a 
remaining systematic error. What is the impact of refining anisotropically?


Good luck,

Jon

Davide Levy wrote:


Dear All,

I have a ”philosophic” question for you: the structure obtained by NPD 
are better than the ones found by XRPD?


I explain a little bit more my question, I studied a MgAlFeO4 spinel 
both by NDP and XRPD from RT to 1000°C. The O coordinate it is 
different for two data set (0.2581 vs.0.25953). The found error on the 
oxygen coordinate is about 10^-5 and 10^-4 for NPD and XRPD data 
respectively. The coordinate calculated from cation partitioning and 
cation radii is similar to the XRPD result.


At the moment I did not found a justification of this and I do not 
know which result is the ‘right one’.


Do you have any suggestion?

Thank you

Davide

Re: FullProf on Ubuntu 7.10

[Jonathan Wright]

Hi there,

Since I just got the graphics card working again after a similar 
upgrade, I'm feeling brave enough to try without wine (running).


$ file fp2k
ELF 32-bit LSB executable, Intel 80386, version 1, statically linked, 
corrupted section header size


... which shows up on google/ubuntu forums as being a upx issue, so:

$ sudo apt-get install upx-ucl
$ upx -d fp2k
  Ultimate Packer for eXecutables
 Copyright (C) 1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006,2007
UPX 3.00Markus Oberhumer, Laszlo Molnar  John Reiser   Apr 27th 
2007


   File size Ratio  Format  Name
     --   ---   ---
  6070937 -   1629094   26.83%linux/386fp2k

Unpacked 1 file.

$ ./fp2k
=**
=** PROGRAM FullProf.2k (Version 3.80 - Jan2007-ILL JRC) **
=**
=   M U L T I -- P A T T E R N
=Rietveld, Profile Matching  Integrated Intensity
= Refinement of X-ray and/or Neutron Data
= (Multi_Pattern: WindowsConsole-version)

 == Give the code of the files (xx for xx.pcr):


I haven't tested it any further than that. For winplotr_2006, after the 
upx -d, I also needed:


$ sudo apt-get install libmotif3

... and winplotr runs too.

What's so amazing about linux? Someone else will have found the problem 
before you, also solved the problem before you; and yet still it is your 
problem to work on! Not like research eh?


Best,

Jon

Wenduo Zhou wrote:

Dear Rietvelders,

I met a problem to use FullProf on Ubuntu 7.10.  I just installed this 
Linux system.  fp2k cannot run right now, but return 127 (-1) without 
any output.  In my another machine with Ubuntu 7.06, fp2k runs just 
fine.  Is there anyone who met this problem before and know how to 
 solve it?   


Thanks for your advices.

Best,

Wenduo Zhou

Re: Fitting 2d image data

[Jonathan Wright]

Phe,

Have you investigated the MFIT menu in fit2d? It should fit a series of 
1D rows of the image to 1D peak shape functions.


Best,

Jon

On Wed, 4 Jul 2007, Phe Man Suherman wrote:





Dear All,

I have some ESRF data of diffraction from a single crystal thin film. The data 
was recorded on a two dimensional image plate (mar plate) and is stored in a 
matrix file (*.mar2300). Do you know if there is any software that I can use to 
fit sets of peaks from such data? At the moment I am picking off the tops of 
the peaks one by one, which can't be the most rigorous way to do it.  I am 
using a FIT2D software for doing this.

Thank you for your attention.

Regards,
Phe



_
The next generation of MSN Hotmail has arrived - Windows Live Hotmail
http://www.newhotmail.co.uk

Embedded plots, was Re: Powder Diffraction In Q-Space

[Jonathan Wright]

From http://www.iucr.org/iucr-top/cif/faq/



# What is DDL3?

DDL version 3 is the name given to some work in progress by Syd Hall and 
his colleagues at the University of Western Australia. It is intended to 
build on the greater consistency and data typing abilities of DDL2 
without tying the data model too closely to that of a relational database. A 
particular goal of DDL3 is to introduce methods into data dictionaries 
through a formal language known as dREL (Dictionary Regular Expression 
Language).


I've not seen a DDL3 example, but many cases can probably be covered with 
what is in pdCIF already.


The application which does the plotting doesn't need to end up inside the 
cif as part of the file, but the equation linking detector pixels to 
Q could be very useful. There has been a good deal of effort already in 
ImageCIF for single crystal experimental data.


I understood Maud can read and plot cifs already, and is written in Java? 
Could there be a browser plugin version for this?


Best,

Jon


On Thu, 22 Feb 2007, Alan Hewat wrote:


Now this sounds interesting. Certainly the raw data should be archived 
and people could then plot it as they wish. But are there examples of 
interactive plotting applications embedded in powderCIF files, and what 
language might they use ? I would like to see a profile plotting package 
in Java or some other really portable language that would read in CIF 
files and plot calculated-observed patterns like Jmol now plots 
structures.

Alan.

_
Dr Alan Hewat, ILL Grenoble, FRANCE[EMAIL PROTECTED]fax+33.476.20.76.48
+33.476.20.72.13 (.26 Mme Guillermet)  http://www.ill.fr/dif/people/hewat/
_

RE: Powder Diffraction In Q-Space

[Jonathan Wright]

Klaus-Dieter was only proposing Q-scale plots for publishing results,


Why this 2pi factor? Why not 1/d or sin(theta)/lambda. During a very 
brief look at SAXS it seemed at least a few authors disagree about the 
units, with s also appearing sometimes. It was confusing and there was 
a lot of swearing.


it would indeed be useful for everyone to report on the same scale for 
comparison. I would personally prefer an (approx) constant density of 
peaks scale


Depends on the lattice? Cubic patterns look great in old Q:
eg: Announcements 1959
Tables of Q as a Function of 2theta (1959) Acta Cryst 12, 421, (1959)
... where Q was 10^4/d^2.

2pi/d just needs a better name than Q?

Best,

Jon

Re: Strange peaks from grainy Si (data re-attached)

[Jonathan Wright]

... The problems bothering me are
the measured peak is much wider than the simulation


Peak widths should be 400 microns (your beamsize) divided by 3.5 cm 
(your distance) in radians, which is about 180*0.4/3.5/PI = 6.5 degrees.


HTH,

Jon

Re: CIF format for powder work

[Jonathan Wright]

The next file I have to make is from a Topas analysis as well.  I'm not 
sure any other program could handle the constraints I constructed for 
that one (how's that for being controvertial?!).


It might be very useful for any future reader of your cif file if you can 
paste the topas inp file in at least. It could either go as a comment or 
perhaps in [core cif]_refine_special_details(?). As impressive as Topas 
is, I didn't realise it is Turing complete. Gone are the days when most 
computer input files were written in fortran ;-)


One might hope that the (volunteer?) cif editors will be very happy to 
hear from you if you can suggest ways to improve the dictionary?


Jon

Re: notes on rietveld method

[Jonathan Wright]

On Mon, 27 Jun 2005, Vikrant Chauhan wrote:

 Hello everyone,
 I am a novice crystallographer ( so to say )..workingon XPERT PLUS..can 
 somebody tell me where to look for notes on rietveld method (online) ..coz 
 wherever I look its all about some other programs for rietveld fitting , 
 analysis etc...I wish to write my own someday .
 
 Kindly do the needful..Thanking you in anticipation.
 
 Vikrant Chauhan
 Physics udergrad.(4th yr )
 Depp of Physics 
 I I T Kharagpur
 

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

[Jonathan Wright]

 Of course, both are eventually linked, so the manner in which applying a
 median filter to the 2-D image prior to producing a histogram affects
 the whole procedure is what I was wondering about.  

Make a radial transform (cake) BEFORE you apply any filters.

 According to Jon's
 comments, there is a body of lore/practice associated with this
 procedure, but whether it has been discussed in print is uncertain.

Wouldn't go so far as to call it a body. There's not much to discuss? For
a texture free, non-grainy powder the signal should not vary around the
Debye Scherrer cone. So you can filter in that direction, removing for
example, a shadow from the beamstop arm.

Best,

Jon

Re: How to output correlation matrix in GSAS

[Jonathan Wright]

Least matrix is in the .CMT, according to the manual.

Alter the printing options in expedt to get it to print correlations on
the normal list file.

HTH,

Jon

On Tue, 30 Nov 2004, Sang-Heon Shim wrote:

 Dear Experts,
 
 This might be an FAQ.  Where (in which file) can I find correlation 
 matrix in GSAS?
 
 Regards,
 
 Dan Shim
 
 

Re: Choosing origins

[Jonathan Wright]

Bill, 

Thanks! Exactly what I was after and I'd never have guessed it from the
title... 

Jon

On Wed, 31 Mar 2004, David, WIF (Bill)  wrote:

 Hi Jon,
 
 A lot of what you'll need is in the back of the International Tables Vol. A
 in Chapter 15 which goes under the snappy title of Euclidean and affine
 normalisers of space groups and their use in crystallography. From memory,
 earlier incarnations of Vol. A do not have this chapter.
 
 Bill

Re: x-ray scattering factors values for B-1

[Jonathan WRIGHT]

Asking purely as someone who once studied chemistry and has a selective
memory about boron; what is the compound you're looking at? I remember
things like (BH4)- and hearing about Wade's rules, but not isolated B-
anions. Isn't boron even less electronegative than carbon? Could you get
away with neutral boron scattering factors and a multipole refinement to
see where the extra electron is going? That might involve something of a
challenge to avoid correlations with absorbtion and thermal factors...

Best wishes,

Jon

At 03:35 PM 9/5/01 +0200, you wrote:
Thank you very much Miguel,
But it doesn't help, because my samples are ionic and the boron has 
-1 or -2 ionic state, while in the atmdata.dat file for GSAS there 
are only x-ray scattering factors values for B.

Dr. Stefano Agrestini

Re: rietveld program (fwd)

[Jonathan WRIGHT]

At 05:51 PM 7/3/01 +0200, Luca Lutterotti wrote:

 - only one type of peak is inside the program but the asymmetry is 
 handled in a much better way than in other programs (is a real 
 convolution as it should be) so I never found a pattern that I was not 
 able to fit very well with my function (from high resolution synchrotron 
 to neutron TOF). This is the reason I never added another function.

The peakshape you're using sounds very interesting... is it written up
somewhere? Sounds like a programmers dream. I'm on the lookout for
something (a function) which could fit hkl dependant peak asymmetry,
possibly due to stacking faults. Ideally I'd just like to get hold of a
functional form for the hkl dependence and asymmetry, without starting off
with a model for the stacking faults. Is there a simple model out there
I've missed?

Thanks in advance,

Jon
---
PS: Apologies for historical nitpicking but there's been a peakshape in
CCSL doing low angle asymmetry effects by convolution, apparently, for more
than 15 years.
[See: Eddy MM, Cheetham AK, David WIF, Powder Neutron-Diffraction Study of
zeolite NA-ZK-4 - An Application of New Functions For Peak Shape and
Asymmetry,
Zeolites (1986) 6, 449.] 
ToF peakshapes are also handled by convolution, as are lorentzian and
gaussian contributions to whichever instrument type. In both cases my
limited understanding is that the functions are evaluated directly in
fourier space, then an FFT is used to put them back into twotheta or ToF,
which saves doing one of the two FFT's needed for numerical convolution. It
also keeps my understanding limited ;)

RE: One GSAS question.

[Jonathan WRIGHT]

Better to work with a single phase and use the red and black symmetry
operators, in my opinion. You might have to lower the symmetry for some
magnetic structures and add contraints on the positions accordingly, but
this saves a lot of headaches, even if it creates a few by making you think
about the symmetry of the magnetic structure. Prodd and fullprof both
handle magnetic structures and multipattern ToF data with slightly more
flexibility than GSAS in terms of the kinds and symmetry of the structures
allowed.

If you insist on P1 then just put all the coordinates which are related
into the same constraint. The fourfold axis will relate x and y for the
atoms in the P1 space group to x or y from the tetragonal. However, if you
have a fourfold site in I4/mmm then it's either 0,1/2,0; 0,1/2,1/4 or 0,0,z
and you only need to constrain z for the latter and fix x and y. In expedt
the constraint would be something like:
1 z 1 1 ! Phase one (I4/mmm), z co-ord, atom one, value 1
2 z 1 1 ! Phase 2 (P1) atom at 0,0,z
2 z 2 -1! Phase 2 atom at 0,0,-z
2 z 3 1 ! Phase 2 atom at 1/2,1/2,z+1/2
2 z 4 -1! Phase 2 atom at 1/2,1/2,-z+1/2

Essentially theres a line added for each thing you want to constrain
together. It gets a bit hair raising if you try to put the same variable in
two different constraints - you can (and should) always put all the related
variables into the same one, this avoids confusion with disappearing or
'ignored' constraints. Remember to enter fixes (expedt; L A F) for the x
and y co-ordinates. I've assumed the magnetic cell is the same size as the
crystallographic. So it could be either ferromagnetic or antiferromagnetic
and the body centring involves time reversal, eg I4/mmm with k=(0,0,1). Or
some evil combination of the two :)

For simple structures you can get away with just refining the atomic
positions from the nuclear phase and updating them in the magnetic phase.
The magnetic model won't have a big impact on the crystal structure if you
have good (any?) data at short d-spacings, unless you are looking for small
structural distortions. If so, then it is indeed a tricky problem.

Best of luck,

Jon

At 02:54 PM 5/17/01 -0400, you wrote:
Thanks a lot for the answer!

Apologize for not making myself very clear. Actually I am refining some
layered manganites data, I have non special postion Mn atoms(4 in one unit
cell for the magnetic phase of Space group P1), I need to make them in 
the same position as the Mn in the atomic structure phase(only one in the
unit cell (I4/mmm) ). 

Thanks again!

Best,

Xiangyun Qiu


On Thu, 17 May 2001, Radaelli, PG (Paolo)
wrote:

 Dear Xiangyun Qiu,
 
 the easiest thing is to create a new purely magnetic phase containing only
 Mn and with P1 symmetry.  Since Mn is in a special position, you don't need
 to refine the coordinates.  You'll have to constrain the reciprocal lattice
 tensor parameters and the phase fraction between the two phases.  The
latter
 are inversely proportional to the cell volume.  Tricky but a good
 exercise...
 
 Paolo Radaelli
 

Xiangyun 

*
Xiangyun Qiu

Dept. of Physics  Astronomy
MSU East Lansing, MI
Http://www.msu.edu/~qiuxiang

*

Re: Resolution in powder diffraction

[Jonathan WRIGHT]

Brian H. Toby wrote:

 ... SOAPBOXBesides, Q
 is the Fourier conjugate of x (the coordinates); d-spaces have no
 physical significance.  D-spaces can mislead a novice into correlating
 reciprocal space distances with real space distances./SOAPBOX

D-spacings are distances between lattice planes and provide me at least
with a nice physical picture of Bragg's law. In this way I guess I am
correlating real space distances with reciprocal space distances, but I
think I prefer remain a novice than give up what little understanding I
have :) 

and thus cannot be compared between techniques and not d-space because
that overemphasizes the low Q (low angle) portion of the pattern which
has minor leverage on most results and further is where one rarely needs
to worry about optimizing instrumental resolution. 

High resolution at low Q is handy for indexing, and is essential for
tackling moderately complex magnetic structures with powder neutron data.
ToF diffractometers which use slow neutrons (eg OSIRIS at ISIS) appear to
be doing particularly well for resolution in the d=3-10 Angstrom region (I
hope we eventually see such machines at SNS and ESS). Peak broadening
effects and splittings can be easier to interpret where there is less peak
overlap, so high resolution in this range can again be useful. It's a
question of applying the right instrument or setup to the particular
problem in mind.

In the plot on my web page, low angle asymmetry is subtracted out -- but it
should not be. For very short wavelength machines, the asymmetry can be
severe for the bulk of the pattern. 

There are a lot of different trade offs to take into account when choosing
a wavelength, with x-rays at least. If low angle asymmetry is a problem for
the experiment in question then you can use a small beam on sample and/or
narrower receiving slits. My recent experience at ESRF is that a lot of the
asymmetry can be removed without destroying the count rate even with a
large unit cell and fairly hard x-rays. (nb. removed by slits, not
deconvolution)

For ToF neutrons the moderator asymmetry is less dominant as ToF increases,
and this is where the resolution is maximised anyway. It can be fitted very
well with the right programs and the advantages of going to very low
d-spacings (high Q) also has to be taken into account. 

Comparing resolution functions only tells part of the story, the real
question is how much information did you gain from the experiment. This can
depend on a lot of other factors, not least background, Q-range and count
rate which are rarely compared in quite the same way. Remember the sample
can still ruin the background and the resolution regardless of the
instrument :)

Cheers,

Jon

Re: Hamilton's test

[Jonathan WRIGHT]

 The observations must be statistically independent, but need not be
 independent in the sense of what they physically measure.

It seems implicit from that sentence that the datapoints must be physically
measuring some aspect of the model, is that the case? For example: Does a
Hamilton test on two crystallographic models give the same results if you
throw out the datapoints which only have background contributions? The
"reducio ad absurdum" would be to use Rwp from a multipattern fit where
only one pattern contains the phase of interest. Maybe that's statistically
valid if some of the least squares parameters depend on all of the patterns? 

Bill David's work on deriving the number of independent peaks in a powder
pattern seems to offer a route to significance testing for different
crytallographic models (J.Appl.Cryst.(1999) 32:654). Perhaps it just adds
to the confusion.

Cheers,

Jon Wright

Re: Neutron diffraction with boron

[Jonathan WRIGHT]

Armel wrote:

And yes, the measurements have been done.

I would not call Science giving the MgB2 atomic
coordinates, already known.

Was this meant to be serious? Checking for any subtle structural changes
around Tc would be (has been?) a worthwhile investigation. Something easily
worthy of the word "science", as I understand it. Knowing what the
structure does or doesn't do around the transition would be a prerequisite
to a deeper understanding of the phenomena. Apologies if it's just that my
sense of irony has been in remission this morning.

Jon

Re: Neutron diffraction with boron

[Jonathan WRIGHT]

At 04:48 PM 3/29/01 +0200, you wrote:

You really think that MgB2 will give more ? Maybe... just routine to do so.

Armel, it was you who asked if boron was possible with neutrons, and when 
you are told that it is, you say that anyway it is borin' (excuse the pun :-)

I hadn't realised there was any problem with x-rays together with magnesium
and boron ;)

Apologies for my previous mail (Re: new gsas), which wasn't supposed to go
to the list, probably this one shouldn't either, but anyway: Refining a
silicon standard is a routine and fairly dull thing to do, but it is
necessary. Being the first group to systematically study the structure of
an unexpected superconductor above, below and around it's transition
temperature does not really fall into the 'routine' category. Is it really
worth trying to belittle what should turn out to be excellent science? 

Jon