Re: Cagliotti and Other Issues

2009-03-24 Thread Alan Hewat
 According to the ccp14 news site the wiki (I guess from apparent lack
 of interest) was recently deactivated after a ccp14 web server upgrade.

In practice, people use whatever is available in the refinement programs
(sometimes blindly :-) The authors of those programs have already spent
considerable effort in writing manuals, and users should be encouraged to
read those as a first step :-)

The Rietveld mailing list http://www.mail-archive.com/rietveld_l@ill.fr/
is also a useful source of different opinions on techniques.

Often wikis are well done, but sometimes represent wacky opinions of a few
individuals. Google itself is often a better source of information. And of
course most refereed papers are now available on the WWW, and can readily
be found with google.

Alan
BTW Mike Glazer is right that people should be more concerned with
physical-chemical tests of their structure, rather than trying to get the
lowest possible R-factor by refining more parameters.
__
Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
alan.he...@neutronoptics.com +33.476.98.41.68
  http://www.NeutronOptics.com/hewat
__



Re: Cagliotti and Other Issues

2009-03-23 Thread Vincent Favre-Nicolin
Hi,

 I wonder if we should, as a community, put some of this stuff on
 wikipedia, or another such place.  In other words, distill the
 community's collective knowledge in a single place that can be updated
 in the future, and also curated for correctness also by the community.
 What are people's thoughts on this?  Rietveldipedia?

   Some time ago I told William Bisson (ccp14 secretary) that it would be 
great to have a CCP14 wiki - which he added quickly (see his message to the 
list on 2007/06/18). Unfortunately this did not get popular (to my great 
shame I must say I did not add any information to that wiki...).

   According to the ccp14 news site the wiki (I guess from apparent lack of 
interest) was recently deactivated after a ccp14 web server upgrade. But I 
guess if there is interest it would be good to have it started again ? CCP14 
seems like a nice place to collect that information, especially as a wiki 
data can be easily duplicated and would not be lost over time.

   The ccp4 project has several wikis which seem to be working quite well: 
- user wiki @ http://strucbio.biologie.uni-konstanz.de/ccp4wiki/
- developper wiki @  http://ccp4wiki.org/

Vincent
-- 
Vincent Favre-Nicolin

CEA Grenoble/INAC/SP2M  http://inac.cea.fr
Univ. Joseph Fourier (Grenoble) http://www.ujf-grenoble.fr

ObjCryst  Fox  http://objcryst.sf.net/Fox


RE: Cagliotti and Other Issues

2009-03-22 Thread Matthew.Rowles


-Original Message-
From: May, Frank [mailto:frank.l@umsl.edu]  
My recollection is the Cagliotti function was adapted to the x-ray case when 
we had low resolution x-ray instruments and slow (or no) computers.  Now that 
we have high resolution instruments and fast computers, why does this 
inappropriate function continue to be used?
 
There's probably a great deal of it's always been done this way in why its 
used, in addtion to a lack of education in when it should be used, as well as 
Let's tick this box and see what happens... :(


On another note, the world is venturing into the infinitely small realm of 
nano-particles As the relative fraction of the bulk becomes smaller, 
both the physical structure as well as the mathematics used to describe the 
bulk suffer from termination-of-series effect, do they not?  Does any of this 
make sense?  Any thoughts?
 
This is talked about by Grey and Wilson*. They show that while you can refine 
diffraction data from nanosize titania particles, the numbers (cell params in 
this case...) that you get out might not represent what is actually there. 
Basically, the assumption that there is an infinite lattice breaks down.





*Titanium vacancy defects in sol-gel prepared anatase
Grey, I; Wilson, N
JOURNAL OF SOLID STATE CHEMISTRY (0022-4596); Volume: 180; Issue: 2; Date: 
2007; pg. 670-678



Cheers

Matthew


Matthew Rowles

CSIRO Minerals
Box 312
Clayton South, Victoria
AUSTRALIA 3169

Ph: +61 3 9545 8892
Fax: +61 3 9562 8919 (site)
Email: matthew.row...@csiro.au



RE: Cagliotti and Other Issues

2009-03-22 Thread Davor Balzar
Dear All:

Indeed, despite some more advanced approaches to modeling diffraction line
shapes, the good, old Cagliotti function is still in use probably for
historical reasons (as it is the case with many other things in sciences).
However, to be fair to (practically all major) Rietveld programs, the
original Cagliotti function (Gaussian term) was a long time ago amended by a
Lorentzian contribution (linear in FWHM as opposed to a quadratic Gaussian
term). This term immensely helps to accurately model high-resolution
measurements, both x-ray and neutron (see, for instance examples of ESRF and
ISIS data in Size-Strain Line-Broadening Analysis of the Ceria Round-Robin
Sample, Journal of Applied Crystallography 37 (2004) 911-924--article and
data available at http://www.du.edu/~balzar/s-s_rr.htm).

As discussed in this thread, the original Cagliotti function often gets into
trouble because of the square root of a negative number. Bill David
described a much better function. Thus, the general approach described by
Bill and in the article cited above is to refine coefficient of a function
used on a pattern obtained from a suitable standard, such as LaB6, and
then fix them (unfortunately, not always possible for all instruments,
because some instrumental parameters depend on the angle in the same way as
the strain term in the Bragg-Brentano geometry). Moreover, for
high-resolution data it might be helpful to add a Lorentzian FWHM to that
expression and then post it to Wikipedia or perhaps publish a paper... :-)

Davor



 -Original Message-
 From: simon.billi...@gmail.com
 [mailto:simon.billi...@gmail.com] On Behalf Of Simon Billinge
 Sent: Sunday, March 22, 2009 2:50 PM
 To: rietveld_l
 Subject: Cagliotti and Other Issues

 Dear Rietvelders

 What is the most complete and authoritative source for issues such as
 profile function definitions, what is their scientific basis, and when
 are they appropriate to use, etc.?  I am guessing there is not
 one-stop-shop solution (Young's book? GSAS manual? Rietveld list
 archive?) but advice on this would be helpful.

 I wonder if we should, as a community, put some of this stuff on
 wikipedia, or another such place.  In other words, distill the
 community's collective knowledge in a single place that can be updated
 in the future, and also curated for correctness also by the community.
 What are people's thoughts on this?  Rietveldipedia?

 S

 2009/3/20 May, Frank frank.l@umsl.edu:
  Back to basics and First Principles
 
  As Alan says, the [use of the Cagliotti function is
 appropriate for the neutron case], but not really for X-ray
 and other geometries.
 
  My recollection is the Cagliotti function was adapted to
 the x-ray case when we had low resolution x-ray instruments
 and slow (or no) computers.  Now that we have high resolution
 instruments and fast computers, why does this inappropriate
 function continue to be used?
 
  On another note, the world is venturing into the infinitely
 small realm of nano-particles.  The classical rules for
 crystallography work very well for ordered structures in the
 macro-world (particles of the order of micron-sizes).  
However, as the particles become smaller, does one not need to  address the
contribution of the surface of the particles?  
 The volume of the surface becomes much greater relative to
 the volume of the bulk of the crystal.  Models today
 account for stress and strain in the macro-world.  As the
 relative fraction of the bulk becomes smaller, both the
 physical structure as well as the mathematics used to
 describe the bulk suffer from termination-of-series effect,
 do they not?  Does any of this make sense?  Any thoughts?
 
  Frank May
  St. Louis, Missouri  U.S.A.
 
  
 
  From: Alan Hewat [mailto:he...@ill.fr]
  Sent: Fri 3/20/2009 2:13 AM
  To: rietveld_l@ill.fr
  Subject: RE: UVW - how to avoid negative widths?
 
 
 
  matthew.row...@csiro.au said:
  From what I've read of Cagliotti's paper, the V term
 should always be
  negative; or am I reading it wrong?
 
  That's right. If
  FWHM^2 = U.tan^2(T) + V.tan(T) + W
  then the W term is just the Full Width at Half-Maximum
 (FWHM) squared at
  zero scattering angle (2T). FWHM^2 is then assumed to
 decrease linearly
  with tan(T) so V is necessarily negative, but at higher
 angles a quadratic
  term (+ve W) produces a rapid increase with tan^2(T).
 
  Cagliotti's formula assumes a minimum in FWHM^2, but if
 that minimum is
  not well defined, U,V,W will be highly correlated and
 refinement may even
  give negative FWHM. In that case you can reasonably constrain V by
  assuming the minimum is at a certain angle 2Tm, which may
 be close to the
  monochromator angle for some geometries. So setting the
 differential of
  Cagliotti's equation with respect to tan(T) to zero at that
 minimum gives:
  2U.tan(T) + V =0   at T=Tm   or   V = -2U.tan(Tm)
  this approximate constraint removes the correlation and
 allows