RE: TOPAS-Academic for Synchrotron and Neutron research centers

[Alan Coelho]

Hi Alan

 

Thanks for the tip; your version certainly sounds better. However, I believe my 
version to be more accurate on two counts:

 

1)  It's in my best interest to distribute the software to such labs and

 

2)  It's not TOPAS that is being considered but TOPAS-Academic

 

>because it is in a company's own interest to introduce their products to 

>the thousands of users of such centres, who will then hopefully buy 

>their own copy to be able to continue refining their data when

 

Maybe I was not clear enough. TOPAS-Academic is not to be used to analyse 
clients data. Synchrotron centres need to purchase TOPAS in order to do this. 

 

The idea is to provide TOPAS-Academic to scientists at these centres in order 
for them to do their own research.

 

Cheers

Alan

 

 

From: Alan Hewat [mailto:alan.he...@gmail.com] 
Sent: Friday, May 19, 2017 2:22 PM
To: Alan Coelho
Cc: rietveld_l@ill.fr
Subject: RE: TOPAS-Academic for Synchrotron and Neutron research centers

 

Alan. Perhaps you could put it this way ?

 

"Bruker-AXS will apply academic prices to purchases of Topaz by neutron and 
synchrotron research centres​".

I have left out "generous" because it is in a company's own interest to 
introduce their products to the thousands of users of such centres, who will 
then hopefully buy their own copy to be able to continue refining their data 
when they get back home.

 

Alan Hewat

_
  From my mobile telephone
 Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE 
 +33.476.98.41.68
  http://www.NeutronOptics.com/hewat
_____

 

On 19 May 2017 02:20, "Alan Coelho"  wrote:

Hi again

 

At least one person misunderstood the TOPAS-Academic message; it’s not free I’m 
afraid. The pricing is the same as for universities. So I will try again:


Bruker-AXS has allowed the purchase of TOPAS-Academic  
(http://www.topas-academic.net/) by Synchrotron and neutron research centers 
for academic research work. Work done for clients or by clients of the 
institution requires the purchase of TOPAS.

Sincerely
Alan Coelho

 

From: Alan Coelho [mailto:alancoe...@bigpond.com] 
Sent: Friday, May 19, 2017 7:16 AM
To: 'rietveld_l@ill.fr'
Subject: TOPAS-Academic for Synchrotron and Neutron research centers

 

Hi all

 

Bruker-AXS has generously granted the distribution of TOPAS-Academic  
(http://www.topas-academic.net/) to Synchrotron and neutron research centers 
for academic research work. Work done for clients or by clients of the 
institution requires the purchase of TOPAS.

 

 

Sincerely

Alan Coelho

 


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RE: TOPAS-Academic for Synchrotron and Neutron research centers

[Alan Coelho]

Hi again

 

At least one person misunderstood the TOPAS-Academic message; it's not free
I'm afraid. The pricing is the same as for universities. So I will try
again:


Bruker-AXS has allowed the purchase of TOPAS-Academic
(http://www.topas-academic.net/) by Synchrotron and neutron research centers
for academic research work. Work done for clients or by clients of the
institution requires the purchase of TOPAS.

Sincerely
Alan Coelho

 

From: Alan Coelho [mailto:alancoe...@bigpond.com] 
Sent: Friday, May 19, 2017 7:16 AM
To: 'rietveld_l@ill.fr'
Subject: TOPAS-Academic for Synchrotron and Neutron research centers

 

Hi all

 

Bruker-AXS has generously granted the distribution of TOPAS-Academic
(http://www.topas-academic.net/) to Synchrotron and neutron research centers
for academic research work. Work done for clients or by clients of the
institution requires the purchase of TOPAS.

 

 

Sincerely

Alan Coelho

 

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TOPAS-Academic for Synchrotron and Neutron research centers

[Alan Coelho]

Hi all

 

Bruker-AXS has generously granted the distribution of TOPAS-Academic
(http://www.topas-academic.net/) to Synchrotron and neutron research centers
for academic research work. Work done for clients or by clients of the
institution requires the purchase of TOPAS.

 

 

Sincerely

Alan Coelho

 

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RE: CrySize error in TOPAS

[Alan Coelho]

Hi Luke

The weight percents should not differ if CrySize is irrelevant. Can you post a 
list of  the weight percents with and without CyrSize as well as Rwp values. 

Also, what peak type are using; I hope it's not PVII as it can give incorrect 
results when the exponent is small leading very long peak tails.
cheers
alan

-Original Message-
From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of 
"Lukasz Kruszewski"
Sent: Thursday, July 28, 2016 3:21 AM
To: Cline, James Dr. (Fed)
Cc: rietveld_l@ill.fr; "Łukasz Kruszewski"
Subject: RE: CrySize error in TOPAS

Thank you very much, Jim. I do appreciate this. I though it is not "allowed" 
not to use the CrySize, maybe because I've mixed crystal size and crystallite 
size... However, I did such a single refinement whthout any CrySize(s) used. 
The residuals were OK (that is, not much worse than when using the CrySize, 
that could possibly overparametrize the refinement and push it towards the 
false-correct Rwp etc.), but the wt.% values obtained differed quite a lot from 
the ones obtained when using the CrySize. This difference in wt.% a bit worries 
me, because I'm working with TOPAS & Rietveld for some years and I still lack 
confidence (-; Patience matters...

Best regards,

Luke Kruszewski



> That means the value is indeterminate with respect to the refinement 
> and the contribution of "CrySize" [crystallite size broadening] to the 
> observation is nearly zero.  Try turning it off and see what the 
> residuals do.
>
> 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: "Łukasz Kruszewski" [mailto:lkruszew...@twarda.pan.pl]
> Sent: Wednesday, July 27, 2016 1:08 PM
> To: Cline, James Dr. (Fed) 
> Cc: rietveld_l@ill.fr; "Łukasz Kruszewski" 
> Subject: RE: CrySize error in TOPAS
>
> Hello James. I just read the error that is reported for each refined 
> parameter in TOPAS. I obtain value like, e.g., 9000 nm, and the error 
> is, e.g., 205006.
>
> Best regards,
>
> Łukasz Kruszewski
>
>
>> By what metric are you determining that the CrySize value is in error?
>>
>>
>> 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 "Lukasz Kruszewski"
>> Sent: Wednesday, July 27, 2016 10:22 AM
>> To: rietveld_l@ill.fr
>> Subject: CrySize error in TOPAS
>>
>> Dera friends,
>>
>> I'm doing Rietveld refinements in TOPAS; I get rather good fit of the 
>> reflections, rather good wt.%, but I've observed large errors for the 
>> CrySize (Lorentzian) values for some introduced Structures. I've 
>> tried to change it by refining CrySize (Gaussian), but it only 
>> changed in few particular cases. I'm rather sure that the intrumental 
>> parameters (geometry of the diffractometer was analyzed with the use 
>> of LaB6, Si, and other standards) and corrections (sample displ. 
>> etc.) are OK and I suppose these factors shouldn't influence (?) the 
>> CrySize values. I always constrain the minimum (20 starting value) 
>> and maximum (1
>> nm) value for CrySize; I usually refine strain, but I've noticed that 
>> it doesn't influence the results (at least the wt.% calculated). Rwp, 
>> goodness of fit and Durbin-Watson statistics R values are OK; also, 
>> the calculated background line is "flat", i.e., there is no mistaking 
>> of the background with reflections; the shapes of the reflections in 
>> the calculated diffractograms seem to be OK, too. I was thus 
>> wondering if these high errors coming from the CrySize are that 
>> important for the refinement?
>>
>> Best regards,
>>
>>
>> --
>> Łukasz Kruszewski, Ph.D., adjunct
>> Polish Academy of Sciences
>> Institute of Geological Sciences
>> Twarda 51/55 str.
>> 00-818 Warsaw
>> Poland
>>
>
>
> --
> Łukasz Kruszewski, Ph.D., adjunct
> Polish Academy of Sciences
> Institute of Geological Sciences
> Twarda 51/55 str.
> 00-818 Warsaw
> Poland
>


--
Łukasz Kruszewski, Ph.D., adjunct
Polish Academy of Sciences
Institute of Geological Sciences
Twarda 51/55 str.
00-818 Warsaw
Poland

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TOPAS-Academic Version 6

[Alan Coelho]

Hi all

TOPAS-Academic Version 6 is now available; see http://www.topas-academic.net/. 
It represents approximately 5 years of improvements.

Bruker-AXS TOPAS will be following in the very near future.

Cheers
Alan

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Capillary data with odd shaped peaks

[Alan Coelho]

Hi all

 

I'm looking  for Capillary Specimen data collected in reflection mode which
shows odd bumps on the peaks. I'm aware that there are supposed to be odd
shaped peaks but I am looking for example data that show it. If anyone has
such data and are willing to part with it then let me know.

cheers
alan

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RE: Unit cell accessible volume

[Alan Coelho]

Hi Othman

 

>I am, however, interested in finding out whether inserting certain
molecules in the voids 

>(without distorting the structure) is geometrically possible

 

Use distance penalties/restraints such anti-bumping etc. and then minimize
on the restraints/penalties by refining the molecular coordinates you want
varied.

alan

 

 

From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf
Of Othman Al Bahri
Sent: Thursday, 11 June 2015 2:41 AM
To: rietveld_l@ill.fr
Subject: Unit cell accessible volume

 

Dear all,

 

I am trying to calculate the void volume in a unit cell. I can estimate the
overall void volume manually by subtracting  the occupied space volume from
the total unit cell volume using VESTA. I am, however, interested in finding
out whether inserting certain molecules in the voids (without distorting the
structure) is geometrically possible. Is there a way to do this given the
complexity of some structures/superstructures and the large number of ways a
molecule can intercalate into a structure ?

 

Kind Regards,

Othman Al Bahri

UNSW - Sydney 

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RE: Powder Diffraction Discussion Group on Facebook

[Alan Coelho]

Radovan wrote:
>Looks like cleavage between troglodyts and tweeters. This of course should
be avoided. 
>How many general scientific questions do you receive, Alan? I remember to
see ~ 1-2 /week on mailing list.

Not called for; people don’t like being called names, no wonder the Rietveld
mailing list is not being used like it once were. They also don’t like the
mediums they use such as twitter being rubbished.

Thanks for the information Othman. 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

I like the look of xrayforum.co.uk.

I remember a while back many questions on the mailing list; if there’s 1-2 a
week now then something is not working. 

Let's have a closer look at the archives at
https://www.mail-archive.com/rietveld_l@ill.fr/mail8.html

In 2014 there were 221 messages

In 2007 there were 593 messages.

In the last 4 months of 2006 there were 211 messages; extrapolating gives
633 messages.

A plot of these numbers and dates would be nice.

Anyway, the Rietveld mailing list is still where the best knowledgeable is
in my opinion; I just wish some members weren’t so grumpy.

Cheers
Alan


-Original Message-
From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf
Of Othman Al Bahri
Sent: Wednesday, 10 June 2015 12:26 AM
To: rietveld_l@ill.fr
Subject: Re: Powder Diffraction Discussion Group on Facebook

This is my fifth month in the field of applied crystallography and as an
undergraduate who is still learning how to learn. I sometimes wish things
were a little more organised. Finding out about this mailing list (by a
totally random lunch-time conversation during an NMR conference) was a
godsend.

Back to the discussion ... http://www.xrayforum.co.uk is a forum to consider
instead of starting something from scratch. Too many options paralyse the
individual, but here's another option
http://www.reddit.com/r/crystallography .
Cheers,
Othman

From: rietveld_l-requ...@ill.fr  on behalf of
Radovan Cerny 
Sent: Wednesday, 10 June 2015 12:03 AM
To: Alan Coelho; rietveld_l@ill.fr
Subject: RE: Powder Diffraction Discussion Group on Facebook

BTW: I will declare my vested interest in this discussion: I would love for
users of programs like GSAS/Fox/TOPAS/Full-prof etc... to ask scientific
questions in scientific forums rather each program having its own web page
trying to hold back the tide. There are so many young scientists asking
questions. No doubt a web page for program specific question is useful but
we are talking general scientific questions. Do I think the Rietveld list
fills the void ? No.

Cheers
Alan

Looks like cleavage between troglodyts and tweeters. This of course should
be avoided.
How many general scientific questions do you receive, Alan? I remember to
see ~ 1-2 /week on mailing list.

Imagine the discussion which has just happened on mailing list to happen on
Facebook or Tweeter. Would be much better with images and even videos of
discussing people. And few seconds of publicity after each tweet ...



Radovan Cerny
Laboratoire de Cristallographie, DQMP
Université de Genève
24, quai Ernest-Ansermet
CH-1211 Geneva 4, Switzerland
Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08 mailto :
radovan.ce...@unige.ch
URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm

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RE: Powder Diffraction Discussion Group on Facebook

[Alan Coelho]

I can never write something and have it interpreted the way I want it to be. 
The written word is so hopeless – in my hands that is.

Alan Hewat wrote:
>Hmm ? Are file servers still OK ? Like the Rietveld archive, where people can 
>already include links to pictures

I'm afraid respectfully that links to picture won't do. People want WYSIWYG  
(You have a twitter account! -  I have never even owned a mobile phone).


Lubomir Smrcok wrote:
>If you argue that 12 yrs old kids can move files between two computers I can 
>only ask..

The point was: how is it a 12 year old can move 100 Mbytes with ease and in a 
manner that didn’t costs a thing (the 3 seconds adverts can be bothersome 
though). Whilst back on the mailing list we are talking bytes rather than 
Mbytes.


Radovan Cerny wrote:
>But I think that the (a)social networks are not a good choice. ...

Agree, that’s why I mentioned wordpress and docuwiki


Radovan Cerny wrote:
>Imagine that I will post one day a short twit (or how you call it?) what is 
>the best way to describe
>a BH4 group in Topas. And Alan has a full right to use it in his publicity 
>campaign 
>saying that even Radovan is now using exclusively Topas and has abandoned 
>Fox (there will be a new version soon thanks to Vincent).

Being so close to Fox you should then know the very many questions,  and indeed 
scientific ones, asked by users. To answer these questions efficiently requires 
attachments and graphics; I can’t imagine answering the 100s of questions I get 
without it. And congratulation to Vincent for the new Fox; can’t wait to have a 
look :).

BTW: I will declare my vested interest in this discussion: I would love for 
users of programs like GSAS/Fox/TOPAS/Full-prof etc... to ask scientific 
questions in scientific forums rather each program having its own web page 
trying to hold back the tide. There are so many young scientists asking 
questions. No doubt a web page for program specific question is useful but we 
are talking general scientific questions. Do I think the Rietveld list fills 
the void ? No.

Cheers
Alan

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RE: Powder Diffraction Discussion Group on Facebook

[Alan Coelho]

Hi again all

I’m no expert but after some quick googling it seems that wordpress, which 
seems to fall under GNU-GPL, may be what a contender. It talks to facebook and 
has 1000s of forum type plugins. 

Or, how about https://www.dokuwiki.org/wiki:dokuwiki

"DokuWiki is a simple to use and highly versatile Open Source wiki software 
that doesn't require a database. It is loved by users for its clean and 
readable syntax. The ease of maintenance, backup and integration makes it an 
administrator's favorite. Built in access controls and authentication 
connectors make DokuWiki especially useful in the enterprise context and the 
large number of plugins contributed by its vibrant community allow for a broad 
range of use cases"

There are certainly options out there but I guess getting someone to administer 
the site is an obstacle.

Cheers
Alan


From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of 
Radovan Cerny
Sent: Tuesday, 9 June 2015 6:36 PM
To: Jonathan WRIGHT; rietveld_l@ill.fr
Subject: RE: Powder Diffraction Discussion Group on Facebook

Jon,

There is no problem to have pictures in the email. Just need to use HTML format 
for your email.

But you have raised an important question: "public perceptions". Uni Geneva has 
already everythink: 
http://www.unige.ch/communication/diffuser/mediassociaux.html

I hope we will not start to discuss this question now.

Jan Rohlicek proposes to link email with (a)social networks. Simple (?) and 
constructive idea.


Radovan Cerny  
Laboratoire de Cristallographie, DQMP
Université de Genève
24, quai Ernest-Ansermet  
CH-1211 Geneva 4, Switzerland
Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08
mailto : radovan.ce...@unige.ch
URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm

De : rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] De la part de 
Jonathan WRIGHT
Envoyé : mardi 9 juin 2015 10:16
À : rietveld_l@ill.fr
Objet : Re: Powder Diffraction Discussion Group on Facebook

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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RE: Powder Diffraction Discussion Group on Facebook

[Alan Coelho]

Radovan 

Interesting discussion, html may allow graphics but doesn't still mean 
e-mailing large files to everyone.

Jon: the IUCR also has a facebook page at https://www.facebook.com/iucr.org

Not recognizing the pull/power of facebook, twitter, Instagram etc… is akin to 
IBM not recognizing the power of personal computers, or like thinking that 3D 
printing is a fad or that drones is a toy or that the newspaper are here 
forever.  

It’s easy to agree with the thought that a small community like ours should not 
have many channels but not having pictures/graphics seems archaic. A 12 year 
old I know used a phone to take a 100Mbyte video and posted it on youtube; 
these are the file sizes being thrown about by kids. 

So great to have a mailing list, thanks Alan, but personally I would love to 
see a medium (I dot care what it is) that allows graphics. 

Cheers
Alan


From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of 
Radovan Cerny
Sent: Tuesday, 9 June 2015 6:36 PM
To: Jonathan WRIGHT; rietveld_l@ill.fr
Subject: RE: Powder Diffraction Discussion Group on Facebook

Jon,

There is no problem to have pictures in the email. Just need to use HTML format 
for your email.

But you have raised an important question: "public perceptions". Uni Geneva has 
already everythink: 
http://www.unige.ch/communication/diffuser/mediassociaux.html

I hope we will not start to discuss this question now.

Jan Rohlicek proposes to link email with (a)social networks. Simple (?) and 
constructive idea.


Radovan Cerny  
Laboratoire de Cristallographie, DQMP
Université de Genève
24, quai Ernest-Ansermet  
CH-1211 Geneva 4, Switzerland
Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08
mailto : radovan.ce...@unige.ch
URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm

De : rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] De la part de 
Jonathan WRIGHT
Envoyé : mardi 9 juin 2015 10:16
À : rietveld_l@ill.fr
Objet : Re: Powder Diffraction Discussion Group on Facebook

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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RE: Very small shift in d-space: insanity check

[Alan Coelho]

Hi Shay

 

>From Bragg's equation we have:

 

   delta_theta = (delta_d/d) Tan(Th)

 

Or, the amount a peak shifts is increases with 2Th but decreases with
d-spacing.

 

So at a d-spacing of 2 Angstroms say (200 pm) for a peak at 20 degrees 2Th
say we would see a shift in 2Th of:

 

(0.1  / 200) Tan(10 Pi/180) 360/Pi

 

= 0.0101 degrees 2Th

   

This is measureable - if my quick calculation is correct that is

 

Cheers

Alan

 

From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf
Of Shay Tirosh
Sent: Wednesday, 8 January 2014 12:23 AM
To: rietveld_l@ill.fr
Subject: Very small shift in d-space: insanity check

 


Dear rietvelders


 


I would like to consult with you as for the possibility to determine small
shift in d-space in the order of 0.1pm in normal Bruker x-ray diffractometer
with
 Bragg Brentano geometry. 


 . 

Detector:

Our  diffractometer equipped with multi-channel Laynex detector. I used
solar slit and 0.6mm advancing slit.

Source:

Cu Kalpha1, Kalpha2.

Experiment:

Step size 0.02o

Time per each step 0.3sec

I used internal standard that has reflection peak at 2teta = 12.71o

I repeat the diffraction experiments 3 times.

Care has been taken not to move the sample between diffraction experiments.

Analysis:

All three diffraction experiments merged, baseline has been subtracted from
the merged data set. Position of the peak has been determined by fitting to
the best peak equation using Fityk. Shift in d-space has been determine with
respect to the internal standard peak reflection. 

Parallel reflections gave similar shifts in the order of 0.1pm with relative
standard deviation of 8.65%. 

 

Dose my result make sense? 

Do I violate the limit of resolution?

 

Please comment.

 

Thank you from advance

 

Shay

 

 

-- 

_

 

Dr. Shay Tirosh

Institute for Nanotechnology & Advanced Materials

Bar Ilan University 

Ramat Gan, 52900

Israel
Phone: +972-(0)30-531-7320

Mobile: +972-(0)54-8834533

Email: stiro...@gmail.com

_

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++

RE: modification of TOPAS reporting macro

[Alan Coelho]

Hi Artem

You can output Xo, Iobs_no_scale_pks and its error as follows:

phase_out file load out_record out_fmt out_eqn
   {
   "%3.0f" = H;
  " %3.0f" = K;
  " %3.0f" = L;
  " %3.0f" = M;
  " %11.5f"   = D_spacing;
  " %11.5f"   = 2 Rad Th;
  " %11.5f"   = Xo;
  " %11.5f"   = Iobs_no_scale_pks;
  " %11.5f\n" = Iobs_no_scale_pks_err;
   }

Iobs_no_scale_pks is calculated using the Rietveld decomposition formulae

cheers
alan


-Original Message-
From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of 
Artem Babaryk
Sent: Tuesday, 3 December 2013 6:57 PM
To: Rietveld_l@ill.fr
Subject: modification of TOPAS reporting macro

Dear Colleagues,

Has anybody tried to modify TOPAS macro Create_hklm_d_Th2_Ip_file(file, wI):

 phase_out file load out_record out_fmt out_eqn
   {
   "%3.0f" = H;
  " %3.0f" = K;
  " %3.0f" = L;
  " %3.0f" = M;
  " %11.5f"   = D_spacing;
  " %11.5f"   = 2 Rad Th;
  " %11.5f\n" = wI;
   }

with xo, yo corresponding to peak positions? 

Regards,
Artem

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++

RE: Instrumental resolution function

[Alan Coelho]

Matt

>I am not sure I understand how you would account for the additional 
>wavelengths in the beam.

Tube tails is spectrally independent and its aberration shape is 2Th
independent. Its realized in TOPAS by a convolution called stacked_hats
which, as its name suggests, convolutes a series of stacked impulse
functions. An intense narrow hat represents the beam and wider hats the
penetration of the electrons in the tube.

Cheers
Alan

-Original Message-
From: Matt Beekman [mailto:matt.beek...@oit.edu] 
Sent: Tuesday, 17 September 2013 2:08 AM
To: Peter Y. Zavalij; Alan Coelho; mariomac...@tux.uis.edu.co;
rietveld_l@ill.fr
Subject: RE: Instrumental resolution function

Alan, Peter,

Would you mind briefly elaborating on the procedure used to "fit tube
tails?" I personally have only used GSAS for Rietveld refinement, and other
than adding another phase(s) with slightly different lattice parameter(s) I
am not sure I understand how you would account for the additional
wavelengths in the beam.

Many thanks in advance!

Matt

--
Matt Beekman, Ph.D.
Assistant Professor of Physics
Department of Natural Sciences
Oregon Institute of Technology
3201 Campus Drive
Klamath Falls, OR 97601
Tel: 541-885-1940
Fax: 541-885-1849
Email: matt.beek...@oit.edu
Web:
http://www.oit.edu/faculty-staff/home-pages/natural-science/matt-beekman



-Original Message-
From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf
Of Peter Y. Zavalij
Sent: Monday, September 16, 2013 6:11 AM
To: Alan Coelho; mariomac...@tux.uis.edu.co; rietveld_l@ill.fr
Subject: RE: Instrumental resolution function

I do exactly the same - fit tube tails using LaB6 standard and use the
parameters (usually w/o fitting) in all other refinements. Although tube
tails fitting helps a lot it's not perfect.
Peter Zavalij

-Original Message-----
From: Alan Coelho [mailto:alancoe...@bigpond.com] 
Sent: Sunday, September 15, 2013 10:05 PM
To: Peter Y. Zavalij; mariomac...@tux.uis.edu.co; rietveld_l@ill.fr
Subject: RE: Instrumental resolution function

Hi Peter, Mario

I happen to have a Ni filter, Cu, LaB6 pattern  that has a very similar look
to the one sent by Mario. Probably best to look at the 21.35 degrees 2Th
peak. The Ni filter cut-off occurs at 20.6 degrees 2Th, the satellite group
is hard to see due to the low angle and hence compression of the emission
profile. What made sense in the pattern was to fit Tube tails. Across the
whole patter the Rwp was reduced by 2.1% where Tube tails was considered and
the fit at the shoulders was good. 

Cheers
Alan


-Original Message-
From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf
Of Peter Y. Zavalij
Sent: Monday, 16 September 2013 10:55 AM
To: mariomac...@tux.uis.edu.co; rietveld_l@ill.fr
Subject: RE: Instrumental resolution function

Hi Mario,
The shoulder you observe is what's left from "white" after it is cut off by
beta-filer. You could check the absorption edge of Ni and it is right at the
shoulder you observe.
Peter

__
Peter Zavalij
X-ray Crystallographic Center
University of Maryland
College Park, MD 20742
Phone/Fax: (301)405-1861
http:/www.chem.umd.edu/crystallography



-Original Message-
From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf
Of mariomac...@tux.uis.edu.co
Sent: Sunday, September 15, 2013 6:08 PM
To: rietveld_l@ill.fr
Subject: Instrumental resolution function

Dear All,

I am calculating the corresponding instrumental resolution function of our
Bruker diffractometer which is operating in Bragg-Brentano geometry with Cu
radiation, using a nickel filter and LynxEye detector.

The calculation is carried out by the Rietveld analysis of the LaB6 (660b)
NIST-standard. We observed the Kbeta peaks, but also some shoulders in the
left part of the peaks. We have some ideas about this but taking into
account that I'm not an actual expert, your comments will be very important
to me.

In the attached file, I send an image to make a better illustration of my
doubts.

Thanks in advance for your help.
Best Regards,

Mario A. Macías
Universidad Industrial de Santander
Bucaramanga-Colombia.


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++

RE: Instrumental resolution function

[Alan Coelho]

Hi Peter, Mario

I happen to have a Ni filter, Cu, LaB6 pattern  that has a very similar look
to the one sent by Mario. Probably best to look at the 21.35 degrees 2Th
peak. The Ni filter cut-off occurs at 20.6 degrees 2Th, the satellite group
is hard to see due to the low angle and hence compression of the emission
profile. What made sense in the pattern was to fit Tube tails. Across the
whole patter the Rwp was reduced by 2.1% where Tube tails was considered and
the fit at the shoulders was good. 

Cheers
Alan


-Original Message-
From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf
Of Peter Y. Zavalij
Sent: Monday, 16 September 2013 10:55 AM
To: mariomac...@tux.uis.edu.co; rietveld_l@ill.fr
Subject: RE: Instrumental resolution function

Hi Mario,
The shoulder you observe is what's left from "white" after it is cut off by
beta-filer. You could check the absorption edge of Ni and it is right at the
shoulder you observe.
Peter

__
Peter Zavalij
X-ray Crystallographic Center
University of Maryland
College Park, MD 20742
Phone/Fax: (301)405-1861
http:/www.chem.umd.edu/crystallography



-Original Message-
From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf
Of mariomac...@tux.uis.edu.co
Sent: Sunday, September 15, 2013 6:08 PM
To: rietveld_l@ill.fr
Subject: Instrumental resolution function

Dear All,

I am calculating the corresponding instrumental resolution function of our
Bruker diffractometer which is operating in Bragg-Brentano geometry with Cu
radiation, using a nickel filter and LynxEye detector.

The calculation is carried out by the Rietveld analysis of the LaB6 (660b)
NIST-standard. We observed the Kbeta peaks, but also some shoulders in the
left part of the peaks. We have some ideas about this but taking into
account that I’m not an actual expert, your comments will be very important
to me.

In the attached file, I send an image to make a better illustration of my
doubts.

Thanks in advance for your help.
Best Regards,

Mario A. Macías
Universidad Industrial de Santander
Bucaramanga-Colombia.

++
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Send commands to  eg: HELP as the subject with no body text
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++

Registration Deadline for EPSRC-ILL Grenoble Spring Conference

[Alan Coelho]

-Original Message-
From: Olga Smirnova [mailto:[EMAIL PROTECTED] 
Sent: Friday, May 13, 2005 8:17 AM
To: Alan Hewat


Dear Dr. Alan Hewat,

I am sorry I got know about the spring conference in Grenoble when the
deadline to apply for a support passed. Would you please write is
there a possibility to register now (with or without a contribution)
and are there funds remaining. I attached my CV and a letter of
recommendation by my supervisor.

Sincerely,

Olga Smirnova
PhD student

mailto:[EMAIL PROTECTED]


- Original Message - 
From: Alan Hewat <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Date: Wednesday, April 20, 2005, 5:14:51 PM

Dear Colleagues,

We already have over 80 participants for the EPSRC-ILL Spring Conference
in Grenoble 25-27 May, with a full list and programme
onhttp://www.ill.fr/dif/epsrc/

If you wish to attend, do NOT delay registration and flight bookings: we
are limited to ~100 participants, accommodation in our guest house is
free, and flights to Grenoble from eg London now start at £34 return -
see http://www.ill.fr/dif/epsrc/travel.html

This is a unique opportunity to see the ILL in action, and some of the
Millennium projects funded by EPSRC nearing completion. We will have
high level representation from both EPSRC and CCLRC, as well as the
Secretary and Vice President of the Royal Society, the Pro Vice
Chancellor of Keele University and other prominent scientists.

But this is a European meeting, and we also have distinguished
speakers from Germany, France, Italy and elsewhere as well as from the
UK.  

Looking forward to a sunny spring in the French Alps, Alan Hewat (local
committee)




Dr Alan Hewat, ILL Grenoble, FRANCE  <[EMAIL PROTECTED]> fax (33)
4.76.20.76.48

(33) 4.76.20.72.13 (.26 Mme Guillermet)
http://www.ill.fr/dif/AlanHewat.htm

___

 

introduction + question

[Alan Coelho]

Peter

It sounds like you were able to refine on the occupancies without
physically unreasonable site occupancies. I am also sure that you have
simplified the discussion for clarity. This is fine but I would add as a
hint to Alexander that making a number of series of samples can assist
greatly in the analysis. 

On a single sample it is a difficult job of determining precise
occupancies; this we all agree upon.

For a series of samples, lets say 6, change a single variable, a dopant
concentration for example. How, the various Rietveld parameters behave
for the various phases involved with respect to the dopant concentration
yields convincing proof of what is happening. The parameters to look at
of course include lattice parameter, bond lengths, temperature
parameters and the total scattering power observed on the sites.

Thus if the scattering power on a particular site changes with dopant
concentration then you can be sure that that site is being affected - a
simple enough deduction to make. If the site in question has a similar
scattering power as the dopant but different ionic radii then the change
in the site occupancy should show up in the trend seen in the average
bond lengths.

Further trends are obtained with many other series of samples with
sometimes only a few peaks being analysed rather than doing full
refinements. Together with refinement and enough series of samles the
trends and site occupancies can be exposed - maybe. 

Thus to end I would recommend looking for trends rather than just
looking at a single sample and believing the refinement results.

Alan


-Original Message-
From: Peter Zavalij [mailto:[EMAIL PROTECTED] 
Sent: Thursday, May 05, 2005 8:16 PM
To: rietveld_l@ill.fr


That's right. The assumption was made just to simplify discussion; in
reality of course there were no assumptions. By the way in that
particular
case it is possible to refine more that 1 occupancy (Ni/Li), e.g. total
metal content.
Peter

Peter Y. Zavalij  
Director, X-ray Crystallographic Laboratory
Department of Chemistry & Biochemistry
091 Chemistry Building
University of Maryland
College Park, MD 20742-4454

Phone: (301)405-1861
Fax:   (301)314-9121
E-mail: [EMAIL PROTECTED]

-Original Message-----
From: Alan Coelho [mailto:[EMAIL PROTECTED] 
Sent: Thursday, May 05, 2005 12:14 PM
To: rietveld_l@ill.fr


Peter

I dont know your chemical system but my first thought is that assuming
full occupancy may be too much of an sssumption. In the system I looked
at vacancies of up to 7% were observed. In fact the vacancy limit
probably determines the stability of a phase and when the limit is
reached there's a phase transition. It may very well be the case that
your system has no vacancies but I would not assume it at first.

alan


-Original Message-
From: Peter Zavalij [mailto:[EMAIL PROTECTED] 
Sent: Thursday, May 05, 2005 6:44 PM
To: rietveld_l@ill.fr


We didn't assume that Ni goes to the Li sites it was the only choice
confirmed by others, and it is not so simple as the full occupancy and
stoichiometry should be measured accurately. BTW sample composition as
well
as sample preparation is a very crucial factor where and what goes.
I believe that Mn1/3Ni1/3Co1/3 is more complex than our composition.

Peter Y. Zavalij  
Director, X-ray Crystallographic Laboratory
Department of Chemistry & Biochemistry
091 Chemistry Building
University of Maryland
College Park, MD 20742-4454

Phone: (301)405-1861
Fax:   (301)314-9121
E-mail: [EMAIL PROTECTED]

-Original Message-
From: Whitfield, Pamela [mailto:[EMAIL PROTECTED] 
Sent: Thursday, May 05, 2005 11:08 AM
To: 'rietveld_l@ill.fr'
Cc: Whitfield, Pamela


Since we're on the subject of battery materials, we published some work
recently where we didn't assume that it was the Ni that went to the Li
site
in LiMn1/3Ni1/3Co1/3O2.  It's logical if it's Ni2+ but we had the data
to
test it in the form of resonant scattering data to add some more
information
to the puzzle.  We could let the TMs (ratios known from XRF) float over
whichever site they wanted together with refining the Li/TM ratio.
Now if you have Li-rich Mn/Co/Ni materials where the Ni isn't
necessarily in
the +2 state then things get a bit more muddy as all of a sudden the TMs
have similar ionic radii. :-)
Monoclinic symmetry also makes it a lot more fun (?!)

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: <mailto:[EMAIL PROTECTED]>
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Peter Zavalij [mailto:[EMAIL PROTECTED]
Sent: May 5, 2005 11:36 AM
To: rietveld_l@ill.fr


Alexander:
I just finished combined X+N refinement of similar battery materials but
w/o
V with Li in 2a site and Mn

introduction + question

[Alan Coelho]

Peter

I dont know your chemical system but my first thought is that assuming
full occupancy may be too much of an sssumption. In the system I looked
at vacancies of up to 7% were observed. In fact the vacancy limit
probably determines the stability of a phase and when the limit is
reached there's a phase transition. It may very well be the case that
your system has no vacancies but I would not assume it at first.

alan


-Original Message-
From: Peter Zavalij [mailto:[EMAIL PROTECTED] 
Sent: Thursday, May 05, 2005 6:44 PM
To: rietveld_l@ill.fr


We didn't assume that Ni goes to the Li sites it was the only choice
confirmed by others, and it is not so simple as the full occupancy and
stoichiometry should be measured accurately. BTW sample composition as
well
as sample preparation is a very crucial factor where and what goes.
I believe that Mn1/3Ni1/3Co1/3 is more complex than our composition.

Peter Y. Zavalij  
Director, X-ray Crystallographic Laboratory
Department of Chemistry & Biochemistry
091 Chemistry Building
University of Maryland
College Park, MD 20742-4454

Phone: (301)405-1861
Fax:   (301)314-9121
E-mail: [EMAIL PROTECTED]

-Original Message-
From: Whitfield, Pamela [mailto:[EMAIL PROTECTED] 
Sent: Thursday, May 05, 2005 11:08 AM
To: 'rietveld_l@ill.fr'
Cc: Whitfield, Pamela


Since we're on the subject of battery materials, we published some work
recently where we didn't assume that it was the Ni that went to the Li
site
in LiMn1/3Ni1/3Co1/3O2.  It's logical if it's Ni2+ but we had the data
to
test it in the form of resonant scattering data to add some more
information
to the puzzle.  We could let the TMs (ratios known from XRF) float over
whichever site they wanted together with refining the Li/TM ratio.
Now if you have Li-rich Mn/Co/Ni materials where the Ni isn't
necessarily in
the +2 state then things get a bit more muddy as all of a sudden the TMs
have similar ionic radii. :-)
Monoclinic symmetry also makes it a lot more fun (?!)

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: <mailto:[EMAIL PROTECTED]>
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Peter Zavalij [mailto:[EMAIL PROTECTED]
Sent: May 5, 2005 11:36 AM
To: rietveld_l@ill.fr


Alexander:
I just finished combined X+N refinement of similar battery materials but
w/o
V with Li in 2a site and Mn, Co and Ni in 2b (or vise versa).
Chemical composition was well known; The problem we were looking for was
migration/exchange of transition metal from 2b to 2a.
That's not so simple problem as basically we have more unknown
parameters
than equations, counting that trans. metals are practically
undistinguishable from x-ray. Fortunately their neutron scattering
coefficients are very different (Mn -.37, Co .25 & Ni 1.03).
It happens that Ni migrates to the Li sites and since it has the largest
Neutron scattering it is the only possibility. 
The logic is simple:
1) X-ray yields that ~ 6% of trans. Metal (but we don't know which)
migrates
to the Li sites.
2) Neutron gives the same 6% only if the migrating metal is Ni.
Thus, in this case the only refined parameter is amount of Ni in Li
site:

Li(1-x)Ni(x) in 2a AND Mn(k) Co(m) Ni(n-x) Li(x) in 2b, 
where k,m,n are known.

It assumes however that: 1) stoichiometry is well established and 2)
both
sites are fully occupied. The latter can be confirmed for example by
measuring density.
Good luck

Peter Y. Zavalij  
Director, X-ray Crystallographic Laboratory
Department of Chemistry & Biochemistry
091 Chemistry Building
University of Maryland
College Park, MD 20742-4454

Phone: (301)405-1861
Fax:   (301)314-9121
E-mail: [EMAIL PROTECTED]

-Original Message-
From: Alan Coelho [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, May 04, 2005 3:03 PM
To: rietveld_l@ill.fr

Alexander:

Your problem is quite similar to one I had to solve in my thesis where I
had a number of mixed valence sites. I also had at my disposal X-ray and
neutron data. The method that I will now mention may be manipulated to
help.

I found the need to match expected stoichiometric results (known
elemental composition) with weight percents obtained with Rietveld
refinement including contributions from impurity phases. Care needs to
be taken in regards to micro-absorption effects. The stoichiometry is
known if you are synthesising the samples; if not then XRF results are
necessary.

The effect of using Stoichiometry is to add another 4 to 6 constraints.

Then like you suggest you can form a number of equation constraints but
some of them are not linear.  Except for a scaling constant the
scattering power amongst the various cations are too similar for X-rays
and non-existent for neutrons.

The

introduction + question

[Alan Coelho]

Alexander:

Your problem is quite similar to one I had to solve in my thesis where I
had a number of mixed valence sites. I also had at my disposal X-ray and
neutron data. The method that I will now mention may be manipulated to
help.

I found the need to match expected stoichiometric results (known
elemental composition) with weight percents obtained with Rietveld
refinement including contributions from impurity phases. Care needs to
be taken in regards to micro-absorption effects. The stoichiometry is
known if you are synthesising the samples; if not then XRF results are
necessary.

The effect of using Stoichiometry is to add another 4 to 6 constraints.

Then like you suggest you can form a number of equation constraints but
some of them are not linear.  Except for a scaling constant the
scattering power amongst the various cations are too similar for X-rays
and non-existent for neutrons.

The most important factor is the synthesising of a series of samples
with an expected vacancy concentration.  In other word working from a
single sample does not generally contain the contrast that you need.
Only from relative changes in phase concentrations can you then
determine the vacancy concentration of the target phase.

It's quite involved and I can send you my thesis on request. A lesser
use of the vacancy concentration process can be found in the
publications: 

Cheary, R. W. & Coelho, A. A.  (1997). "A Site Occupancy Analysis of
Zirconolite CaZrxTi3-xO7". Phys Chem Minearls, 24, 447-454.

Coelho, A. A.,  Cheary, R. W. & Smith, K. L.  (1997). "Analysis and
Structural Determination of Nd Substituted Zirconolite 4M". J. Solid
State Chem., 129, 346-359.

All the best
Alan

-Original Message-
From: Alexander J.M. Schmets [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, May 04, 2005 5:38 PM
To: rietveld_l@ill.fr


Dear users of the Rietveld mailing list,

My name is Alexander Schmets and currently I work as a PhD student in
the
Neutron scattering department at the Delft University of Technology, The
Netherlands. I read this Rietveld already quite some time, but this is
my
first question.

1) I have a range of samples containing Li, V , O and one or more other
transition metal ions (Ni, Co, Mn, Fe). It seems beneficial to do a
combined experiment: neutrons for finding the Li (V hardly visible), and
to distinguish between the transition metal ions; X-rays to get the
vanadium occupation correct.

I have high quality X-ray as well as neutron diffraction (GEM) data.
What
now, is royal way to proceed, such that the 'contrast' is optimally
benifitted from? (there is a topic already about simultaneous refinement
on this list, though it couldn't help me too much).

The structure is a mixed spinel (F D -3 m), where Li,V and the
transition
metals share the 8a, 16d sites and oxygens are as usual on the 32e
sites.

2) I use GSAS to refine the structure. The transition metals can occur
in
a range of oxidation states (eg: V5+, V4+, V3+, V2+, V). Different
oxidation states will contribute differently to the scattered x-ray
intensity. At the same time V's in different oxidation states will have
different 'bond lengths' with their coordinating oxygens.

Consider I know (from other experiments) that V5+ (partly) occupies a
16d
site ...should I attribute instead of V the element that is five places
backwards (Argon) to that site, in order to have the correct scattered
intensity? And then ... the bondlength definately goes wrong...should I
fix it, and where to find an apropiate estimation for such bond length?

May be too many questions for a first appearance on the list. But I
don't
see a way out.

Best Regards,

Alexander


nb) I got already the following advise: put hydrogens on all lattice
sites
..refine the fractional occupations of the sites ... then use a priori
knowledge about which elements/oxidation states reside on these lattice
sites ...and one has a set of linear equations to solve. This would give
a
set of possible structures that could be starting point for further
refinement (with now fixed partial occupancies)



-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
Alexander J.M. Schmets
Departme

RE: fundamental parameters approach & X'celerator

[alan coelho]

>>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?


John, if you had a point source, a point sample and a point receiving
slit then the plane formed by the three points is called the equitorial
plane. Drawing a circle that passes through the three points is called
the focusing circle.  Thus the 2Th arm moves in the equitorial plane.
Perpendicular to the equitorial plane are any number of axial planes. 

Aberrations can therefore be grouped into two categories, axial and
equitorial aberrations. 

Equitorial aberrations include:

The width of the source in the equitorial plane 
The divergence of the primary beam in the equitorial plane
The width of the receiving slit in the equitorial plane 
The length of the LPSD in the equitorial plane 
The length of the sample in the  equitorial plane
Tube tails which shows up in old tubes
Sample penetration (Absorption)
Sample displacement (Goniometer axis not being at the sample
surface)
Sample tilt in the axial plane
   Sample surface roughness

Axial aberrations include:

   The divergence of the primary beam allowed in the axial plane 
  at each point along the source.
   The divergence of the secondary beam allowed in the axial plane
   The length of the source, sample and receiving slit in the axial
plane

   where allowed is limited by Soller slits and the lengths 

There are cross terms which can be reasonably neglected or approximated;
ie. the sine of a small angle is the angle itself in radians etc.

Soller slits are typically inserted to limit axial divergence. In a
parallel beam setup employing a LPSD, an additional secondary Soller
slits (analyser slits) are often inserted to limit eqitorial divergence.
Thus as you pointed out John, Soller slits limit what ever you want but
they do come with their own aberration. 

Of importance when thinking about the effects of these aberrations are
the integral breadths of the aberrations as a function of 2Th and the
centroid shifts of the peak as a function 2Th. 

These relationships are all defined in TA as simple equations and are
simple enough to keep in one's mind. For a more thorough explanation see
for example:

Wilson, A. J. C. (1963), "Mathematical Theory of X-ray Powder
Diffractometry", Gordon And Breach, Science Publishers, New York.

For a more uptodate review and I think the most pertinent is:
 
R. W. Cheary, A. A. Coelho and J. P. Cline. J. Res. Natl. Inst. Stand.
Technol. 109, 1-25 (2004). "Fundamental Parameters Line Profile Fitting
in Laboratory Diffractometers"

Available on line at:

   http://nvl.nist.gov/pub/nistpubs/jres/109/1/j91che.pdf   

This excellent work occupied three out of the last six months of Bob
Cheary's life. 

Alan

RE: fundamental parameters approach & X'celerator

[alan coelho]

Jim Cline wrote:
>Alan???  Are you listening?

Armel wrote:
>>Bruker providing help to analyze Panalytical data ?-).

You have thrown the bait and I will bite.

I am not an employee of a manufacture and as such I am free to implement
as I choose into TOPAS-Academic (TA) and I do this without regard to
manufacture. TA is not institutionally funded (typical), falls far short
of paying its way and thus that classifies it as a hobby. 

Fundamental parameters in regards to a linear PSD (LPSD) was worked out
by myself and Bob Cheary: Cheary, R. W. & Coelho, A. A.  (1994).
"Synthesising and Fitting Linear Position-Sensitive Detector
Step-Scanned Line Profiles". J Appl. Cryst. 27, 673 - 681.

To be humble I should say that such a geometrical analysis is
significant but not world shattering in its own right. The difficulty is
in the massaging of the equations into a form that allows an
implementation in a meaningful sense. This is where Bob and I have
contributed standing on the shoulders of GIANTS in the field like Jim
and Armel.

>Last point, what do you mean by vertical divergence? The Topas 
>manual defines the 'axial divergence' which can be limited by soller 
>slits, and the 'horizontal divergence in the equitorial plane', which
is, 
>I think, the divergence perpendicular to the axial divergence. 
>Whether you call it horizontal or vertical depends on whether you 
>have a horizontal or vertical goniometer .

Its best to use the terms axial plane and horizontal plane to avoid
confusion.

>Is there anybody who has experience with describing peak shapes 
>using the fundamental parameters approach for a typical X'pert-pro 
>diffractometer setup with an X'celerator detector (fixed incident 
>slits, 0.02 rad sollers, no monochromator)?

Arie, I don't know about either the Bruker or Panalytical LPSD's but my
guess is that modern LPSDs reduces or even removes the parallex
aberration which is associated with the depth of the detector. This
would sharpen peaks. If this is the case then my feeling is that TA can
describe modern LPSD step scanned profiles using the peak stack
mechanism and the one_on_x_conv convolution for the case of a flat
sample and not using a primary monochromator. In Laurel Basciano case
the LPSD aberrations is not noticeable due to the small LPSD window
used. 

Thus Arie's query is still unanswered as no one seems to know how these
detectors work or worst still no one reads these mails; maybe the
manufacture's specifications are enough to look into.

In regards to non-standard configurations and in particular geometry
employing a focusing pre-monochromator in a laboratory sense. Such a
setup is sensitive to alignment and often the beam is inhomogeneous in
wavelength in the horizontal plane. This leads to a noticeable change in
expected alpha1 and alpha2 separation at moderate to high angles. Such
an effect can be modeled for the case where alpha2 is not removed but it
needs more investigation.

As usual such an implementation/investigation is non-trivial to do
properly. If someone wants to volunteer GOOD data and time then I am
willing to collaborate - time permitting.

So in addition to Arie's query I would like to know if others have
noticed such alpha1/alpha2 anomalies.

Alan

Re: Size Strain in GSAS

[alan coelho]

Title: Message



Nicolae
>To resume, I think (for example) that is 
better to approximate by a sum of 
>three Lorentzians (involving 
4 profile parameters) than by a sum of two 
>pVs (involving 5 profile parameters). 

 
I 
couldnt agree more.
 
>Concerning the numerical calculation of the profiles, still I'm not 
convinced 
>that is the ideal solution. You have not only the size 
profile to calculate, 
>but also at least two convolutions, with the strain and 
the instrumental 
>profiles. Moreover, what are doing the codes that use 
the gradient 
>calculated analytically?
 
Size 
distribution is a start and Leonie does seem to have worked in some of the other 
effects to his credit. 
 
Whether all this actually helps in the analysis of Size/Strain does not 
seem to concern many - so why not experiment.
 
By 
gradient, I presume you mean the derivatives of the distribution with respect to 
parameters. This would require a mixture of numerical and analytical derivatives 
- very simpe using the chain rule. Dont see why the same cant be done in other 
codes.
 
all 
the best
alan
 
 

  
  -Original Message-From: Nicolae Popa 
  [mailto:[EMAIL PROTECTED] Sent: Monday, April 18, 2005 3:33 
  PMTo: rietveld_l@ill.frSubject: Re: Size Strain in 
  GSAS
  Alen,
  you right, as far as the profile 
  corresponding to a given distribution is accurately described, any 
  representation is good. Nevertheless, at comparative accuracies, it is not 
  better to use a representation with smaller numbers of parameters? 
  
  The profile parameters are 
  functions of the parameters of distribution; in particular for the discussed 
  distributions, lognormal, gamma, the profile parameters are functions of a 
  unique distribution parameter "c". Further, to have a functional 
  formula for profile to be implemented in the Rietveld programs, the 
  dependence on "c" of  the profile parameters must be found (somehow, 
  empirical formulae for example). Now, the number of profile parameters you 
  have used in the primary fit becomes critical. If this number is small the 
  dependence of everyone  on "c" is more or less smoothed. If the number of 
  these parameters is higher than necessary, the dependence on "c" is rather 
  "ugly" and difficult describe. To resume, I think (for example) that is better 
  to approximate by a sum of three Lorentzians (involving 4 profile parameters) 
  than by a sum of two pVs (involving 5 profile parameters). 
   
  Concerning the numerical 
  calculation of the profiles, still I'm not convinced that is the ideal 
  solution. You have not only the size profile to calculate, but also at least 
  two convolutions, with the strain and the instrumental profiles. Moreover, 
  what are doing the codes that use the gradient calculated 
  analytically?
   
  Best wishes,
  Nicolae
   
   
  
  

This is by far the best topic on 
this list for a long time as opposed to requests for Journal papers which as 
pointed out by someone else is inappropriate in the first place and illegal 
in the second.
 
Nicolae 
wrote:
>(i) but a sum of two 
Lorentzians is not sharper than the sum of two pVs 
(Voigts)?
 
This I know, it should not 
matter what is used as long as the 
mapping of the function to a distribution is done accurately. Whether it is 
lognomal, gamma or 
something else does does not matter. 
 
. 
 
As a hint to those who write such code the 
calculation of a profile for an arbitraty distribution operates at around 
5000 profiles per second as I noticed over the weekend - not much slower 
that a gaussian Nicolae. Maybe there's no need for a pseuod-Voigt / 
Lorentzian based approximations after 
all.
 
 
all the best
Alan

Re: Size Strain in GSAS

[alan coelho]

>For the purists, just redo the calculation starting from different
points 
>and you can evaluate the error in the distribution using a 
>MonteCarlo-like approach...

Leonie,

Your error estimation procedure sounds a lot like the "boot strap"
method which I think has now gained credibility, see:

http://www.amazon.com/exec/obidos/tg/detail/-/0412042312/002-2676968-371
2052?v=glance

alan



-Original Message-
From: Matteo Leoni [mailto:[EMAIL PROTECTED] 
Sent: Monday, April 18, 2005 2:00 PM
To: rietveld_l@ill.fr


buna Nicolae,

> Not only arithmetic, I think is clear that both  and c were refined
in a
> whole pattern least square fitting. A private program, not a popular
> Rietveld program because no one has inplemented the size profile
caused by
> the lognormal distribution.

not sure no one did.. we're working with that kind of profiles at 
least since 2000 (published in 2001 Acta Cryst A57, 204), without the
need 
for any approximation going through Voigts or Pseudo Voigts. Using FFT
and 
some math tricks you can compute the "true" profile for a distribution
of 
crystallites almost in the same time you calculate a Voigt curve, so why

the need to use any approximate function? 
I think this agrees with what Alan just pointed out (well 5000 profiles 
per second if you do not include any hkl dependent broadening that has 
to be calculated for each of them (and perhaps for each subcomponent)...

otherwise the speed reduces.. but yes few ms for each profile is the 
current speed for my WPPM code, implementing all this stuff within the 
WPPM frame). 

> > But the most important disadvantage is the necessity to choose the
> > exact type of size distribution. For Sample 1 (which, obviously,
have
> > certain distribution with certain  and c) you got quite different
> > values of  and c for lognorm and gamma models, but the values of
Dv
> > and Da were nearly the same. Don't you feel that Dv and Da values
> > "contain" more reliable information about  and c than those
> > elaborate approximations described in chapter 6?
> 
> Well, this is the general feature of the least square method. In the
least
> square you must firstly to choose a parametrised model for something
that
> you wish to fit.  Do you know another posibility with the least square
than
> to priory choose the model? Without model is only the deconvolution,
and
> even there, if you wish a "stable" solution you must use a
deconvolution
> method that requres a "prior, starting model" (I presume you followed
the
> disertation of Nick Armstrong on this theme).

also in this case it has ben shown possible to obtain a distribution 
without any prior information on its functional shape (J.Appl.Cryst
(2004), 
37, 629) and without taking the maxent treatment into account. 
I'm currently using without much problems for the analysis of 
nanostructured materials... advantages with respect to maxent are the 
speed and the fact that it can coexist with other broadening models
(still  
not possible with maxent and still have to see a specimen where strain  
broadening is absent) and it's able to recover also a polydisperse  
distribution if it's present Just need to test it against maxent (if

data would be kindly provided to do so).
For the purists, just redo the calculation starting from different
points 
and you can evaluate the error in the distribution using a 
MonteCarlo-like approach...

As for the TCH-pV, well, it is no more than a pV with the Scherrer 
trend (1/cos) and the differential of Bragg's law (tan term) plugged in.
This means it is ok as long as you consider a Williamson-Hall plot a
good 
quantitative estimator for size and strain (IMHO).

Mat

PS I fully agree with Alan on the continuous request for Journals, but I

bet the other Alan (the deus ex machina of the mailing list) should warn

the members somehow...

--
Matteo Leoni
Department of Materials Engineering
and Industrial Technologies 
University of Trento
38050 Mesiano (TN)
ITALY

Re: Size Strain in GSAS

[alan coelho]

Title: Message




This is by far the best topic on 
this list for a long time as opposed to requests for Journal papers which as 
pointed out by someone else is inappropriate in the first place and illegal in 
the second.
 
Nicolae wrote:
>(i) but a sum of two Lorentzians 
is not sharper than the sum of two pVs (Voigts)?
 
This I know, it should not matter 
what is used as long as the mapping of the 
function to a distribution is done accurately. Whether it is lognomal, gamma or 
something else does does not matter. 
 
Every thing we are talking about is 
additive meaning that the sum of what ever in 2Th space translates to the sum of 
what ever distributions. From the resulting distribution you are free to extract 
what ever parameter you choose.
 
The idea in Nick Armstrong’s work of 
obtaining a distribution without knowing its functional form is a powerful one. 
But the Baysean approach without a 
functional form results in large errors 
bars in the distribution, see  http://nvl.nist.gov/pub/nistpubs/jres/109/1/cnt109-1.htm
 
What we should be looking 
for are cases where Voigt approximations are not possible. I have only ever seen one 
case where the actual Sinc type ripples are seen in a pattern. This was a 
pattern by Bob Cheary of gold columns. Other reports of ripples do exist in the 
literature (not available to me as I write). We must be careful not to include 
2Th independent bumps produced by 
long narrow Soller slits inserted 
in the axial plane that limits 
horizontal divergence.
 
When sample related ripples are seen 
then you can throw Voigt based approximations out the window. In the case of the 
gold columns we fitted three Sinc functions added together. In other words the 
distribution was really a limited one.
 
The work of Nick et al is sound and 
approaches the problems from a different perspective; it does not however negate 
the need to determine a priori information. The question that is open in my opinion is whether a priori information is 
more easily incorporated into a least squares process or a Bayesian Maxent 
approach.
 
This 
discussion has reinvigorated my interest and 
like Bob, whom is now looking for an equation to approximate the log normal 
disribution, I will resurrect  some code myself that I did a while back which 
calculates profiles from a arbitrary distribution for the Sinc function. Instead 
I will include the equation for spherical crystallites and of course a user 
defined one which can be hkl dependent. 
 
As a hint to those who write such code the calculation 
of a profile for an arbitraty distribution operates at around 5000 profiles per 
second as I noticed over the weekend - not much slower that a gaussian 
Nicolae. Maybe there's no need for a pseuod-Voigt / Lorentzian 
based approximations after all.
 
 
all 
the best
Alan
 

  
  -Original Message-From: Nicolae Popa 
  [mailto:[EMAIL PROTECTED] Sent: Sunday, April 17, 2005 9:00 
  AMTo: rietveld_l@ill.frSubject: Re: Size Strain in 
  GSAS
  Alan,
   
  (i) but a sum of two Lorentzians is not sharper 
  than the sum of two pVs (Voigts)?
   
  (ii) We  fitted the exact size profile 
  caused by the lognormal distribution by a pV (for low lognormal dispersion) or 
  by a sum of maximum 3 Lorenzians (for large lognormal 
dispersion).
  This is "cheaper"  than the sum of 2 
  pVs. It involves the calculation of maximum 3 elementary 
  functions with 4 independent parameters (3 breadths + 2 mixing 
  parameters minus 1 constraint = 4) 
  Sum of two pVs presumes 4 elementary function and 
  5  independent parameters (2 for one pV + 2 for the second one + a mixing 
  parameter).
   
  Best wishes,
  Nicolae
   
   
  
 

A pure peak fitting approach shows that two pV’s (or two Voigts) 
when added with different FWHMs 
and integrated intensities but similar peak positions and eta 
values can almost exactly fit Pearsons II functions that are sharper that 
Lorentzians. This is not surprising as both profiles comprise 6 parameters. 

 
Thus from my observations two pVs added together can fit a 
bimodal distributions quite easily. In fact my guess is that two pVs can fit 
a large range of crystallite size distributions. 
 

  

all the best
alan
 

Re: Size Strain in GSAS

[alan coelho]

Title: Message




Nicolae, Nick, Bob, 
Leonid,
 
I have looked at many patterns (recorded by others) and a few cases 
have shown profiles that are sharper that a Lorentzian; whereby “sharper” means 
that the integral breadth is smaller than that for a unit area lorentzian. 

 
To put a figure on it would be difficult but at a guess I would say 
< 3% of patterns fall into this category in a noticeable manner. 

 
I have no doubt that the work of Nick Armstrong and co. is 
mathematically sound but  a 
simulated data round robin as suggested by Leonid Solovyov may be useful – and I 
am not generally a fan of round robins but this s different as the data is 
simulated. 
 
A pure peak fitting approach shows that two pV’s (or two Voigts) when 
added with different FWHMs 
and integrated intensities but similar peak positions and eta values 
can almost exactly fit Pearsons II functions that are sharper that Lorentzians. 
This is not surprising as both profiles comprise 6 parameters. 

 
Thus from my observations two pVs added together can fit a bimodal 
distributions quite easily. In fact my guess is that two pVs can fit a large 
range of crystallite size distributions. 
 
Thus distinguishing whether a distribution is not 
monomodal is of course possible especially if the two pV approach is taken. 

 
Attempting to determine more than that however takes 
some convincing as two pVs seem to fit almost anything that I have seen that is 
symmetric. Thus introducing more pVs seems 
unnecessary.
 
Thus yes GSAS can determine if a distribution is not monmodal if you 
were to fit two identical phases to the pattern except for the TCH parameters. 
If the Rwp drops by .1% then I wont be convinced.
 
Forgive me Nick but I have not yet read all of your work 
and I am certain that it is sound. Outside of nano particles (and maybe even 
inside) my reservation are that we may well be analyzing noise and second order 
sample and instrumental effects.
 
Thus to show up my naive ness can you categorically say 
that there are real world distributions that two pseudo Voigts cannot fit 
because I have not come across such a pattern. 
 
Once you have done that 
then it would be time to concentrate on strain, micro strain, surface roughness 
and then disloactions
 
all the best
alan
 
 

  
  -Original Message-From: Nicolae Popa 
  [mailto:[EMAIL PROTECTED] Sent: Friday, April 15, 2005 9:30 
  AMTo: rietveld_l@ill.frSubject: Re: Size Strain in 
  GSAS
  Dear Bob,
   
  Perhaps I was not enough clear. Let me be more 
  explicit.
  It's about one sample of CeO2 (not that from 
  round-robin) that we fitted in 4 ways.
   
  (i)    by GSAS with 
  TCH-pV
  (ii)   by another pV resulted from 
  gamma distribution of size
  (iii)  by Lorentz - (the limit of any 
  "regular" pV - eta=1)
   
  All these 3 variants given bad fits. For example 
  (ii): Rw=0.144, similarly the rest. (In principle if one pV works (TCH for 
  example) any other kind of pV must work.)
   
  (iv)  by the profile resulted from lognormal 
  distribution of size; this time the fit was reasonably good: Rw=0.047. It 
  resulted c=2.8, that means a "super Lorentzian" profile (I remember that the 
  Lorentzian limit for lognormal is c~0.4 -  JAC (2002) 35, 
  338).
  Attention, this "super Lorentzian" profile is not 
  constructed as a pV with eta>1.
   
  Sure, such samples are rare, or, perhaps, not so 
  rare. A Jap. group (Ida,, Toraya, JAC (2003) 36, 1107) reported "super 
  Lorentzian" on a sample of SiC. They found c=1.37
   
  Best wishes,
  Nic Popa
   
  
Nic,
This is true for the internal math but the TCH function was assembled 
to reproduce the true Voigt over the entire range of differing Lorentz and 
Gauss FWHM values so it works as if the two FWHM components are independent. 
As for your question, I'm not aware that anyone has actually tried to do the 
fit both ways on a "super Lorentzian" (eta>1 for old psVoigt) sample to 
see if a) the fit is the same and b) the eta>1 was an artifact. Any 
takers to settle this?
Bob
 
 

R.B. Von Dreele
IPNS Division
Argonne National Laboratory
Argonne, IL 60439-4814
 

  
  -Original Message-From: Nicolae Popa 
  [mailto:[EMAIL PROTECTED] Sent: Thursday, April 14, 2005 9:11 
  AMTo: rietveld_l@ill.frSubject: Re: Size Strain in 
  GSAS
  Dear Bob,
   
  If I understand well, you say that eta>1 
  (super Lorenzian) appeared only because eta was free parameter, but if TCH 
  is used super Loreanzians do not occur?
  Nevertheless, for that curious sample of 
  cerium oxide we tried GSAS (with TCH) and the fit was very 
  bad.
  Best wishes,
  Nicolae
   
  PS. By the way, TCH also forces FWHM of the 
  Gaussian and Lorenzian components to be equal, but indeed, eta is not free 
  and cannot be greater than 1.
   
  

Nic,
I know ab

RE: [sdpd] Derivative Difference Minimization

[alan coelho]

Leonid Solovyov wrote:

> The Derivative Difference Minimization (DDM) program is now freely
> available via the web: 


First impressions - "What a nifty idea". 

Haven't given thought to all of the ramifications but it certainly does
seem to have merits. Cant wait to analyze it myself; put it through its
paces so to speak.

cheers
alan

RE: instrumental correction

[alan coelho]

Apu,

The basics of instrument contributions to profile shapes for X-ray
laboratory data should really be well known by now. 

UVW (add Z if you like) is a calibration approach that can never fully
describe X-ray laboratory data as Gaussians and Lorentzians do not
describe the instrument aberrations nor can they describe the specimen
transparency aberration. From memory the UVW approach was developed for
neutron CW data.

Armel wrote:

>People prefer to convolute g (or a model of g) with a model of f in
>order to obtain h, this is much more stable than to deconvolute.
>Nobody works on the f full profile (you would be alone) because
>nobody can obtain a realistic representation of it, without strange
>effects (ripples, etc) due to error propagation (either by Fourier
>inversion method or else).

Convolution like Armel has mentioned needs to be performed in order to
get to the specimen contribution. I do however disagree in that programs
such as XFIT (take note Armel as its free from
http://www.ccp14.ac.uk/tutorial/xfit-95/xfit.htm) and later programs
such as TOPAS-Academic do remove the instrument contribution using
convolution. GSAS also uses some fundamental parameters ideas such as
the Finger and Cox model for axial divergence. Excuse me if I have not
mentioned other note worthy efforts.

Like Armel eluded to deconvolution is difficult for reasons I wont go
into here and it is not the preferred way of doing things in my view. 

Convolution techniques are well known, see: 

Wilson, A. J. C. (1963), "Mathematical Theory of X-ray Powder
Diffractometry", Gordon And Breach, Science Publishers, New York. 
Cheary, R. W. & Coelho, A. A.  (1992).   J Appl. Cryst. 25, 109-121.
Cheary, R. W. & Coelho, A. A.  (1998). "Axial Divergence in a
Conventional X-ray Powder Diffractometer I. Theoretical Foundations". J.
Appl. Cryst. 31, 851-861.

and they do work in practice on whole patterns and have been doing so
for the past 12 years. 

Typically diffractometers are misaligned to some degree (in some cases a
large degree) and refinement of one or two of the key instrumental
parameters are necessary. For a well aligned instrument these key
instrumental parameters should refine to +-10% of their true values.
Otherwise the diffractometer is misaligned.

It is worthwhile to use a standard such as LaB6 and to fit to LaB6 using
convolution in order to ensure proper instrument alignment. 

Having argued the point for the fundamental parameters approach I would
however add that an intelligent calibration can be fruitful for
non-standard diffractometer configurations. ie. it is almost always
possible to use a few generic convolutions with a hint of physical
meaning to fit to LaB6 whilst fixing the specimen contribution in order
to obtain the instrument contribution.

For standard Bragg-Brentano geometry, here are a few things that
fundamental parameters are good at describing:

1) A proper description of the emission profile.
2) Axial divergece. Strong preferred orientaion effects can also lead to
patchy diffraction cones which affect axial divergence.
3) Specimen transparancy especially for specimens that have low linear
absorption coefficients. Total penetration by the primary beam can also
be of signifiance and should be corrected when the sample is thin or
organics are collected with Mo radiation etc...
4) The receiving slit aberration for wide slits in the equitorial plane.
5) Equitorial divergence - important when variable divergence slits are
used.

When one looks at the shapes of these aberrations as a function 2Th, it
seems to not make sense to talk about Voigts in terms of describing the
convoluted effects unless of course the effects are small in comparison
to the sample related Voigt effects.

regards
alan

RE: convertion to a z-matrix model in TOPAS

[alan coelho]

Simon,

>Presumably the translation component is just the fractional 
> coordinates of the first atom in my Z-matrix, something 
>like 
>
>Translate(@ .1, @ .2, @ .3)
>
>if my first atom is at .1, .2, .3.
>
>Does anyone know how to go about getting the rotation part, 
>ie the '?' parts in:
>
>Rotate_about_axes(@ ?, @ ?, @ ?)



If you wanted to rotate atoms A, B and C about an origin of (u, v, w)
then you need to first translate A, B, C by an amount of (-u, -v, -w),
perform the rotation and then translate A, B, C again by an amount (u,
v, w). 

For example, to rotate A, B, C around the 'a' lattice vector with a
rotation origin defined at atom D, then the following could be used:

   translate
  ta = -Point(D, rx);
  tb = -Point(D, ry);
  tc = -Point(D, rz);
operate_on_points "A B C"

roate @ 10 qa 1 
operate_on_points "A B C"

   translate
  ta = Point(D, rx);
  tb = Point(D, ry);
  tc = Point(D, rz);
operate_on_points "A B C"

Using the Translate_point_amount macro simplifies the above but it is
good to spell it out first.

Thus the question to ask when performing a rotation is! What is the
rotation origin. For refinement purposes it is often desirable to rotate
a molecule around its geometric center, or something close to it. This
can be achieved by using the translate operator.

If you need more information then let me know but maybe off the list.
cheers
alan

differences between TOPAS-Academic (TA) and TOPAS

[alan coelho]

dear all

thought I was clear on the differences between TOPAS-Academic (TA) and
TOPAS. In any case to save me a lot of writing of separate e-mails I
have spelt it out here:

http://pws.prserv.net/Alan.Coelho

regards
alan

RE: troublesome unit cell

[alan coelho]

Title: Message



Pam,
 
If the 
other programs are in error at the hkl stage then my suggestion is to send the 
hkls from the apparently working programs to the authors of the apparently not 
working programs. 
 
Or 
better yet those authors should contact you as I for one am always on the look 
out for "apparent" discrepencies.
alan

  
  -Original Message-From: Whitfield, 
  Pamela [mailto:[EMAIL PROTECTED] Sent: Tuesday, 
  October 19, 2004 12:05 AMTo: '[EMAIL PROTECTED]'Subject: 
  RE: troublesome unit cell
  Alan
   
  In the original 
  simulations I used them exactly as you describe :-)
  I modified that file to be able to start refining the TM 
  x and y positions for some data I have.  Topas is still seeing them as 3a 
  and 3b positions, so internally they are still 1/9, 5/9 etc, as they started 
  out.  In any case it doesn't make a massive difference.  
  The problems I refer to in some software are not subtle, they're 
  huge, and seem to reflect a problem in hkl-related 
  multiplicities.
   
  Pam  
   
  Dr Pamela Whitfield CChem MRSCEnergy Materials 
  GroupInstitute for Chemical Process and Environmental TechnologyBuilding 
  M12National Research Council Canada1200 Montreal 
  RoadOttawa ON K1A 0R6CANADATel: (613) 998 8462 Fax: (613) 991 2384Email: 
  <<mailto:[EMAIL PROTECTED]>>ICPET 
  WWW: <http://icpet-itpce.nrc-cnrc.gc.ca/> 
  
-Original Message-From: alan coelho 
[mailto:[EMAIL PROTECTED]Sent: October 18, 2004 5:36 
PMTo: [EMAIL PROTECTED]Subject: RE: troublesome unit 
cell
Pam,
 
I 
looked at your INP file and there was a problem in regards to how atomic 
coordinates were defined. As you know TOPAS uses computer algebra with a 
tollerance of 1.0e-15 for checking the equivalence of equivalent positions. 
If I use
 
x 
= 1/9; y = 5/9;  etc,,,
 
then the structures are similar.
 
It 
is not often obvious these equations but it is easy to check using the 
number of equivalent positions or by inspecting the bond 
lengths.
 
My 
guess is that the other programs may have conventions that are also not 
obvious.
 
it 
is always good to do some checking
cheers
alan
 
 

  
  -Original Message-From: Whitfield, 
  Pamela [mailto:[EMAIL PROTECTED] Sent: Monday, 
  October 18, 2004 10:32 PMTo: 
  '[EMAIL PROTECTED]'Subject: RE: troublesome unit 
  cell
  AlanI'm afraid that the cif files weren't overly 
  good ones - I don't normally use them.  For the R-3m the Li 1/2 
  fractional coordinate is for the z, not y.  The structures are 
  related by a Ö3a x Ö3a 
  relationship with Z = 3 for the R-3m and Z = 9 for the P3112.Here are 
  the STR files.  You can refine the 3a and 3b positions for the P3112, 
  but there is a strict relationship that has to be maintained between the x 
  and y coordinates - I have to do it in launch mode to make it work.  
  It's a very picky space group to work with.PamDr 
  Pamela Whitfield CChem MRSCEnergy Materials GroupInstitute for 
  Chemical Process and Environmental TechnologyBuilding M12National 
  Research Council Canada1200 Montreal RoadOttawa  
  ON   K1A 0R6CANADATel: (613) 998 
  8462 Fax: (613) 991 
  2384Email: <mailto:[EMAIL PROTECTED]>ICPET 
      WWW: http://icpet-itpce.nrc-cnrc.gc.ca-Original 
  Message-From: alan coelho [mailto:[EMAIL PROTECTED]]Sent: 
  October 18, 2004 4:16 PMTo: [EMAIL PROTECTED]Subject: RE: 
  troublesome unit cellPam,As a developer and someone 
  who uses other software to test against, Ihave been following the 
  discussion with interest. This is a complex areaand it goes to show 
  the importance of having a few programs if only fortesting 
  purposes.I am puzzled by your cif data however as I cant get past 
  verifying theequivalence of the number of equivalent positions for the 
  Li site.In R-3m you have as fractional atomic coordinates for 
  Li1:  x = 0    y = 0.5  and  z = 
  0For P3112 you have three Li sites with x, y, z's 
  as0.77780 0.0 0.833300.0 0.88890 0.833300.0 
  0.55560 0.83330which translates to:0.77780 0.0 
  5/60.0 0.88890 5/60.0 0.55560 5/6Listed below are 
  equivalent positions for a general site.What I dont understand is 
  that for R-3m I get 9 non-overlapping fullyoccupied equivalent 
  positions within the unit cell with a volume of101.2975.For 
  P3112 I get 18 non-overlapping equivalent positions with a volumethree 
  times as large of 303.8968. I was expecting to get 27 if the 
  twostructure were to be equivalent.Thus, from your cif data I 
  am left to conclude that I am generating thewrong number of equivalent 
  positions, or, if I am gene

RE: troublesome unit cell

[alan coelho]

Bob and Pam,

Hope others on the list dont consider this topic as spam but the
checking across programs are a critical part of developent.

and a thanks by myself to the both of them for hand checking the
equivalent poistions - no wonder Bob made a goof.
regards
alan



-Original Message-
From: Von Dreele, Robert B. [mailto:[EMAIL PROTECTED] 
Sent: Monday, October 18, 2004 10:39 PM
To: [EMAIL PROTECTED]


Alan,
One of your operators is a typo.
"-x+y, y, -z+1/3" should be " Y-X Y  1/3-Z"
Bob


____

From: alan coelho [mailto:[EMAIL PROTECTED]
Sent: Mon 10/18/2004 3:16 PM
To: [EMAIL PROTECTED]



Pam,

As a developer and someone who uses other software to test against, I
have been following the discussion with interest. This is a complex area
and it goes to show the importance of having a few programs if only for
testing purposes.

I am puzzled by your cif data however as I cant get past verifying the
equivalence of the number of equivalent positions for the Li site.

In R-3m you have as fractional atomic coordinates for Li1:

  x = 0y = 0.5  and  z = 0

For P3112 you have three Li sites with x, y, z's as

0.77780 0.0 0.83330
0.0 0.88890 0.83330
0.0 0.55560 0.83330

which translates to:

0.77780 0.0 5/6
0.0 0.88890 5/6
0.0 0.55560 5/6

Listed below are equivalent positions for a general site.

What I dont understand is that for R-3m I get 9 non-overlapping fully
occupied equivalent positions within the unit cell with a volume of
101.2975.

For P3112 I get 18 non-overlapping equivalent positions with a volume
three times as large of 303.8968. I was expecting to get 27 if the two
structure were to be equivalent.

Thus, from your cif data I am left to conclude that I am generating the
wrong number of equivalent positions, or, if I am generating the correct
number of equivalent positions then the two cif data sets should indeed
give different powder patterns.

Have you checked what the number of non-overlapping fully occupied
equivalent positions for Li should be for the two structures.

alan





P3112
xyzs
{
-x+y, -x, z-1/3
-x+y, y, -z+1/3
-y, -x, -z-1/3
-y, x-y, z+1/3
x, y, z
x, x-y, -z
} 6


R-3m
xyzs
{
-x, -x+y, -z
-x, -y, -z
-x+y, -x, z
-x+y, y, z
-y, -x, z
-y, x-y, z
y, -x+y, -z
y, x, -z
x-y, -y, -z
x-y, x, -z
x, y, z
x, x-y, z
' +(-1/3, 1/3, 1/3) -
-x-1/3, -x+y+1/3, -z+1/3
-x-1/3, -y+1/3, -z+1/3
-x+y-1/3, -x+1/3, z+1/3
-x+y-1/3, y+1/3, z+1/3
-y-1/3, -x+1/3, z+1/3
-y-1/3, x-y+1/3, z+1/3
y-1/3, -x+y+1/3, -z+1/3
y-1/3, x+1/3, -z+1/3
x-y-1/3, -y+1/3, -z+1/3
x-y-1/3, x+1/3, -z+1/3
x-1/3, y+1/3, z+1/3
x-1/3, x-y+1/3, z+1/3
' +(1/3, -1/3, -1/3) -
-x+1/3, -x+y-1/3, -z-1/3
-x+1/3, -y-1/3, -z-1/3
-x+y+1/3, -x-1/3, z-1/3
-x+y+1/3, y-1/3, z-1/3
-y+1/3, -x-1/3, z-1/3
-y+1/3, x-y-1/3, z-1/3
y+1/3, -x+y-1/3, -z-1/3
y+1/3, x-1/3, -z-1/3
x-y+1/3, -y-1/3, -z-1/3
x-y+1/3, x-1/3, -z-1/3
x+1/3, y-1/3, z-1/3
x+1/3, x-y-1/3, z-1/3
} 36



/* Fractional atomic coordinates for for R-3m
Li1
 0.0  0.5  0.0
 0.5  0.0  0.0
 0.5  0.5  0.0
 0.7  0.8  0.3
 0.16667  0.3  0.3
 0.16667  0.8  0.3
 0.3  0.16667  0.7
 0.8  0.7  0.7
 0.8  0.16667  0.7
*/


/* Fractional atomic coordinates for P3112
Li
 0.0  0.0  0.5
 0.77780  0.0  0.8
 0.77780  0.55560  0.16667
Li
 0.77780  0.88890  0.5
 0.0  0.88890  0.8
 0.0  0.0  0.16667
Li
 0.11120  0.55560  0.5
 0.0  0.55560  0.8
 0.0  0.0  0.16667
*/

RE: troublesome unit cell

[alan coelho]

Title: Message



Pam,
 
I 
looked at your INP file and there was a problem in regards to how atomic 
coordinates were defined. As you know TOPAS uses computer algebra with a 
tollerance of 1.0e-15 for checking the equivalence of equivalent positions. If I 
use
 
x = 
1/9; y = 5/9;  etc,,,
 
then 
the structures are similar.
 
It is 
not often obvious these equations but it is easy to check using the number of 
equivalent positions or by inspecting the bond lengths.
 
My 
guess is that the other programs may have conventions that are also not 
obvious.
 
it is 
always good to do some checking
cheers
alan
 
 

  
  -Original Message-From: Whitfield, 
  Pamela [mailto:[EMAIL PROTECTED] Sent: Monday, 
  October 18, 2004 10:32 PMTo: '[EMAIL PROTECTED]'Subject: 
  RE: troublesome unit cell
  AlanI'm afraid that the cif files weren't overly good 
  ones - I don't normally use them.  For the R-3m the Li 1/2 fractional 
  coordinate is for the z, not y.  The structures are related by a Ö3a x Ö3a relationship with Z = 3 
  for the R-3m and Z = 9 for the P3112.Here are the STR files.  You can 
  refine the 3a and 3b positions for the P3112, but there is a strict 
  relationship that has to be maintained between the x and y coordinates - I 
  have to do it in launch mode to make it work.  It's a very picky space 
  group to work with.PamDr Pamela Whitfield CChem 
  MRSCEnergy Materials GroupInstitute for Chemical Process and 
  Environmental TechnologyBuilding M12National Research Council 
  Canada1200 Montreal RoadOttawa  ON   K1A 
  0R6CANADATel: (613) 998 
  8462 Fax: (613) 991 
  2384Email: <mailto:[EMAIL PROTECTED]>ICPET 
  WWW: http://icpet-itpce.nrc-cnrc.gc.ca-----Original 
  Message-From: alan coelho [mailto:[EMAIL PROTECTED]]Sent: 
  October 18, 2004 4:16 PMTo: [EMAIL PROTECTED]Subject: RE: troublesome 
  unit cellPam,As a developer and someone who uses other 
  software to test against, Ihave been following the discussion with 
  interest. This is a complex areaand it goes to show the importance of 
  having a few programs if only fortesting purposes.I am puzzled by 
  your cif data however as I cant get past verifying theequivalence of the 
  number of equivalent positions for the Li site.In R-3m you have as 
  fractional atomic coordinates for Li1:  x = 0    y 
  = 0.5  and  z = 0For P3112 you have three Li sites with x, 
  y, z's as0.77780 0.0 0.833300.0 0.88890 0.833300.0 
  0.55560 0.83330which translates to:0.77780 0.0 
  5/60.0 0.88890 5/60.0 0.55560 5/6Listed below are 
  equivalent positions for a general site.What I dont understand is that 
  for R-3m I get 9 non-overlapping fullyoccupied equivalent positions within 
  the unit cell with a volume of101.2975.For P3112 I get 18 
  non-overlapping equivalent positions with a volumethree times as large of 
  303.8968. I was expecting to get 27 if the twostructure were to be 
  equivalent.Thus, from your cif data I am left to conclude that I am 
  generating thewrong number of equivalent positions, or, if I am generating 
  the correctnumber of equivalent positions then the two cif data sets 
  should indeedgive different powder patterns.Have you checked what 
  the number of non-overlapping fully occupiedequivalent positions for Li 
  should be for the two 
  structures.alanP3112xyzs{    
  -x+y, -x, z-1/3    -x+y, y, 
  -z+1/3    -y, -x, 
  -z-1/3    -y, x-y, 
  z+1/3    x, y, 
  z    x, x-y, -z} 
  6R-3mxyzs{    
  -x, -x+y, -z    -x, -y, 
  -z    -x+y, -x, 
  z    -x+y, y, 
  z    -y, -x, 
  z    -y, x-y, 
  z    y, -x+y, 
  -z    y, x, 
  -z    x-y, -y, 
  -z    x-y, x, 
  -z    x, y, 
  z    x, x-y, 
  z    ' +(-1/3, 1/3, 1/3) 
  -    
  -x-1/3, -x+y+1/3, -z+1/3    -x-1/3, 
  -y+1/3, -z+1/3    -x+y-1/3, -x+1/3, 
  z+1/3    -x+y-1/3, y+1/3, 
  z+1/3    -y-1/3, -x+1/3, 
  z+1/3    -y-1/3, x-y+1/3, 
  z+1/3    y-1/3, -x+y+1/3, 
  -z+1/3    y-1/3, x+1/3, 
  -z+1/3    x-y-1/3, -y+1/3, 
  -z+1/3    x-y-1/3, x+1/3, 
  -z+1/3    x-1/3, y+1/3, 
  z+1/3    x-1/3, x-y+1/3, 
  z+1/3    ' +(1/3, -1/3, -1/3) 
  -    
  -x+1/3, -x+y-1/3, -z-1/3    -x+1/3, 
  -y-1/3, -z-1/3    -x+y+1/3, -x-1/3, 
  z-1/3    -x+y+1/3, y-1/3, 
  z-1/3    -y+1/3, -x-1/3, 
  z-1/3    -y+1/3, x-y-1/3, 
  z-1/3    y+1/3, -x+y-1/3, 
  -z-1/3    y+1/3, x-1/3, 
  -z-1/3    x-y+1/3, -y-1/3, 
  -z-1/3    x-y+1/3, x-1/3, 
  -z-1/3    x+1/3, y-1/3, 
  z-1/3    x+1/3, x-y-1/3, z-1/3} 
  36/* Fractional atomic coordinates for for 
  R-3mLi1 0.0  
  0.5  0.0 
  0.5  0.0  
  0.0 0.5  
  0.5  0.0 
  0.7  0.8  
  0.3 0.16667  
  0.3  0.3 
  0.16667  0.8  
  0.3 0.333

RE: troublesome unit cell

[alan coelho]

Pam,

As a developer and someone who uses other software to test against, I
have been following the discussion with interest. This is a complex area
and it goes to show the importance of having a few programs if only for
testing purposes.

I am puzzled by your cif data however as I cant get past verifying the
equivalence of the number of equivalent positions for the Li site.

In R-3m you have as fractional atomic coordinates for Li1:

  x = 0y = 0.5  and  z = 0

For P3112 you have three Li sites with x, y, z's as

0.77780 0.0 0.83330 
0.0 0.88890 0.83330 
0.0 0.55560 0.83330 

which translates to:

0.77780 0.0 5/6
0.0 0.88890 5/6
0.0 0.55560 5/6

Listed below are equivalent positions for a general site.

What I dont understand is that for R-3m I get 9 non-overlapping fully
occupied equivalent positions within the unit cell with a volume of
101.2975.

For P3112 I get 18 non-overlapping equivalent positions with a volume
three times as large of 303.8968. I was expecting to get 27 if the two
structure were to be equivalent.

Thus, from your cif data I am left to conclude that I am generating the
wrong number of equivalent positions, or, if I am generating the correct
number of equivalent positions then the two cif data sets should indeed
give different powder patterns.

Have you checked what the number of non-overlapping fully occupied
equivalent positions for Li should be for the two structures.

alan





P3112
xyzs
{
-x+y, -x, z-1/3
-x+y, y, -z+1/3
-y, -x, -z-1/3
-y, x-y, z+1/3
x, y, z
x, x-y, -z
} 6


R-3m
xyzs
{
-x, -x+y, -z
-x, -y, -z
-x+y, -x, z
-x+y, y, z
-y, -x, z
-y, x-y, z
y, -x+y, -z
y, x, -z
x-y, -y, -z
x-y, x, -z
x, y, z
x, x-y, z
' +(-1/3, 1/3, 1/3) -
-x-1/3, -x+y+1/3, -z+1/3
-x-1/3, -y+1/3, -z+1/3
-x+y-1/3, -x+1/3, z+1/3
-x+y-1/3, y+1/3, z+1/3
-y-1/3, -x+1/3, z+1/3
-y-1/3, x-y+1/3, z+1/3
y-1/3, -x+y+1/3, -z+1/3
y-1/3, x+1/3, -z+1/3
x-y-1/3, -y+1/3, -z+1/3
x-y-1/3, x+1/3, -z+1/3
x-1/3, y+1/3, z+1/3
x-1/3, x-y+1/3, z+1/3
' +(1/3, -1/3, -1/3) -
-x+1/3, -x+y-1/3, -z-1/3
-x+1/3, -y-1/3, -z-1/3
-x+y+1/3, -x-1/3, z-1/3
-x+y+1/3, y-1/3, z-1/3
-y+1/3, -x-1/3, z-1/3
-y+1/3, x-y-1/3, z-1/3
y+1/3, -x+y-1/3, -z-1/3
y+1/3, x-1/3, -z-1/3
x-y+1/3, -y-1/3, -z-1/3
x-y+1/3, x-1/3, -z-1/3
x+1/3, y-1/3, z-1/3
x+1/3, x-y-1/3, z-1/3
} 36



/* Fractional atomic coordinates for for R-3m
Li1 
 0.0  0.5  0.0 
 0.5  0.0  0.0 
 0.5  0.5  0.0 
 0.7  0.8  0.3 
 0.16667  0.3  0.3 
 0.16667  0.8  0.3 
 0.3  0.16667  0.7 
 0.8  0.7  0.7 
 0.8  0.16667  0.7 
*/


/* Fractional atomic coordinates for P3112
Li 
 0.0  0.0  0.5 
 0.77780  0.0  0.8 
 0.77780  0.55560  0.16667 
Li 
 0.77780  0.88890  0.5 
 0.0  0.88890  0.8 
 0.0  0.0  0.16667 
Li 
 0.11120  0.55560  0.5 
 0.0  0.55560  0.8 
 0.0  0.0  0.16667 
*/

Re: TOPAS-Academic

[alan coelho]

Jon,

The plans for Plugins is as concrete as I and those in the scientific
community make it. What I am eventually looking for is to involve others
in writing Plugins. This is the only way to guarantee a long term future
for the system; the truth of the matter is that a program of this size
needs input from many sources; a sole developer usually develops the
core routines as in this case but its the frills provided by others that
keeps the system going.

I have been experementing with Java and being able to integrate it with
c++ code. It is possible but there are problems. I am also aiming for
making TA paltform dependent. This may mean settling for a little less
in terms of graphics but I think that the trade off may well be worth
it. At present TA is only dependent on Windwows for some of its
graphics; the Kernel is written in ANSI c++ and it should compile under
any platform.

Anyway, for TA the editor jEdit may already provide the functionality
you need to automatically generate restaints by writing one of its
macros. Modern editors of this type, and there are many, makes life easy
in regards to writing scripts. 

I spent a lot of time looking at XML versus a scripting language and in
the end I decided that the INP format is closer to a scripting language.
Because of this I have decided to stick with the INP format as it seems
the simplest. If XML writers progress to a point where there are easier
to use then it would be a simple matter of incoorporating tags into the
INP format as the INP format is virtually XML without tags.
all the best
Alan



-Original Message-
From: Jon Wright [mailto:[EMAIL PROTECTED] 
Sent: Friday, September 24, 2004 12:37 PM
To: [EMAIL PROTECTED]


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-granting institutions comprising universities, university run
>institutes, laboratories and schools at:
>
>   http://pws.prserv.net/Alan.Coelho 
>
>The main aim of TOPAS-Academic (TA) is to provide a low cost but
>powerful and easy to use program for the academic community. One that
>will grow through a planned Plugin Architecture.
>
>BRUKER-AXS TOPAS will continue to be developed in parallel employing
the
>latest in Windows GUI Dialog technology.
>
>regards
>alan
>
>
>
>  
>

TA download problems

[alan coelho]

Dear all,

My apologies for those whom may have downloaded the TOPAS-Academic
demonstration version as there was an error in the ZIP file due to ftp
problems. The problem has been fixed, see:

http://pws.prserv.net/Alan.Coelho

regards
alan

TOPAS-Academic

[alan coelho]

Dear all,

An academic version of BRUKER-AXS TOPAS is now available to
degree-granting institutions comprising universities, university run
institutes, laboratories and schools at:

http://pws.prserv.net/Alan.Coelho 

The main aim of TOPAS-Academic (TA) is to provide a low cost but
powerful and easy to use program for the academic community. One that
will grow through a planned Plugin Architecture.

BRUKER-AXS TOPAS will continue to be developed in parallel employing the
latest in Windows GUI Dialog technology.

regards 
alan

Re: Philosophical vein

[alan coelho]

Picking up on Bob’s point. 

As an author of a commercial program I don’t see the world coming to an
end. In this melodramatic discussion the idea of encouraging young
scientists to write the type of software that the community is demanding
is fraught with difficulty. Unless of course a scientist can be found
who enjoys drawing bitmaps.

A hobby is supposed to be related to an activity that is enjoyable. In
the days of command line programs it was possible to concentrate on the
part I consider enjoyable, the algorithms, and to still function as a
scientist in crystallography. 

In the present day and from my experience computer literacy is in fact
decreasing rather than increasing. If a modern program did not comprise
colorful buttons, context sensitive help, ease of use, very little
thought in regards to its use then that program no matter how brilliant
in the algorithmic sense would find it difficult to survive.

XFIT a public domain program that I wrote in 6 months has been heavily
used and I suspect that the reason is not just because of the numeric
algorithms but more for the GUI and the computing science ideas behind
it.

Bob’s work is exceptional in the algorithmic sense, to then demand
computing science ideas and bells and whistles without institutional
support is an anathema. 

Thus my advice to those who seek to encourage your scientist to write
more than scientific algorithms is to do so with support and respect.

alan


-Original Message-
From: Von Dreele, Robert B. [mailto:[EMAIL PROTECTED] 
Sent: Friday, March 19, 2004 11:16 PM
To: [EMAIL PROTECTED]


I would only add that much of the software development is done as a
"hobby" by many us, i.e. with only grudging institutional support.
Bob


-Original Message-
From: L. Cranswick [mailto:[EMAIL PROTECTED]
Sent: Fri 3/19/2004 3:44 PM
To: [EMAIL PROTECTED]
 

[hope this is not a resend - Email software went beserk with
previous effort]

>"What happens in the future?" When Bob Von Dreele and Brian Toby, to
>name two, join Al Larson in retirement, (and Al finally stops working)
>what happens then? 

A number of single crystal members on the IUCr Commission on
Crystallographic Computing have been quite concerned about this as well
(their observations being based on the field of small molecule
crystallography).

A result of these concerns is putting renewed effort into the IUCr
computing schools. (next one is in Siena in 2005 - just prior
to the IUCr Florence congress)

   http://www.iucr.org/iucr-top/comm/ccom/siena2005/

The Siena School webpage states:
  "The aim of the school is to have the crystallographic computing
experts
  of the present, help train and inspire a new generation of experts in
  crystallographic computing."

As well as IUCr Computing Commission newsletters for publishing software
crystallographic programming information and help with community
building.

   http://www.iucr.org/iucr-top/comm/ccom/newsletters/

---

>I will be very interested in your responses. Is my prediction of coming
>disaster too pessimistic? Probably. After all, the late Jose Donnay of
>Johns Hopkins University always claimed that crystallography was ruined
by
>the invention of the computer. I never learned to what extent his
opinion
>was effected by the conflicts I had with his wife.

Overall, I am not as pesimistic on this issue: as we have seen
analytical software gaps get filled once they have become too annoying
to kludge solutions from existing software packages. Examples of this
could be the recent advances in powder indexing software to handle
impurity peaks, new or updated software for structure solution from
powder diffraction data, and new advances in fundamental parameters
based Rietveld packages.

One old-school Prof in London stated the personal opinion that black
button that is Direct Methods (1960's?) wrecked the fun and challenge in
solving crystal structures from single crystal data. This does not seem
the case in solving structures from powders? The black buttons are not
yet that routine(?) Though programs like EXPO and Fox are working well
in that direction.

Lachlan.

---
Lachlan M. D. Cranswick
Contact outside working hours /
  Coordonnees en dehors des heures de travail:
E-mail / courriel: [EMAIL PROTECTED]   Home Tel: (613) 584-4226
Mobile/Cell: 613 401 3433   WWW: http://lachlan.bluehaze.com.au/
P.O. Box 2057, Deep River, Ontario, Canada, K0J 1P0

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Re: Combined neutron/x-ray refinements

[alan . coelho]

I would like to add my two cents to the discussion on ESDs and
weightings. 

Paolo wrote:

> Clearly, the ESD on x1 have worsened in this simple case.  This does not
> prove the general case, but there might be a proof for that as well.

This conclusion was reached by applying non-linear least squares to
solving for x1 and x2 in the following:

^I1=x1+x2; I2=x1+2*x2, I3=x2, and assuming unitary weights.

ESDs squared were calculated as
2 and 2/3 for x1 and x2 respectively:
and 5 and 2 for x1 and x2 respectively excluding I3

This change in ESDs makes perfect sense to me. Excluding I3 lessens the
certainty in determining x2 which in turn lessens the certainty in
determining  x1. My conclusion is that there is nothing wrong with the
ESDs calculated. 

Now,  for x1 and x2 to be independent of I3 then I3 should not contain
any parameters that are also in equations that are functions of x1 and
x2; for example:

I1 = x1 + x2
I2 = x1 + 2 x2
I3 = x3

I3 here is now independent of I3. And the A and B matrices becomes:

A = {{2, 3, 0}, {3, 5, 0}, {0, 0, 1}}
B = {{5, -3, 0}, {-3, 2, 0}, {0, 0, 1}}

Excluding I3 means excluding x3 as well; the A and B matrices here are:

A = {{2, 3}, {3, 5}}
B = {{5, -3}, {-3, 2}}

As you can see that in both cases the ESDs for x1 and x2 are the same.

Some other points I would like to clear up,

> 1) You construct the Aij matrix (also sometimes called the Hessian matrix)
> 
> Aij=D^2chi^2/DxiDxj (D is the partial derivative sign.  E-mail is
> still too primitive)

The term Hessian matrix refers to the second order terms obtained when
expanding a function in a Taylor series.

Typically Chi^2 is written as:

 Chi^2 = Sum[  w(i)^2 (Io(i) - Ic(i))^2 , i]

where Io(i) an the observed data point
Ic(i) a calclated data point
w(i)^2 the weighting term for data point I
and the summation is over i

Ic(i) is expanded to a first order Taylor approximation, or:

Ic(i) = Ic(i, P) + Sum[ dIc(i)/dP(p) Del(p) , p]

where P is the parameter vector 
Del(p) the change in parameter P(p)
dIc(i)/dP(p) is the derivative of the Ic(I) wrt parameter P(p)
 
Chi^2 becomes

 Chi^2 = Sum[  w(i)^2 (Io(i) - Ic(i, P) - Sum[ dIc(i)/dP(p) Del(p) ,
p])^2 , i]

Differentiating Chi^2 wrt to each parameter P(p) and equating these
equation to zero yields the normal equations which in matrix form looks
like:

A Del(P) = Y

where Aij = Sum[  w(i) dIc(i)/dP(i)  dIc(i)/dP(i)  , i]

These equations are then solved for the changes in the parameters
Del(P). This term for Aij is different to the one given by Paolo and is
applicable to single crystal data. It is also applicable to powder data
by replacing i by 2Th and I by the intensities as a function of 2Th.
Thus I do not know where the following term by Paolo came from:

^   Aij=D^2chi^2/DxiDxj 

Note that it is sometimes useful to expand Chi^2 itself but not in the
analysis of XRD data.

Alan