RE: Parafocussing definition?

[Yokochi, Alexandre]

I just read through the rest of the discussion.  He only thing to add is that I 
think the flat sample does play a role in the para part of the focusing.

A real focusing experiment includes the light source entrance slit, “curved 
diffraction grating” (what we call our sample), and exit slits all on the 
perimeter of a Rowland circle (the center is the center of the goniometer, 
technically).  Since it clearly would be a significantly difficult exercise to 
a) create a sample that has the right radius of curvature (and it would have to 
be infinitesimally thin to boot), and b) continuously change the diffraction 
grating to exit slit distance, the BB geometry uses a) a flat diffraction 
grating and b) a fixed grating to exit slits distance, which almost looks like 
an experiment with a flat diffraction grating and a Rowland circle of changing 
diameter.

Therefore, parafocusing  geometry as in “almost focusing geometry” describes 
the arrangement of a BB optical bench quite nicely.

Alex Y
___
Dr. Alexandre (Alex) F. T. Yokochi
Professor of Chemical Engineering
Laboratory for innovative Reaction Engineering for Materials and Sustainability 
(iREMS lab)
School of Chemical, Biological and Environmental Engineering
Oregon State University
Corvallis, OR 97331 - 2702

From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of 
ian.mad...@csiro.au
Sent: Monday, May 2, 2016 1:06 AM
To: rietveld_l@ill.fr; rowle...@gmail.com
Subject: Re: Parafocussing definition?


Hi Matthew,



I've got some nice figures from an old XRD Basics presentation from decades ago 
- the problem is that all this stuff is in my CSIRO office and I'm at home!



However, I will do my best to recall the basic principles of parafocusing In a 
Bragg-Brentano instrument:-

  1.  The source (tube target) and receiving slit are both on the 
diffractometer circle (not to be confused with the focusing circle) and are 
equidistant from the diffractometer (rotation) axis.
  2.  The beam is divergent (strictly speaking, a parallel beam instrument is 
not Bragg-Brentano geometry).
  3.  The sample is an extended flat plate.
  4.  The centre line of the incident beam will strike the sample at the centre 
of the diffractometer rotation axis (assuming the instrument is well aligned 
and the sample properly presented - not always a given!) at some angle theta. 
This beam will diffract from crystal planes parallel to the surface to the 
receiving slit also at an angle theta (yippee - theta + theta = 2theta - I'm a 
maths wiz)
  5.  The lower extremity of the diverging incident beam will strike the sample 
on the tube side of the diffractometer rotation axis at some angle (theta + 
phi). Now (and this is where the magic comes in) this beam will diffract from 
planes rotated phi degrees to the surface - for the same reflection as in 4. 
above, this means that the diffracted beam now makes an angle of (theta - phi) 
to the surface. Now (theta + phi) + (theta - phi) = 2theta - still amazing.
  6.  The upper extremity of the diverging incident beam will strike the sample 
on the detector side of the diffractometer rotation axis ... follow reasoning 
above for planes rotated -phi with respect to the sample surface.
  7.  This works because (this is the important bit) within a circle equal arcs 
make equal angles - a simple ray tracing diagram will help here.
  8.  Part of the reason Bragg-Brentano instruments have good intensity is due 
to the fact that the diverging beam will diffract from a wider range of 
crystallite orientations than say a parallel beam instrument.
  9.  There is no true 'focusing' of the X-ray beam in this context - the 
apparent focusing is happening because of 4 - 6 above in the context of 
diverging beams.
  10. I don't think that flat vs curved sample needs to come into this 
explanation.

I hope this helps.

​


Cheers



ooo0ooo

 Ian Madsen
 Honorary Fellow
 CSIRO Mineral Resources Flagship
 Private Bag 10,  Clayton South 3169
 Victoria,   AUSTRALIA
 Phone +61 3 9545 8785 direct
 +61 3 9545 8500 switch
 +61 (0) 417 554 935 mobile
 FAX+61 3 9562 8919
 Email ian.mad...@csiro.au

ooo0ooo

From: rietveld_l-requ...@ill.fr 
> on behalf of 
Matthew Rowles >
Sent: Monday, May 2, 2016 3:52 PM
To: RIETVELD_L Distribution List
Subject: Parafocussing definition?

Hi all

I've been trying to find a good explanation of what parafocussing (wrt 
Bragg-Brentato geometry) actually is, but haven't been able to find one.

Klug and Alexander just reference Brentano's papers.

"The Basics of Crystallography and Diffraction" 2nd ed 

RE: software for correcting peak positions in capillary XRD data

[Yokochi, Alexandre]

Angel,

Don't correct peak positions.  Rather, use the appropriate parameter in
your refinement software (in Fullprof, usually a combination of zero and
sysin, but then again I usually have data from position sensitive
detectors)(if your instrument was properly aligned, zero should refine
to close to 0).

Alex Y


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia

 -Original Message-
 From: alor...@unex.es [mailto:alor...@unex.es]
 Sent: Saturday, November 21, 2009 6:27 AM
 To: rietveld_l@ill.fr
 Subject: software for correcting peak positions in capillary XRD data
 
 Dear colleages:
 
 could any of you indicate to me where to find free software to perform
the
 absortion correction for XRD data taken in the capillary geometry? I
need
 this to correct the peak positions.
 
 Thanks a lot,
 
 Angel L. Ortiz
 University of Extremadura, Spain
 

RE: Re : HT XRD calibration

[Yokochi, Alexandre]

Hi all,

I've never used one of these Anton Paar furnaces, but with some of my 
instruments (externally heated, not Pt resistive foil heated) I could actually 
use the thermocouple as the sample mount.  I also had an instrument that had a 
thermocouple in contact with the powder sample, which due to thermal expansion 
mismatch would upon heating expand and split the sample surface giving rise to 
ugly split peaks so be careful... (you can imagine that implementation lasted 
as many samples as it took me to figure out what the peak splitting problem 
was).

Alex Y


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia

 -Original Message-
 From: Payzant, E. Andrew [mailto:payza...@ornl.gov]
 Sent: Thursday, October 15, 2009 6:27 AM
 To: Rietveld list
 Subject: Re: Re : HT XRD calibration
 
 Patrick,
 
 That is a good idea. Note that to actually get rid of the uncertainty you
 need to be certain that the thermocouple is either reading the temperature
 of the actual sample volume contributing to the diffraction pattern, or
 that it is reading the temperature of a location where the temperature is
 exactly the same as the sample volume.
 
 Andrew
 
 
 On 10/14/09 11:25 AM, Patrick Weisbecker weis...@yahoo.fr wrote:
 
 Hi,
 
 One way to get rid of the temperature uncertainty is to introduce a second
 thermocouple inside the furnace and to fix it as close as possible from
 the sample. If the sample is a bulk sample:Drill a hole inside the sample
 and put the thermocouple inside the hole and if the the sample is made of
 powder put it inside the powder.
 The are some miniature thermocouple (0.25-0.5mm diameter), mineral
 insulated which are unlikely to react with the samples.
 
 Patrick
 
 
 
 
 - Message d'origine 
 De : Payzant, E. Andrew payza...@ornl.gov
 À : Mikko Heikkilä mikko.j.heikk...@helsinki.fi
 Cc : Rietveld list rietveld_l@ill.fr
 Envoyé le : Mer 14 Octobre 2009, 16 h 39 min 58 s
 Objet : Re: HT XRD calibration
 
 All,
 
 The two calibration standard method was described by Andy Drews (Ford
 Research Lab) in Advances in X-ray Analysis (the proceedings of the Denver
 X-ray Conference), vol. 44, page 44 (2001).
 
 Scott Misture (Alfred Univ), Stephen Skinner (Imperial College), Christian
 Resch (Anton Paar), and I ran a workshop on non-ambient diffraction at the
 Denver X-ray Conference in 2008, where we discussed many of these issues.
 There was a lively discussion with the attendees regarding various
 experiences with HTXRD, and the difficulty in abtaining the right
 answer. Too often we are so focused on the precision and accuracy of our
 refinements that we neglect the temperature issue, to our peril.
 
 One issue with the HT16 hot stage is that you will likely need to
 recalibrate with every new heater strip - don't rely on them behaving the
 same. Even for a particular strip, use of an internal standard is best if
 you can use one that does not react with either the strip or the sample.
 If you push this furnace to temperatures above 1200degC or so, the
 platinum will creep and the tensioning will change, so that the
 height/temperature calibration may subsequently be off.
 
 I agree fully with the suggestion to use parallel beam optics to eliminate
 the sample height error. You do lose some angular resolution of course, at
 least on a laboratory diffractometer, but you take one variable (sample
 height) out of the refinement.
 
 The other BIG problem with the HT16 (and many other non-ambient stages) is
 knowing the temperature of the SAMPLE (as opposed to the strip). Powders
 have hopelessly poor thermal conductivity, and the gradients in these
 furnaces can be substantial. We rarely measure the temperature of the
 sample directly, and this is another reason why internal standards are
 very useful - you can use either a known CTE to estimate the delta T over
 the full temperature range, or a known phase transformation to determine
 delta T at a single point. I personally prefer the former approach myself.
 Note that a solid-solid transformation may give a different result than a
 melting point standard, since the liquid will change the thermal
 conductivity between the strip and the sample. You can find more
 discussion of these issues in Mark Rodriguez's chapter in the book
 Industrial Applications of X-ray Diffraction, or mine in Principles and
 Applications of Powder Diffraction.
 
 I chair the non-ambient diffraction subcommittee of the ICDD, and in
 that capacity I am looking for ways we can develop and standardize these
 methods. If any of you would like to participate in this exercise please
 let me know. Perhaps a special issue of Powder Diffraction could be
 devoted to in-situ high-temperature diffraction papers? Always looking for
 good ideas...
 
 Andrew
 
 
 On 

RE: Question about Fullprof

[Yokochi, Alexandre]

Hi all,

I just remembered the answer:  if you use an instrument resolution file
then the program automatically generates the desired output.

Sorry for taking up space in your mailbox with the original question -
should have gone for a swim earlier...

Alex Y


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia

 -Original Message-
 From: Yokochi, Alexandre [mailto:alexandre.yoko...@oregonstate.edu]
 Sent: Wednesday, July 22, 2009 3:10 PM
 To: rietveld_l@ill.fr
 Subject: Question about Fullprof
 
 Hi everyone,
 
 Does anyone remember offhand how to turn on the output that includes
 calculated particle size when refining with a symmetry specific size
 model in Fullprof?  I haven't looked at the program in a few years and
 am afraid I can't quite remember...
 
 Alex Y
 
 
 Dr. Alexandre (Alex) F. T. Yokochi
 Assistant Professor
 Department of Chemical Engineering
 Oregon State University
 Corvallis, OR 97331-2702
 
 Voice:  (541) 737-9357
 Fax:  (541) 737-4600
 http://oregonstate.edu/~yokochia

Question about Fullprof

[Yokochi, Alexandre]

Hi everyone,

Does anyone remember offhand how to turn on the output that includes
calculated particle size when refining with a symmetry specific size
model in Fullprof?  I haven't looked at the program in a few years and
am afraid I can't quite remember...

Alex Y


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia

RE: error in peak positions that is linear in theta

[Yokochi, Alexandre]

Hi all,

Does the error maximize at 2-theta = 90 then decrease again?  Back when
I was an actual crystallographer and used an INEL system, this was
observed when the capillary position was not coaxial with the detector
(in fact, when it was behind the proper position).

Alex Y


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia

 -Original Message-
  *From:* Kurt Leinenweber [mailto:ku...@asu.edu]
  *Sent:* Thursday, January 08, 2009 6:09 PM
  *To:* Rietveld_l@ill.fr
  *Subject:* error in peak positions that is linear in theta
 
 
 
  Dear Rietvelders,
 
 
 
  (I hope this list is appropriate for this question).  I am trying to
set
  up a new D8 diffractometer from Bruker, and have it set up with a
Vario
  monochromator focusing on a sample in a capillary.  Of course I hope
to
  do Rietveld refinement on the samples eventually.  But there is an
error
  in two theta of the peak positions on all samples, and the error is
  linear in two theta.  At 40 degrees the error (measured minus
expected)
  is about 0.020 degrees, at 80 degrees the error is about 0.040
degrees,
  etcetera.
 
 
 
  Has anyone ever seen anything like this and do you know where it
could
  come from?
 
 
 
  Thank you very much,
 
 
 
  - Kurt
 
 
 
 
 
  *
 
  Kurt Leinenweber
 
  Dept. of Chemistry and Biochemistry
 
  Arizona State University
 
  Tempe, AZ 85287-1604
 
 
 
  phone (480)-965-8853
 
  fax (480)-965-2747
 
 
 
  ***
 
 
 
 

RE: source for Y2O3?

[Yokochi, Alexandre]

Kurt,

 

Back when I was doing this I just purchased Y2O3 from a conventional
chemical supplier and annealed it at high temperature (as high as you
can easily get to, usually something like 1150C unless you have really
fancy furnaces and crucibles) for a few days.

 

Alex Y

 


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia 

- Original Message - 

From: Kurt Leinenweber mailto:[EMAIL PROTECTED]  

To: rietveld_l@ill.fr 

Sent: Tuesday, October 14, 2008 8:17 PM

Subject: source for Y2O3?

 

Dear Rietvelders,

 

In September there was a discussion of refining the polarization
of an instrument, and Lachlan and Matthew both suggested Y2O3.  The time
has come to do the measurement, and I was wondering if anyone has
suggestions for a good source and annealing schedule for the Y2O3?  Is
the already annealed material available as an XRD standard?

 

Thank you very much,

 

- Kurt

 

 

*

Kurt Leinenweber

Dept. of Chemistry and Biochemistry

Arizona State University

Tempe, AZ 85287-1604

 

phone (480)-965-8853

fax (480)-965-2747

 

***

 

RE: PDF refinement pros and cons

[Yokochi, Alexandre]

Pam and all,

I too have been looking at materials using in house lab data.  Using an
Ag rotating anode (I actually used Ag-k beta for simplicity of the lack
of peak splitting) and an MSC curved imaging plate, and very long
exposures we got data we found quite useful.  However, I stopped playing
in that particular corner of the sandbox a while ago to focus on other
stuff (more process engineering than materials science related) and
would be interested in learning what's new in lab based data.

Alex Y


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia

 -Original Message-
 From: Whitfield, Pamela [mailto:[EMAIL PROTECTED]
 Sent: Friday, June 13, 2008 6:26 AM
 To: Matteo Leoni; Jonathan Wright
 Cc: rietveld_l@ill.fr
 Subject: RE: PDF refinement pros and cons
 
 I'm only going to stick my big toe in here on a practical note for
 lab-based studies.
 I managed to get the Bruker Vantec detector to work with MoKa quite
 nicely for some non-ambient work and decided to see if I could get
 useful data for PDF from some battery cathode materials (I think it
was
 up to 17A-1 or so).  The PSD means the data collection time is more
 reasonable to get low noise and the data did show the metal-oxygen
bond
 splitting that was supposed to be there from synchrotron studies.
 Next step is AgKa for a more demanding non-ambient application I'm
 working on so I'll find out if the Vantec works or whether an high
 energy optimized Si-strip detector is the way to go.  Should be fun!
 
 Pam
 

RE: Analysis of data from instruments with theta-compensating slits

[Yokochi, Alexandre]

Patrick,

The usual thing is to correct the data using a 1/(sin theta) correction.
Notice that you'll have to create an ESD format file for GSAS and
calculate what your ESDs (or SUs or whatever) in the corrected data is
or you'll get funny statistics.  The goal is I/sigma I stays constant -
figure out from there and from what GSAS assumes the ESDs are (or maybe
you already have a file with explicit ESDs...) how make this
transformation.

Alex Y


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia

 -Original Message-
 From: Patrick D Burton [mailto:[EMAIL PROTECTED]
 Sent: Friday, March 07, 2008 2:34 PM
 To: rietveld_l@ill.fr
 Subject: RE: Analysis of data from instruments with theta-compensating
 slits
 
 Yes, I'm working with an X'Pert Pro with constant illumination length,
and
 I was wondering if there is a software correction for it in GSAS.  The
 patterns I have worked with so far can only be refined by changing the
 thermal parameter to impossible values.
 
 Thanks,
 Patrick Burton
 
 On Sat, 8 Mar 2008 [EMAIL PROTECTED] wrote:
 
  Patrick
 
  Do you mean like constant illumination length slit settings?
 
 
  Matthew Rowles
 
 
 
  -Original Message-
  From: Patrick D. Burton [mailto:[EMAIL PROTECTED]
  Sent: Sat 08/03/2008 5:54
  To: rietveld_l@ill.fr
  Cc:
  Subject: Analysis of data from instruments with
theta-compensating
 slits
 
 
  Reitvelders,
 
  I was wondering if anybody is performing Reitveld analysis on
data
 collected using theta compensating slits.
  If so, what sort of intensity correction are you using?
 
  Thank you,
 
  Patrick Burton
 
 
 
 
 --
 Patrick D. Burton
 Graduate Research Assistant
 [EMAIL PROTECTED]
 --

RE: occupancy

[Yokochi, Alexandre]

Igor,

 

Back when I used to do this a lot, the easiest way was to just start the
occupancy of the two sites at 1 (e.g., 95% + 5%)  then give one site a
given variable and the second the opposite sign for the same variable
(e.g., 20.5 and -20.5).  I've been out of the XRD game for a few years,
so there may be a better way in Fullprof nowadays...

 

Alex Y

 


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia 



From: Igor Djerdj [mailto:[EMAIL PROTECTED] 
Sent: Tuesday, December 04, 2007 3:45 PM
To: rietveld_l@ill.fr
Subject: occupancy

 

Dear all,

The following question is addressed more to FULLPROF users. I want to
refine atomic occupancies of Fe-doped TiO2 for instance. Assuming that
Ti is substituted with Fe at some sites, how can I provide that the sum
of occupancies of Fe and Ti is 1 or 100%?

Regards,

Igor Djerdj

 

RE: Jorge González

[Yokochi, Alexandre]

Jorge,

 

I purchased a Rigaku Rapid a few years ago (now superseded by the Spider, I 
believe) which I use extensively for single crystal, powder and thin film work. 
 Unless you are extremely careful, the powder patterns can have somewhat 
broadened peaks which makes doing very high quality size/strain, for example, a 
bit of a challenge.  On the other hand, I can collect a powder pattern on a few 
mg of material in a matter of minutes (so it is great for phase ID, etc).

 

Alex Y


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia 



From: Jorge Gonzalez [mailto:] 
Sent: Wednesday, November 28, 2007 1:12 PM
To: rietveld_l@ill.fr
Subject: Jorge González

 

 

Dear Friends,

 

I would like to contact with people familiar with x-ray diffractometers capable 
of performing both powder and single crystal measurements. We are planning to 
buy one and we need some information.



Thank you.


 
Jorge González González
Escuela de Ciencias Químicas
Universidad de Colima, Colima, México.
TLF: (0052) 312 135 6426
Fax: (0052) 312 315 6585

 
 






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RE: [sdpd] Material for calculation of IRF or IRP

[Yokochi, Alexandre]

SM,

Having had INEL instruments, I would like to point out that you should
carefully determine the angle between the primary beam and the sample
when you make measurements on both standards and samples.  This has a
huge effect on line profiles.  Peaks, especially very low angle ones,
will have a surprisingly anisotropic shape.  

I usually used annealed In2O3 as both a line profile standard as well as
a detector linearization standard:  I always preferred conceptually the
fact that this material has a large number of peaks, which should give a
much better linearization curve (but make sure to measure the
diffraction pattern on a separate instrument prior to trusting two theta
peak positions - we used our D5000 - or use a well known material like
the SRM materials).

Alex Y


Dr. Alexandre (Alex) F. T. Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Voice:  (541) 737-9357
Fax:  (541) 737-4600
http://oregonstate.edu/~yokochia
 -Original Message-
 From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of
 Murugesan S
 Sent: Tuesday, August 21, 2007 12:43 AM
 To: rietveld_l@ill.fr
 Cc: [EMAIL PROTECTED]
 Subject: [sdpd] Material for calculation of IRF or IRP
 
 Dear Rietveld useres,
 
 I need one help,
 
 I need to calibrate the machine, and instrumental parameters of our
INEL
 diffractometer,
 
 I don't have  the LaB6 powder, whether I can use the well grinned,
 annealed
 CeO2 powder to get the Instrumental Resolution Parameter.  Or What
type of
 material suitable for to get the good instrumental parameters from the
XRD
 data.
 
 Mostly we used it for the size / strain analysis purpose.
 
 please suggest me the good materials,
 
 i expect your comments and suggestions
 
 Thank you,
 
 
 with best regards
 SM
 
 
 [Non-text portions of this message have been removed]
 
 
 
 
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Re: Introductory presentation on PDFs

[Yokochi, Alexandre]

Hi Simon,

Is this presentation part of the materials in your web site?  If not, I would 
really like to look at it.

Alex Y


Dr. Alexandre (Alex) Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Phone:  (541)-737-9357
Fax:  (541)-737-4600
 

-Original Message-
From: Simon Billinge [mailto:[EMAIL PROTECTED] 
Sent: Tuesday, April 26, 2005 6:21 AM
To: rietveld_l@ill.fr

Hi Radovan,

I am happy to oblige. You are welcome to use part or all of it for non 
commercial purposes provided, as normal, credit is properly ascribed. I 
will send it in a following email that doesn't go to the list.

If anyone else wants a canned talk on the PDF (without the words) 
please let me know and I will send you a copy. btw, the talk forms the 
basis of a chapter (with the words) in the upcoming IUCr classic on 
powder diffraction.  Look for it in the fall in your local quality bookshop.

Take care,

S


Radovan Cerny wrote:
 Dear Simon and Angus,
 
 I admit openly that I would be also very gratefull for some slides on 
 the PDF.
 
 With many thanks in advance
 
 Radovan
 
 Angus P. Wilkinson a écrit:
 
 Dear Simon,

 do you have any canned material that I could use (with 
 acknowledgement) to give a brief introduction (45 minutes) to the PDF 
 method. This is for use with Chemistry grad students at the end of 
 crystallography course so that they have some feel for the information 
 that is in the scattering data, but not in the Bragg peaks. Some of 
 the material that you used at the NICEST workshop might be appropriate.

 Thanks, Angus


 At 09:57 AM 4/22/2005 -0400, you wrote:

 SNS is developing a rather elaborate Portal (I think it is Al Geist 
 again, who did the enotebook, working on this) system and ISIS is 
 pioneering software for data curation.  These may exceed your 
 needs, and right now I have the impression that it is as much 
 research as construction.  Only when we start using these things 
 will be find out the value.  You can get more information from Steve 
 Miller at SNS. It would certainly be great to have some nice software 
 application to take care of archiving and cataloging data...we 
 perennially fight with this and have not found a satisfactory 
 solution.  Let me know when you do...

 Angus P. Wilkinson wrote:

 Thanks for the e-notebook suggestion. Do none of the user facilities 
 have a data management system in place for their instruments?
 Angus

 At 05:17 AM 4/22/2005 +0100, you wrote:

   Are any of you using a Laboratory Information Management 
 Systems
  (LIMS) to keep track of powder diffraction and related 
 measurements in a
  university or government laboratory environment?
Alternatively, is there any good (and free) software 
 available
  for archiving and managing large numbers of diffraction data sets 
 from a
  multi-user instrument?

 While not exactly a LIMS system - you might like to check out
 the freeware Oak Ridge National Laboratory  - Electronic Notebook
 Project:

   http://www.csm.ornl.gov/~geist/java/applets/enote/

 It is a perl script that works via a webserver (windows or UNIX)

 We use it for the C2 neutron powder diffractometer at Chalk River
 (inside our intranet - so not viewable to the outside world) and it is
 brilliant. (especially if you have a habit of forgetting where you put
 down your paper notebook - or have multiple people using an 
 instrument)
 If travelling or moving from building, (or overseas at a conference)
 it is easy to find and add information. It
 does not have 100% of the features I would like (and a few annoying
 nuances) - but it gets the job done (ability to search text,
 notarise entries (so they cannot be modified or deleted) - add photos,
 zip files, EXCEL files, zipped data, zipped GSAS results files, etc).

 It does require some discipline to use it - especially if in a rush
 or multi-tasking.

 For adding hand drawn pictures - using a USB INTUOS drawing tablet is
 probably the most appropriate as it does not need extra batteries.

   http://www.wacom.com/

 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

 (please use clear titles in any Email - otherwise messages might
 accidentally get put in the SPAM list due to large amount of junk
 Email being received. If you don't get an expected reply to any
 messages, please try again.)

 (Essayez d'utiliser des titres explicites - sans quoi vos messages
 pourraient aboutir dans un dossier de rebuts, du fait de la quantite
 tres importante de pourriels recue. Si vous n'obtenez pas la reponse
 attendue, merci de bien vouloir 

Re: Change format

[Yokochi, Alexandre]

Hi,

One issue to consider is that many programs, when esd's of each datum
are not given explicitly, estimate these as sqrt(I).  Further, many
programs weigh the data using these esd's.  Therefore, since it is
desired that esd/I remain a constant, if you do multiply your data by a
constant, the easiest thing is to build a GSAS data file in ESD format
with the esd's given as c*sqrt(I).  Implement this and you will avoid
screwing up your meaningless numbers r (do most journal reviewers and
editors share that opinion?).  It can be done in a few lines of fortran.

Given that I do collect almost all high quality data with a locally
adapted variable counting time method, almost all my data have different
statistics in different areas of the pattern, so implementing this
properly was fairly important to me...

Alex Y


Dr. Alexandre (Alex) Yokochi
Assistant Professor
Department of Chemical Engineering
Oregon State University
Corvallis, OR 97331-2702

Phone:  (541)-737-9357
Fax:  (541)-737-4600
 

-Original Message-
From: Jon Wright [mailto:[EMAIL PROTECTED] 
Sent: Thursday, March 31, 2005 12:53 AM
To: rietveld_l@ill.fr

Brian Toby wrote:

 If the numbers are real values then they are not counts. They may be 
 counts per second or something else. One needs to have uncertainty 
 estimates for these intensities before one can do a meaningful 
 Rietveld refinement (with any code). Following the above procedure, by

 multiplying them by an arbitrary constant and then inputting them to 
 GSAS as if they were counts will cause GSAS to compute the 
 uncertainties as the square-root of the intensities, something that is

 quite unlikely to be true. This will cause the refinement to be 
 weighted improperly and the r-factors to be wrong.

Assuming you model a single pattern, then multiplying the data by some 
constant should not alter the esd's on refined parameters for programs 
which derive them conventionally (using a chi^2 factor), since 
sqrt(cI)=sqrt(c)sqrt(I). This can be a very good approximation if the 
statistics are about the same over the whole pattern. If the statistics 
are different in different regions of the pattern, then problems could 
arise. However, in the majority of published refinements the 
distribution of misfits is not Gaussian and all bets are off anyway, 
so having the right error model for your data is not a great help, as 
you have no error model for your model. One can sympathise with anyone 
who wants to get on with the science ;-)

If the major difficulty is screwing up r-factor statistics, why would 
that be a problem? Isn't it better to abandon these meaningless numbers 
sooner rather than later? Lower powder R-factors are normally an 
indicator of lower data quality, either higher background or more peak 
overlap. As far as the major players (GSAS and fullprof) are concerned, 
they aren't even the same thing. Just stop reporting them please!

I agree that one should try to get the errors on the data right, but it 
won't stop the refinement being weighted improperly and it won't make 
the r-factors right ;-)

Jon

RE: Bond lengths calculation by Fullprof

[Yokochi, Alexandre]

Armel, Irini, and all,

The option to do bond length calculations and BVS calculations, etc,
is not explicitly given in the HTML fullprof manual.  It is, however,
described in the appendix included with the more recent releases of Fullprof
(you know, the big ol pdf file called something like app_fp2k_man.pdf, right
about page 20).  I only caught onto it after I had a lead from someone here.
Below, is a slice of a prf file that does the bond lengths and stuff
correctly.  Also, if you're really interested in the BVS calculations, you
may be better off using Brown's Valist program.

AlexY




!  ZeroCodeSycosCode   SysinCode  Lambda Code MORE
-Patt# 1
 -0.01583   0.50  0.0   0.10  0.0   0.10 0.000.00   0
!   Background coefficients/codes  for Pattern#  1
  138.71 -4.4682 0.53262  0.  0.  0.
   0.500   0.500   0.500   0.100   0.100   0.100
!---

!  Data for PHASE number:   1  == Current R_Bragg for Pattern#  1: 0.00
!---

2H-CuScO2

!
!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ   Nvk Npr More
   4   0   0 0.0 0.0 1.0   0   0   0   0   00.00   0   7   1
!
!Jvi Jdi Hel Sol Mom Ter  Brind   RMuaRMubRMuc   Jtyp
   2   3   0   0   0   0  1.  0.  0.  0.   1
!
! Max_dst(dist) (angles)  Bond-Valence Calc.
  2.9000180.BVS
!  N_cations   N_anions Tolerance(%) / Name or cations/ and Anions
   3   1   80.00
CU+1 SC+3 MG+2
O-2 
!
P 63/m m c   --Space group symbol
!Atom Typ   XYZ Biso  Occ In Fin N_t Spc
/Codes
!beta11   beta22   beta33   beta12   beta13   beta23  /Codes
Cu   CU  0.35645  0.71293  0.25000  0.0  2.0   0   0   20
   10.2010.40 0.00 0.10 0.00

Negative displacement params in neutron refinement

[Yokochi, Alexandre]

Hi all,

I have neutron data (constant wavelength) I have been working on and
the displacement parameters of most atoms turn out to be negative along one
axis (c in hexagonal setting).  The material has relatively low absorption
coefficient (mu*r approx .5), and (as expected) when a cylindrical
absorption correction is applied, the displacement parameters are still
negative.  I would like to hear any suggestions of possible causes.  Though
the structure is well known and refined multiple times (including by me from
single crystal for related systems) I favour wrong symmetry / space group as
the cause.

Thanks, AlexY


Dr. Alexandre F. T. Yokochi
Assistant Professor (Senior Research)
Director, X-ray Crystallographic Facilities
Department of Chemistry
Oregon State University
Corvallis, OR 97331-4003

Ph#  (541) 737-6724 Email: [EMAIL PROTECTED]
Fax# (541) 737-2062 Web Page: crystal.chem.orst.edu/~alexy (temporarily
unavailable)

Crystallographic data for Sucrose

[Yokochi, Alexandre]

Hi everyone,

I have been interested on how well one of my diffractometers would
do with organic samples (i.e., would it be useful for phase matching, or
even SDPD) and am currently collecting a data set on Sucrose (table
variety).  I wonder if any of you that has access to the CSD database would
be so kind as to give me a reference, or even all the relevant data for this
compound.

Also, if anyone knows what all do the food companies add to this
fundamental foodstuff (a veritable staple in some people's diets) I would
like to know, seieng as I have some nice sharp peaks at 120 degrees 2-theta
and above (and I have only been collecting data for 15 minutes so far - the
wonders of area detectors).

Thanks, AlexY

Dr. Alexandre F. T. Yokochi
Assistant Professor (Senior Research)
Director, X-ray Crystallographic Facilities
Department of Chemistry
Oregon State University
Corvallis, OR 97331-4003

Ph#  (541) 737-6724 Email: [EMAIL PROTECTED]
Fax# (541) 737-2062 Web Page: crystal.chem.orst.edu/~alexy (temporarily
unavailable)

Toroidal atom displacement factors?

[Yokochi, Alexandre]

Hi everyone,

I have some data where I suspect that an atom rather than sitting
exactly on a special position is actually displaced off of it, and should
essentially form a torus around it.  I think I overheard that there is the
possibility of using toroidal displacement factors in one of the more common
programs.  Could someone give me a pointer in that direction if it is
possible at all?

Thanks, AlexY

Dr. Alexandre F. T. Yokochi
Assistant Professor (Senior Research)
Director, X-ray Crystallographic Facilities
Department of Chemistry
Oregon State University
Corvallis, OR 97331-4003

Ph#  (541) 737-6724 Email: [EMAIL PROTECTED]
Fax# (541) 737-2062 Web Page: crystal.chem.orst.edu/~alexy (temporarily
unavailable)

RE: Re: Powder patterns from single crystal intensity data

[Yokochi, Alexandre]

Sean,

Thanks, I'll give it a try.  I am also to the point where I think
writing a quick utility to do it would be trivial, so maybe I'll do it as
soon as instrumentation quits breaking down (I've almost reached steady
state!).

Did you ever get an answer to your GSAS question?

AlexY

Powder patterns from single crystal intensity data

[Yokochi, Alexandre]

Hi everyone,

I am wondering whether there is an easy to use tool that will take a
SHELX format intensity file and instrumental parameters (or even without
these) and calculate a powder pattern out of that.

I know that sometime ago someone asked exactly the question I am now
asking, but if I recall correctly the answer involved using Koalariet, which
is a program with which I am not conversant.

Thanks, AlexY

Dr. Alexandre F. T. Yokochi
Assistant Professor (Senior Research)
Director, X-ray Crystallographic Facilities
Department of Chemistry
Oregon State University
Corvallis, OR 97331-4003

Ph#  (541) 737-6724 Email: [EMAIL PROTECTED]
Fax# (541) 737-2062 Web Page: crystal.chem.orst.edu/~alexy (temporarily
unavailable)

RE: none

[Yokochi, Alexandre]

Joe,

You'll have fun and learn a lot of strange things playing with powders (I know 
I have).

We have both a Siemens (Bruker) D5000 and two INEL systems.  Both give 
excellent data, etc.  The INEL systems, due to the parallel beam optics are way more 
sensitive to alignment.  However, because of the fact that we have a flat plate 
monochromator, we have peak profiles that are a lot easier to fit (only Kalpha1 and no 
'tube wings') even if the low angle peaks are a bit asymmetric.  I understand that by 
coupling a mirror to the monochromator of the INEL systems you can double or triple 
the X-ray flux, but I have no first hand experience of that.  Besides, right now I am 
working on hooking up one of our INEL systems to a rotating anode generator, which 
should be even better (Lee can tall you I'm always wanting to use 'the other port' in 
any rotating anode generator).

Let me know if you'd like more comments.

AlexY


Dr. Alexandre F. T. Yokochi
Assistant Professor (Senior Research)
Director, X-ray Crystallographic Facilities
Department of Chemistry
Oregon State University
Corvallis, OR 97331-4003

Ph#  (541) 737-6724 Email: [EMAIL PROTECTED]
Fax# (541) 737-2062 Web Page: crystal.chem.orst.edu/~alexy (temporarily 
unavailable)

RE: a few words about pdCIF

[Yokochi, Alexandre]

Howdy everyone,

Concerning the data storage formats, Brian Toby wrote that (some time ago)

am not sure that I would use CIF as my internal format, if I were to
create a database, since it is not designed for searching, but I would
certainly want the ability to both import and export data to/from CIF.

As I recall, someone maintains an in-house database of single crystal work 
that is stored in CIF, using a public domain database search software, and on Linux.  
The someone may have been Paul Boyle at North Carolina State, if my memory serves, but 
this query of my internal database is attempting to access stuff at least a couple 
years old.

AlexY

Dr. Alexandre F. T. Yokochi
Director, X-ray Crystallographic Facilities
Department of Chemistry
Oregon State University
Corvallis, OR 97331-4003

Ph#  (541) 737-6724 Email: [EMAIL PROTECTED]
Fax# (541) 737-2062 Web Page: crystal.chem.orst.edu/~alexy (temporarily 
unavailable)