Re: fractional occupancy and composition within GSAS
The short answer here is read the code that does this, which I have not done anytime recently. What I recall is the unit cell composition is simply the sum of site multiplicities times the fractional occupancy for each site grouped by atom type. The way I come up with z is something of a kludge -- I think I look for the largest integer divisor for all the non fractionally occupied sites. If anyone has a better suggestion on how to do this, I'd like to hear it. Brian Sent via BlackBerry from T-Mobile -Original Message- From: Irvin Telepeni irvin.telep...@nottingham.ac.uk Date: Wed, 02 Dec 2009 17:07:02 To: rietveld_l@ill.fr Subject: fractional occupancy and composition within GSAS Hi, I'd like to know how GSAS (EXPGUI) calculates the atomic composition (through the RESULTS menu) of one phase with respect to the atomic fractional occupancy? How can I get to the same composition values from my fractional occupancies? Cheers, Irvin This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Re:
Dear Milinda, I have added you to my mailing list for information about EXPGUI (the GSAS user interface). When I have time, I make updates and send out mail to that list. If you have questions, you likely want to join the Rietveld mail server, where people have discussions on the technique and software. That list is at rietveld_l@ill.fr and you can find instructions on how to subscribe at http://ccp14.sims.nrc.ca/ccp/ccp14/ftp-mirror/howardflack/pub/soft/crystal/stxnews/riet/using.htm (the ccp14 site also has many good tutorials, plus there are a few on my site, see link below) There is also an archive of the Rietveld list: x-tad-biggerhttp://www.mail-archive.com/rietveld_l@ill.fr/ Brian/x-tad-bigger Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8563 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8563 http://www.ncnr.nist.gov/xtal On Jul 1, 2005, at 1:32 PM, milinda a wrote: Hello Brian, I am a graduate student at University of Houston. I use GSAS to model Nanoclusters embedded in zeolite. I have some questions regarding my refinments. Please add me to the GSAS mailing list. Thank you. Regards! Milinda __ Yahoo! Mail Mobile Take Yahoo! Mail with you! Check email on your mobile phone. http://mobile.yahoo.com/learn/mail
Re: DBWS vs other refinement programs
http://danse.cacr.caltech.edu/polls/results.php?sid=22 Of course, the number of people using Rietveld software is more than 269 (number of answers in the survey) The number of respondents to the survey is ~150, but Rietveld users (at least the ones who took the time to participate) on average use more than one package, which is why there are >>150 answers. Brian
Re: mismatch between ICSD cif file and GSAS
On May 17, 2005, at 12:31 AM, Donald Wang wrote: x-tad-biggerAfter 1/8 offset, it appears that the pattern from live plot is a good match to ICSD-generated pattern, which basically solved my problem. I am very happy and grateful./x-tad-bigger x-tad-bigger /x-tad-bigger x-tad-biggerThere is still a little problem. The multiplicity column did not change at all (in EXPGUI). Please explain./x-tad-bigger Yes -- this one is a known EXPGUI bug. EXPGUI does not compute the multiplicity values directly, but rather it reads them from the .EXP file. GENLES will update them, but only if the atom [coordinate?] is varied. When you move an atom in EXPGUI from one site to another by editing coordinates the multiplicity does not get updated, but as you found the diffraction intensity calculation comes out right. The right way to address this problem would be to have EXPGUI invoke the section of EXPEDT that computes multiplicities, but that is not going to happen any time soon. One thing that I could do fairly easily would be to set the multiplicity to zero when an atom position is edited. Anyone want to speak in favor or against this idea? Brian
Re: Laboratory Information Management Systems (LIMS)
At 14:43 22/04/2005, Angus P. Wilkinson [EMAIL PROTECTED] wrote: Do none of the user facilities have a data management system in place for their instruments? Well yes Angus :-) For the past 30+ years ILL has stored all instrument data as simple ASCII files with a data format described in the first few lines of the file. I presume we all archive data files -- but a data management system records far more about the data and sample (metadata as the informatics folks like to say) than what shows up in the run header. We can locate all the data that were collected at 1500 K, but how about finding studies on all the samples that were quenched from 1500 K prior to measurement? Brian
Re: Change format
your data are free format with intensities as a real variable. Using excel or any equivalent you can convert in integer intensities (e.g. multiplying by ten to avoid errors with low values) which is the usual data input (counts). Step 2 is then to convert the free 2th-I (real-integer) file into GSAS format (no 2th, 10 int per line) using any of the conversion programs. 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. I can sympathize with the temptation to skip the details (like understanding exactly what your data represent) to get on with the science, but the eventual result is a study that is not suitable for publication. Brian
Re: RIET:CLAY: IUCr 2005: Crystallographic Software Fayre at IUCr Florence, Italy 2005 Congress
I should think about doing something -- what makes most sense CMPR, EXPGUI, GSAS2CIF or pdCIFplot? I tend to think CIF is the most important with the Acta's now asking for powder CIFs. What to you think? BTW, at least for me, invited talks matter and other talks don't. As part of my goal of self promotion, err, as improving recognition for software generators, I suggest that people be invited to make presentations in future Congresses. Brian On Sunday, March 13, 2005, at 02:19 AM, L. Cranswick wrote: Crystallographic Software Fayre at IUCr Florence, Italy 2005 Congress (Wednesday 24th August until Tuesday 30th August 2005) http://www.ccp14.ac.uk/projects/iucr2005-softwarefayre/ Thanks to PC hardware arranged by the conference organisers, there will be a non-Commercial Crystallographic Software Fayre at the IUCr Florence 2005 Congress (http://www.iucr2005.it/) from Wednesday 24th August until Tuesday 30th August 2005. This is being organised by Richard Stephenson (CCP14, University College London) and Lachlan Cranswick (NRC Canada, Chalk River Laboratories). The Software Fayre was the following for general usage: 8 PCs running Windows and Linux connected by a local area network A computer projector system and microphone system will also be available for formal software demonstrations (E-mail Richard Stephenson at [EMAIL PROTECTED] if you would like to book some time slots). Besides making informal use of the computers in between booked time slots, non-commercial software authors and interested users are invited to to book time slots to allow the presentation of formal software demonstrations. Bookings of time slots are done through Richard Stephenson (E-mail: [EMAIL PROTECTED]). Current bookings are viewable at: http://www.ccp14.ac.uk/projects/iucr2005-softwarefayre/software.htm More detailed information is available at the 2005 Crystallographic Software Fayre homepage at: http://www.ccp14.ac.uk/projects/iucr2005-softwarefayre/ Please Email [EMAIL PROTECTED] if you have any queries, or bookings you would like to make. Richard and 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 renvoyer un message.)
Re: Rigid body constraints on perovskite structured materials
I will wade in on this topic quickly. Rigid body constraints can be used for two linked bodies pretty easily -- what one does is define the origin of each body as an atom that shared between each body (note that this atom needs to be present in the atom list twice, so adjust occupancies to total accordingly.) Then one can constrain the origin for each body to be the same and but still give each body independent orientations. This trick could be used for more complex situations where more than two bodies share a single atom, but off-hand, I don't see this helping in the case of a perovskite. One other idea that could help is the following: you could define your perovskite blocks individually without any regard to linkages, but then use soft-constraints (really strong ones!) to keep the linking atoms tied together. Again, you will need to define the linking atoms multiple times (so some many need to be dummy atoms or split occupancies), but this should work for any arbitrarily complex arrangement of bodies. Brian On Friday, November 12, 2004, at 10:50 AM, Sang-Heon Shim wrote: I wonder if the rigid-body constraints of GSAS can be used for the polyhedra which are linked each other, such as octahedra in perovskite structured materials. Or is the application of the rigid-body constraints strictly restricted to isolated polyhedra in crystal structures?
Re: Instument parameter file
Theoretically U,V,W should not be refined at all as they describe instrumental broadening This is true only when there is no Gaussian strain present. Brian
Re: Sequential refinement with GSAS
I need to make Rietveld analysis with big amount of data files and I would
like to ask you if you know is it possible to make GSAS refinement for many
files at the same time or is there some procedure to do analysis
automatically for some consequence of files.
I agree that this is a valuable task, but I seem to have enough to do
already. I will suggest, though, that a fair amount of the groundwork in
reading writing GSAS files, as well as running GSAS programs can be
performed using code in EXPGUI. I am happy to help, if someone else
wants to take this task on.
As an example, below is a short tcl script that creates a new .EXP file
based on a template, changing the data file, the title, a,b c and then
runs
POWPREF GENLES. I wrote it quickly, so the script would need some
neatening up so that it could be run on Windows Unix.
# basic definitions needed by EXPGUI routines
set expgui(gsasdir) /home/gsas
set expgui(gsasexe) /home/gsas/exe
set env(GSASBACKSPACE) 1
set expgui(autoiconify) 0
set expgui(debug) 0
# source files
source ${expgui(gsasdir)}/expgui/readexp.tcl
source ${expgui(gsasdir)}/expgui/gsascmds.tcl
# load exp file
cd /home/toby/test/
expload GARNET.EXP
mapexp
# make changes
expinfo title set GARNET 300K
histinfo 1 file set GARNET300.RAW
phaseinfo 1 a set [expr 1.0001 * [phaseinfo 1 a]]
phaseinfo 1 b set [expr 1.0001 * [phaseinfo 1 b]]
phaseinfo 1 c set [expr 1.0001 * [phaseinfo 1 c]]
# save run
expwrite GARNET300.EXP
forknewterm POWPREF $expgui(gsasexe)/powpref GARNET300
forknewterm GENLES $expgui(gsasexe)/genles GARNET300
Anyone who has read this far without losing their last meal is welcome
to contact me.
Brian
