Re: GSAS - p 63/m m c
[EMAIL PROTECTED] wrote: > > Dear All, > > I am trying to do Rietveld refinement of Zirconium using GSAS. Its space > group is p 63/mmc (194). It is a hexagonal closed packed system with two atoms > per unit cell. Position of the one atom is (0, 0, 0) and that of the other is > (2/3, 1/3, 1/2). > > I am also giving the atom coordinates i.e. x,y,z as (0, 0, 0) for Zr1 and > (0.666, 0.333, 0.5) for ZR2 in GSAS. > > I think I am doing wrong because it is giving very bad result.. > > Please suggest what should I give as the atom coordinates. > > Thanking you all. > > Regards, > > Apu > > /_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ > Apu Sarkar > Research Fellow > Variable Energy Cyclotron Centre > Kolkata 700 064 > phone: 91-33-2337-1230 (extn. 3190) > Fax: 91-33-2334-6871 > INDIA > /_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ I personally would use 2/3, 1/3, 1/2 for the Zr2 coordinates. With out digging into the code I do not know if the 0.666 is recognized as 2/3. If you must use the decimal fraction, at least use 0.667 or 0.6667. The GSAS code used to recognize fractions and convert them properly and that would guarantee proper values for the coordinates. Also since the space group listed in the literature is P6/mmc, you might have better luck with a change of space groups. The 63 translation is placing both Zr1 and Zr2 at z=0 and at z=1/2. Allen Larson
Re: New versions of GSAS
Hi! I might note that part of the work in correcting problems with the TLS model in GSAS added a the transformation of anisotropic thermal parameters to the unit cell change program, CllChg. One should now be able to easily transform rhombohedral cell data to the hexagonal representation or make any other similar transformation that is desired. Concerning Bob's point 2, it might be noted that I found when I began development of the Macintosh version of GSAS that DOS GSAS files are 82 characters(records terminated with ), not 80 as noted by Bob below. Incidentally the Macintosh version normally uses 81 character files for easy examination with standard editor programs, records terminated with . It will read the 80 character UNIX files and the 82 character DOS files and if a new version is produced as in GenLes and ExpEdt, the new file has 81 characters. If you are interested in obtaining the Macintosh version of GSAS, please contact me at '[EMAIL PROTECTED]'. Allen C. Larson 14 Cerrado Loop Santa Fe, NM 87505-8248 Phone: (505)466-4792 - Bob Von Dreele wrote: > > Hi, > There are now new versions of both the MS-DOS/Windows and Linux versions of > GSAS. They are essentially identical. The major changes are: > 1. The rigid body TLS model has been changed to be properly based on a > Cartesian > coordinate system (thanks to Allen Larson). This is only noticable in > refinements of TLS in nonorthogonal crystal systems (hexagonal, monoclinic > & triclinic). > 2. GSAS is now more tolerant of raw data files, iprarm files and exp files > that are > not in the "proper" 80 character fixed length direct access format. This is > not completely > fool proof but EXPEDT (and other programs) will detect either files with > incorrect > length records or those transferred from unix (i.e. Linux) and convert raw > and iparm > files to scratch before attempting to read them; the original files are > left unchanged. > EXP files with incorrect record are converted; the original file is > retained with the > extension changed to "CRP". CNVFILE has also been modified to handle Unix > format > direct access files transferred to MS-DOS (Windows). Similarly convstod has > been modified to convert MS-DOS files to unix direct access. (thanks to > Brian Toby for putting forward the original changes for this). > > Enjoy, > Bob Von Dreele
Re: Question on GSAS
Riccardo, In looking through the GSAS source, I find that there are two criteria used to determine if a problem has reached convergence. First all variable groups, such as lattice constants or atom variables, must have a sum of (esd/shift)**2 of less than 0.01 and secondly the total sum of all (esd/shift)**2 must be less than 10**ICNVRG where INCVRG is the number being requested with the 'V' option. I don't know if the 'V' has been removed in the six years since I turned GSAS over to Bob Von Dreele or if it never got into the menu, I suspect the latter. I have modified the menus in the Macintosh version to show the 'V' and added to the data request a statement intended to indicate that an integer is required as the data to be changed. I will admit that I was a bit confused when I tried to enter 0.01 and got told that there was an error in the string. Allen C. Larson Riccardo Vivani wrote: > > Dear all, > in GSAS, L-S control editing option menu appears as follows > Enter L-S control editing option (,A,B,C,D,E,J,L,P,X) > > > By entering "V" (which is not in the list) a new convergence criterion is > asked: > Enter the new convergence criterion > > > Can I have more information on this, and also the more appropriate answer to > that question? > Thank you in advance > > Riccardo Vivani > Laboratiorio di Chimica Inorganica > Dipartimento di Chimica > Perugia - Italy
Re: Bonds calculations....
Distances and angles in crystal structures are calculated using the DisAgl program unit of the GSAS package. Allen C. Larson "[EMAIL PROTECTED]" wrote: > > Does anyone can provide me a software to calculate bonds and angles in > crystal structure (input: space group , atomic positions and unit cell > parameter). > > Thanks. > > > Laurent CHAPON > LPMC, UMR 5617 CNRS, CC003 > Université Montpellier II > 5, place E. Bataillon > 34095 Montpellier Cedex > FRANCE > Mail to : [EMAIL PROTECTED] > Phone :+33-4-67-14-48-88 (ask for Mr CHAPON)
GSAS has been ported to Macintosh
I have ported GSAS to the Macintosh computer. This was developed on a PowerPC Mac with a 604 processor and has been tested machines with the 601e and the G3 processor. Run times are very similar to those on PC's with similar clock speeds. Older Mac's with 680x0 processors are not currently supported. It is now available as shareware. Since the anticipated user base for this software is small, the price is a bit high for shareware. The license fee has been set at US$100 for academic users. And at US$500 for industrial users. A site license fee has not been defined. The software package is available by FTP from 'MacGSAS.CNCHOST.COM'. Unfortunately Concentric, my IP does not allow anonymous FTP access to this site. So I have set it up with two users, one with full privileges and one with read only access. Please contact me for further details. I am willing to discuss any and all details of this project. Allen C. Larson 14 Cerrado loop Santa Fe, NM USA 87505-8248 Email: [EMAIL PROTECTED] Phone: (505)466-4792
Re: Difference in GSAS and DBWS/Fullprof
This sounds like something that someone familiar with both DBWS and GSAS could be able to work out. As the author of the symmetry operation code in both GSAS and DBWS perhaps I can help out. And I have an interest in trying to insure that both of these codes produce proper results. I have source code for both systems here on my personal computers and can thus sort out any problems that exist. I would be quite happy to try to sort out the problem. Privately and report my conclusions to the Rietveld list when the task is completed. Allen C. Larson 14 Cerrado Loop Santa Fe, NM 87505-8248 USA email: [EMAIL PROTECTED] "Magnus H. Sørby" wrote: > > I'm somewhat reluctant to give out my files to "the public" as they are an > important part on somethink I've been working on for a long time and it is > soon to be published. > > As soon as it is published, however, I would be happy to give out the files. > > Best wishes > Magnus >
Re: GSAS code
Armel, There are other people who should be consulted concerning placing GSAS code in any archive. In particular one must note that the code used to generate symmetry operations were developed by me while working at Los Alamos in the late '60s and then revised by me while working at the National Research Council of Canada in the mid '70s. The magnetic symmetry operations were developed at Los Alamos, again by me still later in the evolution of the GSAS software package. Allen C. Larson Armel Le Bail wrote: > > Unfortunately, no benefit at all until now. Still no permission for > putting it in the source code museum. Bob possibly considers > that his code is not old enough and may post an obsolete version > some day ?-). I don't know. Anyway, I have kept it in a highly secured > place ;-). > > Armel > http://www.cristal.org/museum/ > > PS - Who said that we do not need faster computers but only > new ideas ? We need both, don't we ?
Re: Rietveld question - EXPGUI
Alan Hewat wrote: > > >I'm trying to do some refinement on Zr-Y-O powders. I keep getting an error for > >the space group P 42 / n m c S when I try to import the *.cif file for ICSD 90885 > >into EXPGUI. Can someone tell me why? > > >It seems I may have answered my own question. A space seems to be needed between > >the 4 and the 2. This seems to work. OK? > > I would be interested to hear what Brian Toby has to say, since 42/n is one of the > symmetry elements and I would not expect it to be broken up with spaces (but then I > am not sufficiently familiar with how GSAS does that). I would also be interested to > know what EXPGUI/GSAS does with the trailing S in "P 42/n m c S" since this S is > special to ICSD and means that the axes have been chosen to be not at a center of > symmetry. > > 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 > ___ As Alan notes a space which breaks up the 42/n symmetry operator is disastrous in the generation of the matrices which define the group. I might also note that the code recognizes a space as a delimiter in interpreting the group. As for the fifth field in the space group symbol, the code would never see it. Only 4 blocks of data, delimited with spaces, are examined by the space group interpreting code. Allen Larson
Re: Defining the origin of P2/n
[EMAIL PROTECTED] wrote: > > Dear Rietvelders, > > I used GSAS to refine my structure in P2/n, however the program automatically > fixed the the XYZ positions of the first atom during refinement. To my > surprise, this atom is not seen in the "fixed atom list" in the atom parameters > menu of GSAS. > > Please advise and many thanks, > > stephen I am amazed by the flow of miss information that flows on this list whenever an apparent problem with a space group comes up. I am forced to wonder if the correspondents in these exchanges have ever looked at 'The International Tables, Volume A(1983)' or Volume 1(1969) or the earlier volume which dates in the 1930's. Or any of the several other treatises that can also serve as a source for this information. The GSAS package contains a program, SpcGroup, that can be used to list the symmetry operations of any possible string defining a possible space group. In general the space group symbol consists of 2 or more groups of characters delimited by spaces. Please note that the spaces separating axial operations are required in the GSAS interpretation of the space group symbol. Thus 'R3c' must be written as 'R 3 c' or taking advantage of the fact that the lattice type can only occupy one character, 'R3 c', is accepted, but not recommended. I might also note that all of this is based on the use of keyboards in general use in English speaking countries. And I did have no information concerning what you might get using other keyboards. Now for P2/n is a centric space group for which there, in my mind, there exists no reasonable origin choice that the 1bar site. Therefore the software would always choose that for the origin of the unit cell. Allen C. Larson
Re: Defining the origin of P2/n
Peter Zavalij wrote: > > Bob, > Thank you for the clarification. I never had doubts that GSAS handles fixed origin > issue properly but also never understand how it > is done. This way has one big advantage over user fixed origin -- it yields standard > uncertainties for all atoms and therefore for > all distances, etc. > Peter Zavalij > When there is a 1bar site it is automatically chosen as the origin of the unit cell. Any other choice would require adding a extra shift parameter to the X, Y and Z notation in generation the matrices which perform the symmetry operations. Allen
Re: Defining the origin of P2/n
Stephen and Bob, The issue very simply is once you define a site as 'x,y,z', are -x, -y, and -z all used in the definition of other sites in the group? If so the origin has been defined. If not the origin is arbitrary in those directions lacking a minus sign on their operator. This may be over simplifying things, but it might clear up some of this discussion. For P2/n the 2-fold axis defines the x and z origin and the n-glide defines the y origin. Allen C. Larson "Von Dreele, Robert B." wrote: > > Stephen, > Whether the space group is centrosymmetric or not isn't the issue. The question is > whether it is polar or not. P2/n is not polar (i.e. origin defined relative to some > symmetry element) but P2 is polar (i.e y coordinate not chosen relative to a > symmetry element). > Bob Von Dreele > > > > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > Sent: Wed 3/31/2004 9:23 PM > To: [EMAIL PROTECTED] > > Dear Robert B.Von Dreele > > Thank you for your explanation. > Therefore GSAS could do the origin fixing for us when the space group is not > centrosymmetric. Can I boardly say that? > > regards, > stephen
Journals available for shipping
Dear All: I am about to move to the Mesa, AZ, and we won't have space for my complete collection of Journals in our home there. Hence I would like to find a home for them other than the County landfill. The Journal that takes up the most space is Acta Crystallographica. I have bound volumes 1-7, 9-62(Parts A,B & C only) and unbound volumes 8 and 53-57(Parts A,B & C only). I also have The Journal of Applied Crystallography, volumes 6-29, bound, and 30-34, unbound. Sincerely, Allen C. Larson Email: [EMAIL PROTECTED] Phone: (505)466-4792
