November 2003 - Ifeffit - millenia.cars.aps.anl.gov

A question
by H H 06 Nov '03

06 Nov '03

I have tried to use artemis to fit some data. I faced some problem and I am not sure if I am doing the right thing or not. Here is the problem, after I perform the fit then I can save the data and also the fit in K, R, and Q. However, when I do the phase correction using the option(path to use for phase correction), it did the job, but I did not allow me to save the fit. I am using the latest version posted oonline. I would appreciate if someone tell me if I am doing something wrong or the way to save it. Thanks, Hedy __________________________________ Do you Yahoo!? Protect your identity with Yahoo! Mail AddressGuard http://antispam.yahoo.com/whatsnewfree

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iMol for Mac OSX
by Charles Bouldin 04 Nov '03

04 Nov '03

This may be of some use to the Mac OSX users here: http://www.pirx.com/iMol/index.html

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quick Artemis ?
by k-kupiecki＠northwestern.edu 04 Nov '03

04 Nov '03

Hi, Just a quick Artemis question... I've been pulling in my FEFF8 paths by selecting the feff.inp in the appropriate folder with all the paths.... I've noticed that when I load in my path files this way that all of them are automatically selected to "Include feffNNN.dat in the fit". Is there a way I can get these all turned off at the same time (other than manually to each path)? So that I can add the paths one by one to the fit while they are all listed in Artemis? Thanks, Kristine Northwestern University

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Re: [Ifeffit] quick Artemis ?
by k-kupiecki＠northwestern.edu 04 Nov '03

04 Nov '03

Thanks Mark and Peter for your quick responses.... you just saved me a ton of time today! Thanks! -Kristine

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Inconsistency in generaton of feff.inp by atoms
by Carlo U. Segre 04 Nov '03

04 Nov '03

Bruce: I have just run up against an odd error in atoms. I am not sure why it happens but it is consistent among all my computers. I start tkatoms and set up a structural model fo rthe wurtzite structure as follows: ----------------- atoms.inp ---------------- ! This atoms input file was generated by TkAtoms 3.0beta8 ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = ZnS Wurtzite structure space = p 63 m c a = 3.820 b = 3.820 c = 6.260 alpha = 90.0 beta = 90.0 gamma = 120.0 core = Zn edge = K rmax = 7.0 shift 0.0000 0.0000 0.0000 atoms ! elem x y z tag occ. Zn 0.3333 0.6667 0.0000 1.0000 S 0.3333 0.6667 0.3748 1.0000 ----------------- Then I run atoms from within tkatoms and get a feff.inp file: ----------------- first feff.inp (top lines only)---------------- * This feff input file was generated by TkAtoms 3.0beta8 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 761.06 cm^-1, delta_mu = 589.98 cm^-1 * specific gravity = 4.091 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00045 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE ZnS Wurtzite structure HOLE 1 1.0 * Zn K edge (9659.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 7.0 *CRITERIA curved plane *DEBYE temp debye-temp *NLEG 8 POTENTIALS * ipot Z element 0 30 Zn 1 30 Zn 2 16 S ATOMS * this list contains 68 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Zn 0.00000 2.20546 0.00004 -0.78375 2 S_1 2.34058 -1.10276 -1.90996 -0.78375 2 S_1 2.34058 -1.10276 1.91004 -0.78375 2 S_2 2.34064 0.00000 0.00000 2.34625 2 S_3 2.34625 3.30822 1.91000 0.00000 1 Zn_1 3.82000 -3.30822 1.91000 0.00000 1 Zn_1 3.82000 0.00000 3.82000 0.00000 1 Zn_1 3.82000 3.30822 -1.91000 0.00000 1 Zn_1 3.82000 -3.30822 -1.91000 0.00000 1 Zn_1 3.82000 0.00000 -3.82000 0.00000 1 Zn_1 3.82000 ----------------------------- Then I save the atoms.inp file and when I read it in again and run atoms, I get a completely different result: ------------------- second feff.inp (top lines only) -------------- * This feff input file was generated by Atoms 3.0beta8 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 1522.11 cm^-1, delta_mu = 1179.96 cm^-1 * specific gravity = 8.182 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00045 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE ZnS Wurtzite structure HOLE 1 1.0 * Zn K edge (9659.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 7.0 *CRITERIA curved plane *DEBYE temp debye-temp *NLEG 8 POTENTIALS * ipot Z element 0 30 Zn 1 30 Zn 2 16 S ATOMS * this list contains 136 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Zn 0.00000 0.00011 0.00006 0.00000 1 Zn_1 0.00013 -1.10274 1.90987 -0.78375 2 S_1 2.34049 -1.10274 -1.90987 -0.78375 2 S_1 2.34049 2.20548 0.00013 -0.78375 2 S_2 2.34060 2.20548 -0.00013 -0.78375 2 S_2 2.34060 -1.10274 1.91013 -0.78375 2 S_3 2.34070 -1.10274 -1.91013 -0.78375 2 S_3 2.34070 0.00000 0.00000 2.34625 2 S_4 2.34625 0.00011 0.00006 2.34625 2 S_4 2.34625 -3.30811 -1.90994 0.00000 1 Zn_2 3.81987 -3.30811 1.91006 0.00000 1 Zn_3 3.81994 0.00011 -3.81994 0.00000 1 Zn_3 3.81994 3.30822 1.91000 0.00000 1 Zn_4 3.82000 ----------------------------------------------- You can see that the total mu, specific gravity and delta mu are different! I can run atoms from teh command line as well and I get the same incorrect result. I am running atoms-3.0beta8 but I tested beta9 and got the same result. I don't have this problem with the zincblende structure which is cubic so there must be a problem with the hexagonal lattice. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)agni.phys.iit.edu http://www.iit.edu/~segre

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Inconsistency in generaton of feff.inp by atoms
by Bruce Ravel 04 Nov '03

04 Nov '03

Carlo, Peter, There is certainly a problem with your example. It seems likely that any hexagonal group will have this problem. Drat! I am very busy this week with some administrative responsibilities, but will look into the problem just as soon as I can and hopefully announce a fixed atoms soon after that. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Tk804.025_beta
by J. M. An 04 Nov '03

04 Nov '03

Until then, I recommend that you use the work-around I suggested earlier today. As a reminder, I have an older version of perl/Tk on my web site: http://leonardo.phys.washington.edu/~ravel/misc/Tk-800.024.tar.gz <http://leonardo.phys.washington.edu/%7Eravel/misc/Tk-800.024.tar.gz> If you install that, Athena and Artemis should work. If you have other software that requires the very latest perl/Tk -- I apologize for the inconvenience. Thanks, Bruce. Now, my previous problems with Tk804.025_beta disappears, when I install an older version Tk-800.024. I uninstalled the latest version, and intalled the older one. Joon An

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Tk804.025_beta
by J. M. An 03 Nov '03

03 Nov '03

On Sunday 02 November 2003 06:43 pm, J. M. An wrote: >> (3) in using artemis, here is the problem >> >> Typing "artemis" brought up a window, but in "import a Feff calculaton" >> window under menu-bar "File", >> I couldn't move to any directory where "feff.inp" is, causing the >> following error message: >> >> Tk::Error: Can't locate Tk/Unselect.pm in @INC (@INC > > >Hi, >Yours is the second email this morning reporting this problem. I >don't know the answer, but I'll look into it and make an announcement >to the mailing list when I figure it out. Dear Bruce, As for the inability to move into/out of directories, the following error message may help to track down its cause: Tk::Error: Can't locate Tk/ListBrowse.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/Tk/Widget.pm line 270. I suspect that some ListBrowse.pm and Unselect.pm files are missing. Joon >From LBL

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Regarding IFEFFIT updates and WIN98
by k-kupiecki＠northwestern.edu 03 Nov '03

03 Nov '03

Hi, I've been using IFEFFIT etc. on a Win98 machine. When I went to use Artemis today I received the message regarding an IFEFFIT update being available. I went to install it but it froze... so I figured it might be because of it being Win98..... So I just uninstalled my old version of IFEFFIT and installed the new version - which works great.... But I'm still getting this IFEFFIT prompt for updates even though I have the updated version of everything.... I'm just wondering if there is a way for me to turn that off.... Thanks, Kristine Northwestern University

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Tk804.025_beta
by J. M. An 03 Nov '03

03 Nov '03

Dear helper, Sorry to interrupt to this installation procedure for questions, but it was definitely helpful to install horae-025 package. I'd like to report a problem in using artemis. I use RH 8.0 to install the package, following all your instructions. Log in as a normal user. (1) For Tk804.025_beta installation, xhost + localhost su export LANG=lang_us perl -MCPAN -e shell cpan>install Tk In the installation process, I encountered the following warnings: cc1: warning: changing search order for system directory "/usr/local/include" cc1: warning: as it has already been specified as a non-system directory But the installation was successful after all. (2) For horae-025 intallation, perl Makefile.PL make make intall I also encountered the same warnings as the above, but the installation seems ok. (3) in using artemis, here is the problem Typing "artemis" brought up a window, but in "import a Feff calculaton" window under menu-bar "File", I couldn't move to any directory where "feff.inp" is, causing the following error message: Tk::Error: Can't locate Tk/Unselect.pm in @INC (@INC contains:/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/Tk/Widget.pm line 270. Joon An From LBL.

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