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

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 03 Nov '03

03 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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[Ifeffit] problems using Athena and Artemis with perl/Tk 804.025 on linux and other unixes
by Bruce Ravel 03 Nov '03

03 Nov '03

Hi folks, The problem I am reporting in this email mostly effects users of linux and other unix systems. This does not effect Windows users of Athena and Artemis. There seem to be some severe problem in how Athena and Artemis interact with the latest version of perl/Tk. At least a couple of people have done the very sensible thing of installing the latest version of perl/Tk and then installing my software. Unfortunately, if you do so, you will run into lots of problems. As soon as possible, I will release new versions of Athena and Artemis that will play well with the latest version of perl/Tk. Until then, the best advice I can give is to "downgrade" your version of perl/Tk. Here is a copy of a version that I believe will allow you to use Athena and Artemis fully: http://leonardo.phys.washington.edu/~ravel/misc/Tk-800.024.tar.gz If this conflicts with other programs or projects for any individual user, I apologize and, as I said, will fix the problems with Athena and Artemis ASAP. So, to summarize, Athena and Artemis currently do not work with the most recent version of perl/Tk. This is my fault not the fault of perl/Tk. The solution is either to wait for me to fix the problems or to install an older version of perl/Tk. Regards, Bruce -- 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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Re: [Ifeffit] ... and lots of new stuff in Athena and Artemis, too!
by SCalvin100＠aol.com 31 Oct '03

31 Oct '03

Yippee!!! Many thanks to Matt and Bruce for the new releases! --Scott Calvin Sarah Lawrence College

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Ifeffit 1.2.4 Debian Linux packages
by Carlo U. Segre 31 Oct '03

31 Oct '03

Hello all: The latest version of Ifeffit is now available as a Debian packge. There is also an update package of horae 024 with a recompiled wrapper for Ifeffit 1.2.4. 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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RE: [Ifeffit] relation between DW factors in uranyls
by Kelly, Shelly D. 30 Oct '03

30 Oct '03

> This is in response to Shelly's post for MS references. For > linear multiple scattering, I like to use this paper: > > Hudson, EA; et. al. (1996) Phys Rev B 54(1) 156-165 > > It uses the uranyl ion specifically in this example and has a > short section in the introduction about the relations between > single and multiple scattering D-W parameters. > > Hope this is vaguely what you were looking for.... > > > Sam Hi Sam and John, I just wanted to say thank-you to the ifeffit mailing list. Sam, the reference was indeed helpful. And thanks to John for his derivation. This is what I learned about relating sigma2 values for the uranyl. For a linear uranyl moiety (UO2), where the atoms are all in a line O1-U-O2, the sigma2 values can be approximated like this: U-O1-U: sigma2-s.s. (single scattering sigma2) U-O1-U-O1-U: sigma2 = 4 * sigma2-s.s. U-O1-U-O2-U: sigma2 ~ 2 * sigma2-s.s. U-O1-O2-U: sigma2 ~ 2 * sigma2-s.s. This information has been published in Hudson et al. PRB V54 n1, pg 156 (1996). Shelly

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