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

Icosahedral cluster coordinates
by Patrick Kluth 17 Aug '05

17 Aug '05

Hi All, Since this is my first message to the mailing list, I`d like to say thanks very much to Bruce, Matt and everyone else who is involved for this great piece of software. It makes life in the EXAFS world so much easier. I am working with metal clusters and would like to do some FEFF calculations on icosahedral clusters. Is there anyone out there who has a FEFF input file (or equivalently a list of coordinates) for an icosahedral cluster (147 atoms is probably sufficient for my purpuses). Thanks Patrick --------------------------------------------------------------------------------- Dr. Patrick Kluth ARC Australian Postdoctoral Fellow Department of Electronic Materials Engineering Research School of Physical Sciences and Engineering The Australian National University Canberra, ACT 0200 AUSTRALIA Phone: +61 2 6125 0358 Fax: +61 2 6125 0511 Mobile: +61 408 66 31 04 Email: Patrick.Kluth(a)anu.edu.au http://www.rsphysse.anu.edu.au/eme ---------------------------------------------------------------------------------

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Bug in artemis of horae-053
by Paul Fons 16 Aug '05

16 Aug '05

I have had been bitten by surprisingly few bugs in the latest version of artemis, but I thought I would pass along an observation of one that should be easy to confirm. I am doing multiple edge fits and have in the past imported new data by using the project data item in the file menu. Selecting this brings up a dialog which asks if the new (path) data should replace the old data or should it be new (e.g. a new feff calculation). It doesn't appear to make any difference which option is selected, it always replaces the existing data. I seem to remember that this used to work in earlier versions... In any case, a work around is just to use the open item under the file menu which then does generate a new feff calculation entry. Oh, one more thing, as I recall Calculation is misspelled in the theory menu (it hurts to look at it as I live in a land with a lot of broken English (Japan))! Paul

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RE: [Ifeffit] Athena plotting multiple k-weights; confusion about "k" and "k-weight"
by Kelly, Shelly D. 15 Aug '05

15 Aug '05

Hi Charles, I think that you understand correctly and that Athena doesn't label the axis correctly when multiple k-weights are being plotted. The FT are different when different k-weights are used because different regions of chi(k) are emphasized differently. Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Charles Chusuei Sent: Mon 8/15/2005 12:23 PM To: 'XAFS Analysis using Ifeffit' Subject: [Ifeffit] Athena plotting multiple k-weights; confusion about "k" and "k-weight" Hello all: I'm confused about what is meant by "k-weight" and "k" and how they are used in the Athena plotting. As I understand it, "k" refers to the photo-electron wavenumber, k = [2m(E-E0)]/(h/2pi)^2]^ 0.5. A "k-weight" is the degree that chi(k) can be amplified. For instance k-weight of "2" in the Athena program plots a k^2*chi(k) versus k. A k-weight of "3" plots a k^3*chi(k) versus k, etc. However, in plotting multiple "spectra" using the same data file of different k-weighting one can see the different lineshapes for each k-weight [for instance assigning k-weights = 1,2 and 3]. Yet, the Athena output has the labels of "k^2*chi(k)" versus "k" even though there are multiple k-weights used. Is this a typo in the ordinate label where it would be more appropriately labeled as "k^n*chi(k)" versus "k" where n = weight, or am I fundamentally misunderstanding the relationship between "k" and "k-weight"? I'd appreciate assistance in understanding if the latter is the case. Thank you for your thoughts. Charles _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Athena plotting multiple k-weights; confusion about "k" and "k-weight"
by Charles Chusuei 15 Aug '05

15 Aug '05

Hello all: I'm confused about what is meant by "k-weight" and "k" and how they are used in the Athena plotting. As I understand it, "k" refers to the photo-electron wavenumber, k = [2m(E-E0)]/(h/2pi)^2]^ 0.5. A "k-weight" is the degree that chi(k) can be amplified. For instance k-weight of "2" in the Athena program plots a k^2*chi(k) versus k. A k-weight of "3" plots a k^3*chi(k) versus k, etc. However, in plotting multiple "spectra" using the same data file of different k-weighting one can see the different lineshapes for each k-weight [for instance assigning k-weights = 1,2 and 3]. Yet, the Athena output has the labels of "k^2*chi(k)" versus "k" even though there are multiple k-weights used. Is this a typo in the ordinate label where it would be more appropriately labeled as "k^n*chi(k)" versus "k" where n = weight, or am I fundamentally misunderstanding the relationship between "k" and "k-weight"? I'd appreciate assistance in understanding if the latter is the case. Thank you for your thoughts. Charles

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problem with the new version of athena
by Carmelo Prestipino 11 Aug '05

11 Aug '05

Hi I have a really strange problem with the new version of athena. After updating to iffefit 1.2.7 I lose the possibility to use athena, but the rest of the package works well. I already try do deinstall everything and install ifeffit again but nothing changed. This problem is present only on my computer while in the computer of my colleagues athena works well. The file 1.txt is the answer of calling from the shell "athena.exe" the file 2.txt is the answer of calling from the shell "athena.bat" I'm using a windows 2000 sistem Any idea? Bye Carmelo -- ************************************************************************ Carmelo Prestipino(*) Department of Inorganic, Physical and Material Chemistry Via P. Giuria 7 I-10125 Torino Italy Tel +39011-6707841> Fax +39011-6707855 E-mail carmelo.prestipino(a)unito.it (*) also with INFM UdR di Torino Universita' ************************************************************************* C:\Programmi\Ifeffit>athena.bat Ifeffit checked for updates recently. Untagged opnames: recv i_predec localtime sassign rewinddir untie sockpair scope seekdir ucfirst fteowned i_negate rv2cv leave accept ge redo stringify substcont index right_shift aelem hex sservent send gt multiply bit_or unlink gv wantarray i_ne exi t lcfirst semctl open rv2sv gprotoent backtick syswrite getlogin grepstart subtract ftsize eof warn ehostent nextstate dofile aassign ftatime gvsv null gmtime shift stat flip substr postinc open_dir cond_expr atan2 left_shift time hslice leaveeval ret urn grepwhile socket preinc telldir seq link ftfile setstate sysread chdir each av2arylen ioctl reset ftewrite refgen gpwuid ord join modulo chown pop padav shmread ftsvtx pos and pow sgrent oct rindex chr sge aelemfast regcomp andassign fteexec rv2gv ftpipe ftsuid sort i_divide sprotoent fork entersub sgt ftbinary chmod unpack fteread bind tell eservent entertry semop push getpriority flock rv2hv lc ftrowned gpwnam system le gsbyport dump concat pushmark ftctime lt mapstart i_postdec repeat pack leaveloop stub exists sin threadsv syscall utime quotemeta ftchr padsv bit_xor log mapwhile rcatline sysopen readdir alarm truncate seek const padany sselect entereval abs ftzero ne helem close ftblk i_eq gpwent gpbynumber values pushre leavesub proto type die dbmclose aslice binmode wait complement list reverse flop snetent gsbyname fttty ftrexec leavetry match unstack eprotoent i_preinc gpbyname shutdown ftrwrite crypt postdec iter listen anoncode trans lineseq ftrread length ftsgid sprintf print chomp or add enter predec lock epwent tie fttext chop i_ge sle schop umask closedir gnetent subst tied i_add setpgrp i_modulo defined scmp negate getpeername undef rmdir ftlink slt regcreset i_gt rename ghostent msgsnd method_named kill orassign requ ire sqrt method ftis lstat splice mkdir leavesublv gsockopt ftdir i_ncmp scalar getpgrp chroot padhv ncmp vec exp unshift caller qr dbstate ggrnam cos sne ftmtime symlink srefgen ftsock enterloop schomp keys msgrcv msgget shmget anonhash exec waitpid xor sleep read range goto getppid delete prtf shostent int next fcntl getsockname shmwrite i_multiply setpriority gelem sysseek regcmaybe getc enterwrite semget not gservent ggrent anonlist formline glob fileno ssockopt rv2av spwent i_subtract ggrgid tms gnbyname rand divide srand enteriter bit_and study eq dbmopen gnbyaddr leavewrite i_le pipe_op ghbyname connect ref lslice bless uc readline enetent select readlink msgctl i_lt i_postinc split last egrent ghbyaddr shmctl Can't locate Tk/Popup.pm in @INC (@INC contains: C:\DOCUME~1\lello\IMPOST~1\Temp\par-lello\cache-5d90d4330465c124b0c34b24a7275a8a36486b2a/inc/lib C:\DOCUME~1\lello\IMPOST~1\Temp\par-lello\cache-5d90d4330465c124b0c34b24a7275a8a36486b2a/inc CODE(0x12d32 6c) .) at Tk/Widget.pm line 259. BEGIN failed--compilation aborted at -e line 835. C:\Programmi\Ifeffit> C:\Programmi\Ifeffit>athena.exe can't open \perl\Xray\space_groups.db: No such file or directory at Xray/Xtal.pm line 115 Compilation failed in require at Ifeffit/Files.pm line 50. BEGIN failed--compilation aborted at Ifeffit/Files.pm line 50. Compilation failed in require at script/athena line 86. BEGIN failed--compilation aborted at script/athena line 86. BEGIN failed--compilation aborted at -e line 835. C:\Programmi\Ifeffit>

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Athena
by gfabbris＠lnls.br 09 Aug '05

09 Aug '05

Hi! My name is Gilberto Fabbris, I`m from LNLS, that stay in Campinas-SP, Brazil. I installed the Ifeffit (the last version) today. I runned the Athena, but when I tried to align, or calibrate energy, the Windows (XP) accused a error in the program and closed it. How can I fix it? Thank you! Gilberto Fabbris

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ifeffit 1.2.7
by Matt Newville 25 Jul '05

25 Jul '05

Hi Folks, I've posted Ifeffit 1.2.7, including a new Windows installer, source code, and a Mac Binary installer (currently OS 10.3 only) on the IFeffit Web Page. I'll post these to sourceforge.net as soon as I can. For Windows users, there is also an automatic update that may be downloaded and installed. The changes to the ifeffit library are small: a few bugfixes, added a 'penalty()' math function (as per a discussion on this list about restraints) and an improved mechanism for ifeffit to report its status to a calling program like Athena and Artemis. The Windows and Mac installers also include the latest versions of Bruce's Athena, Artemis, and Hephaestus. There are still some known issues with "PAR-" files from Bruce's codes on Windows. Bruce and I think we can solve this, and are aiming to release a new Windows installer sometime in the next month (or so) that fixes this and cleans up some of the messiness of the Windows installer. --Matt

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RE: [Ifeffit] surface EXAFS
by Kelly, Shelly D. 21 Jul '05

21 Jul '05

Hi Matt, I should have given these details right away. My trick is to parameterize the feff paths in terms of an x, y, z coordinate for the atom on the surface. Then I refine three different polarization dependent data sets to find the best x, y, and z position of the atom on the surface. Thanks for the references! Shelly > -----Original Message----- > From: Matt Newville [mailto:newville@cars.uchicago.edu] > Sent: Thursday, July 21, 2005 11:13 AM > To: Kelly, Shelly D.; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] surface EXAFS > > Hi Shelly, > > > I am working on a project were I trick feffit into moving an > > atom around on the surface of a plane to refine polarization > > dependent surface EXAFS data. I made a quick literature > > search and have not found any other EXAFS papers that do such > > a thing. Are you aware of similar work? I would like to give > > credit in our manuscript. > > I know of other work in progress (some in progress for a pretty > long time!!). I also believe there are a few surface XAFS > papers that used feffit. I think these may count, though I > don't have a copy of any of these in front of me: > > L. Y. Zhao et al, Applied Surface Science 228, p 257 (2004) > P. Luches et al, Surface Science 566, p 84 (2004) > L. Damoc, et al J. Applied Physics 92, p 1862 (2002) > S. K. Kim, et al, PRB 62, p 3025 (2000). > > I think there are probably others. > > I'm not sure what the 'trick' you're using is. Doing a polarized > calculation (with feff or in feffit) for an atom on a surface > doesn't seem like such a big deal, but maybe you're doing > something fancier. > > One paper that I know is in progress (and a just-completed > thesis) measures the 'height above the surface' of a sorbed atom > by defining several different distances in terms of this height. > > --Matt

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surface EXAFS
by Kelly, Shelly D. 21 Jul '05

21 Jul '05

Hello all, I am working on a project were I trick feffit into moving an atom around on the surface of a plane to refine polarization dependent surface EXAFS data. I made a quick literature search and have not found any other EXAFS papers that do such a thing. Are you aware of similar work? I would like to give credit in our manuscript. Shelly

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feff doesn't like cluster
by Juraj Majzlan 21 Jul '05

21 Jul '05

Hello, I collected As K EXAFS data and created a cluster which could represent the "probable geometry". I have an ATOMS file with coordinates of the atoms in a triclinic unit cell. ATOMS did its thing but FEFF refused to process the data and generated an error: Feff 6L.02 No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. Fatal Error: at RDINP Then I filled the empty space around the cluster with hydrogen atoms on a grid, hoping that FEFF would like it more, but the same error came. Short of creating a complete structure (of some sort) with the cluster embedded in it, what can I do to make this work? Thank you, Juro Majzlan ---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de

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