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

Regarding XANES spectra of Manganese oxides
by Grant Bunker 17 Jun '04

17 Jun '04

This is in response to Prof. Gang Ho Lee's question. There is indeed a spinel form of Mn2O3 which is isostructural with Mn3O4, except (as I recall from twenty years ago) that the +2 and +3 ion populations are reversed (2/3 of the ions are in octahedral sites, and 1/3 in tetrahedral). So even though the average charge state is changed, the structure isn't. The XANES and XRD are virtually the same because the structures are virtually the same. grant bunker On Thu, 17 Jun 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: a few words... (scalvin(a)slc.edu) > 2. A very quick question (Ahmed M Shahin) > 3. Re: A very quick question (Bruce Ravel) > 4. Reagrding Xanes spectra of manganese oxides (Gang Ho Lee) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Jun 2004 14:01:28 -0400 (EDT) > From: scalvin(a)slc.edu > Subject: Re: [Ifeffit] a few words... > To: ravel(a)phys.washington.edu, "XAFS Analysis using Ifeffit" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <2823.138.110.111.207.1087495288.squirrel(a)mail.slc.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Bruce said: > > > I also wanted to comment on a couple of things that made me laugh out > > loud. One was was Paul's comment to Chris Derr asking him to inform > > the list of the answer once he gets EXAFS all figured out. (Is it > > 42?) > > > > Bruce! I'm shocked at you! Everyone knows that legitimate EXAFS results > must always be reported with the uncertainty; the answer is actually 42 > +/- pi. > > --Scott Calvin > Sarah Lawrence College > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jun 2004 14:17:38 -0500 > From: "Ahmed M Shahin" <shahin(a)umr.edu> > Subject: [Ifeffit] A very quick question > To: <Ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <001a01c4549f$c0ece3a0$fc689783(a)chem.umr.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > I would like to ask a very quick question and I would appreciate if someone can help me. > While running XANES fitting for mixed valence state metals such as cerium (3/4), should I use two arctangent functions with selected group of Lorentzian functions or I have to use only one arctangent function with a group of Gaussian functions? > I would appreciate if someone give some advice. > Yours, > Ahmed > >

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Reagrding Xanes spectra of manganese oxides
by Gang Ho Lee 17 Jun '04

17 Jun '04

Dear Sirs I am writing to you because we are not familiar with xanes. We took xanes spectra of both sample (synthesized by us and we think it as gamma-Mn2O3 ) and Mn3O4 (reference) to make sure that we synthesized gamma-Mn2O3 nanoparticles. The particle diameters ranged from 10 to 15 nm. By using XRD pattern, the structure of sample was determined to be tetragonal with lattice constants of a=5.79 A and c=9.4 A, similar to Mn3O4. From the XRD patterns, we can not distinguish between gamma-Mn2O3 and Mn3O4 because both show nearly identical XRD patterns (JACS 72, 856 (1950)). We attached a data file. Could you please tell us whether the sample is gamma-Mn2O3 nanoparticles or not. Sincerely, Prof. Gang Ho Lee Department of Chemistry College of Natural Sciences Kyungpook National University Taegu 702-701, South Korea tel: 001-82-53-950-5340 fax: 001-82-53-950-6330 e-mail: ghlee(a)bh.knu.ac.kr

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A very quick question
by Ahmed M Shahin 17 Jun '04

17 Jun '04

Hello, I would like to ask a very quick question and I would appreciate if someone can help me. While running XANES fitting for mixed valence state metals such as cerium (3/4), should I use two arctangent functions with selected group of Lorentzian functions or I have to use only one arctangent function with a group of Gaussian functions? I would appreciate if someone give some advice. Yours, Ahmed

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Artemis: Error in laoding additional FEFF paths?
by Carlo U. Segre 17 Jun '04

17 Jun '04

Hello All: One of my students is just trying Scott's ZnO tutorial and we are finding a consistent problem when trying to work with the third project file. When we get to the point of adding an additional path, (feff0011.dat), artemis crashes with the following message: --------------------------------- The following message was trapped by Artemis: Artemis0.7.006warn/home/segre/.horae/stash/ARTEMIS.TRAPCODE(0x9652e54)/home/segre/.horae/stash/artemis.project.2/ at /usr/bin/artemis line 1562 main::__ANON__('Use of uninitialized value in string eq at /usr/bin/artemis l...') called at /usr/bin/artemis line 7313 main::read_feff('^^') called at /usr/lib/perl5/Tk.pm line 225 eval {...} called at /usr/lib/perl5/Tk.pm line 225 Tk::__ANON__('Tk::Menu=HASH(0x974a060)', 'active') called at /usr/lib/perl5/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 1) called at /usr/lib/perl5/Tk.pm line 347 eval {...} called at /usr/lib/perl5/Tk.pm line 347 Tk::MainLoop() called at /usr/bin/artemis line 1707 -------------------------------- This is happening on all of my Linux machines. They are using my Debian packages and so I have not tried with the tarball installation. Has anyone else had this problem? I hesitate to report it as a bug until it is confirmed. In a previous version of horae, it worked fine. 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 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Re: [Ifeffit] Iffeffit1.5.2a compilation troubles
by Stefano Ciurli 16 Jun '04

16 Jun '04

Hello folks, I said earlier: "Apparently, I need to restart the PC any time that somethig goes wrong with aquaterm" No, the problem is really with the ZnO tutorial .apj files. I get aquaterm starting when I open a Cu.chi file, but I do not get it to open when I try to read the ZnO1.apj file. I think this is due to some bug in horae, which makes the programs not really good at managing project files. I think Bruce said something like that some time ago. Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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Re: [Ifeffit] Iffeffit1.5.2a compilation troubles
by Stefano Ciurli 16 Jun '04

16 Jun '04

Hello folks, following the "lost" message from yesterday, and in order to solve the apparent bug that aquaterm does not start automatically etc etc, I reinstalled 1.2.5a using the binary installer AND, this time, restarted the computer (the same old trick). This time aquaterm opens again.... Then, after running the horae_update --force command, aquaterm does not open automatically. BUT, if I restart again the PC, the aquaterm opens. Apparently, I need to restart the PC any time that somethig goes wrong with aquaterm. Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 15 Jun '04

15 Jun '04

Matt, as to the following question: QUESTION: I do not seem to have, in tcsh, the command "configure" I think I solved this one by entering the /Users/stefano/Tk-804.027/ifeffit-1.2.5 directory I am proceeding with the resto of the indicated protocol, so far not caring about the downloading directory (I am using my home directory right now). Please let me know whether I can change the Tk-804.027 directory from my home directory to where it is more right to move it (which I do not know). Thanks, Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 15 Jun '04

15 Jun '04

Paul, this is my .cshrc file: bindkey -k up history-search-backward bindkey -k down history-search-forward if (! $?DISPLAY) then setenv DISPLAY :0.0 endif source /Library/Scripts/iterminal_custom.tcsh source /sw/bin/init.csh source /Users/stefano/Programs/XtalView/XtalView.env setenv PATH `echo $PATH`:/usr/local/sparky/bin:/usr/local:/usr/local/molscript:/usr/local/bin:/Users/stefano/Programs/modeller6v2:/Users/stefano/Programs/o/bin/:/Users/stefano/Programs/autodock/dist305/bin:/Users/stefano/Programs/autodock/dist305/share/:/Users/stefano/Programs/Validation_suite/validation-v0.904-beta-prod-bin-darwin/bin:/Users/stefano/Programs/XtalView/bin/powerpcDarwin5/ defaults write com.apple.x11 wm_ffm true defaults write com.apple.x11 no_quit_alert true setenv RCSBROOT /Users/stefano/Programs/Validation_suite/validation-v0.904-beta-prod-bin-darwin setenv SPARKYHOME /Users/stefano/Programs/Sparky setenv EDENHOME /usr/local/eden setenv ODAT /Users/stefano/Programs/o/data setenv PGPLOT_DIR /etc setenv PGPLOT_DEV /AQT source /Library/Scripts/settitle.csh source /Users/stefano/Programs/NMRPipe/com/nmrInit.mac.com alias ono osx_ono ### begin MODELLER6v2 ###################################################### setenv MODINSTALL6v2 /Users/stefano/Programs/modeller6v2 setenv EXECUTABLE_TYPE6v2 mac10v2-absoft setenv LIBS_LIB6v2 $MODINSTALL6v2/modlib/libs.lib setenv KEY_MODELLER6v2 MODELIRANJE alias mod mod6v2 set path=($path $MODINSTALL6v2/bin) limit stacksize unlimited ### end MODELLER6v2 ######################################################## # this line was added by Ifeffit Installation Script source /Applications/Ifeffit/bin/iff_init.csh ~ so I think I do have the instruction for aquaterm. It is not a very nasty bug. I just have to remember to start aquaterm first... and the only bugging idea is that it worked once... Ciao, Stefano > In my case, aquaterm opens automatically. I did set in my .cshrc >(shell script initialization file), the variable >PGPLOT_DEV=/AQT >I do know that aquaterm started even automatically even when I was >building horae using the pgplot in fink as well. > > Paul -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 13 Jun '04

13 Jun '04

Hello Matt, after having installed 1.2.5a, the aquaterm is now opening ok: am currently trying artemis ZnO tutorials... Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 13 Jun '04

13 Jun '04

Hello again, after running horae_update, and having now horae-036, I still do not get aquaterm to open.... SHould I reinstall ifeffit1.2.5a??? Trying to do so... Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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