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

Re : EXAFS analysis of a sample having two metal centres with different coordination geometry
by Abhijeet Gaur 22 Jul '11

22 Jul '11

<Abhijeet, <This seems like a system which might require more information before using EXAFS analysis. How did you come to the conclusion that there are <two metal centers? You begin by asking how to model two metal centers with different coordination and then in question 3, you lead the list to <believe that there might not be two metal centers? I assume you have found structural data for the sample? You have different geometry as <well as different ligands (atoms). Do the metal centers only contain the absorbing metal or is it mixed? If you had a bit more information <about the material through other methods, I am sure several people could suggest helpful ideas for your analysis. <Chris -- Christopher J. Patridge PhD. 405 NSC - Dept of Chemistry University at Buffalo State University of New York Buffalo, NY 14260 Office:(716)645-4137 Contact:(315)529-0501 <E-mail: patridge at buffalo.edu<http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> Dear Chris, I am sorry for making my problem a bit difficult to understand. Let me clarify the problem: 1. Yes, I have the crystal strcuture of the sample with me, from which I know that there are two metal centers. With this crystal strcuture data, I have generated the theoretical model for the two metal sites. 2. Yes, the metal centers only contain the absorbing metal, i.e., copper but with with different coordination. And my question is whether by using EXAFS analysis of experimetal data, the contribution of two metal center present in sample can be confirmed? Also, is it possible to calculate that how much one metal center contribute to the experimetal data? If, one of the theoretical model does not fit to the experimetal EXAFS data, what does it signify about the corresponding metal center? I hope this will make my problem clear to the members of the mailing list. With thanks Abhijeet Gaur

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EXAFS analysis of a sample having two metal centres with different coordination geometry
by Abhijeet Gaur 21 Jul '11

21 Jul '11

Hi all, I am doing EXAFS analysis of a sample having two metal centres with different coordination geometry. In my sample two (Cu) metal centres are present and these metal centres are surrounded by different ligands (atoms) in different coordination geometry. As I understand the EXAFS data of such sample will have contributions from both the metal centres. So, in order to analyse the EXAFS data, I have generated theoretical model (using Artemis) for both the metal centres. Then, I have fitted these theoretical models to the experimetal data. But, I have some questions regarding this type of analysis as I am not sure whether I going in right direction or not: 1. I have to fit these theoretical models one by one or simultaneously to the experimetal data. 2. How can I confirm that whether the EXAFS data of the sample has contributions from both the metal centres. 3. If one of the model does not fit well to the exp data, does this mean that the corresponding metal centre is not present or the metal centre is present but not contributing. 4. Is it possible to calculate the percentage of contributions from different metal centres to the experimetal data. If someone can suggest some available literature on this problem, it will be really helpful to me. With thanks Abhijeet Gaur Research Scholar School of Studies in Physics Vikram University, Ujjain, India

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Re: [Ifeffit] Scripting - Python
by Andrew Korinda 21 Jul '11

21 Jul '11

Thanks for the help. Sorry it took so long to report back but I can only do must of my work on this on weekends. The corrected code worked great and I'm moving forward again. No message was given when the code wasn't working. Andy Korinda On Nov 1, 2010 1:55 PM, "Matt Newville" <newville(a)cars.uchicago.edu> wrote: Hi Andrew, On Mon, Nov 1, 2010 at 12:01 PM, Andrew Korinda <a-korinda(a)northwestern.edu> wrote: > I'm looking t... This is almost certainly due to space in the filename, and is really more of a problem with the fortran than python (or perl for that matter). That is, with a space in the file name, you should explicitly use read_data(file=...., group=...) This should work better:: import Ifeffit iff = Ifeffit.Ifeffit() ret = iff.ifeffit("read_data(file=C:\Program Files\Ifeffit\examples\Ifeffit\data\cu.xmu, group=c)") If it doesn't, let use know. > >From this experience I have some questions: > > ~First does anyone have some debugging tips for ... There should have been a printed message that might have altered you that the file hadn't been read in correctly: *** read_data: no file name given! was that message not given? > ~Secondly, Does anyone have any example Python scripts for Ifeffit > that they would like to shar... I sort of deliberately have left the base Ifeffit python module bare-bones. It would certainly be possible to add more functionality to that, or distribute add-on packages. It sort of depends what people would find desirable. I have many example scripts using Ifeffit + Python, mostly scripts, not documented, reliable code. Of course, there is also sixpack. I had some older GUIs as well. Would it be helpful to add some small examples on a wiki page? > ~Finally, would I be better off coding in Perl and using Demeter? That's a difficult question. The relative merits of Perl v Python are sort of a topic all on their own. For what it's worth, I believe (far) more people have used Python than Perl, but several very notable Ifeffit programs are written in Perl ;). --Matt PS: The next version of Ifeffit will be in python. Progress is slow, and when it will start to look like an EXAFS analysis program is a fair question. It probably shouldn't sway your decision much. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.g...

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Bond length to ATOM conversion
by Nicholas.Tse＠csiro.au 15 Jul '11

15 Jul '11

G'day Listed Members, Does anyone know how to convert bond length and bond angles into Cartesian coordinates to input into ATOM in Artemis. The space group is number 176 a P63/m (ie hexagonal dipyramidal) with a a=b=6.3 A, c=3.6 A. Apical Equatorial M-O2 M-O1 O1-O2 O1-O2 O2-O2 O1-M-O2 O1-M-O2 O2-M-O2 Gd(OH)3 2.462(3) 2.465(4) 2.910(6) 2.761(7) 2.879(8) 72.4(1) 68.18(6) 71.6(1) * G. W. Beall and W. O. Milligan, J. Inorg. Nucl. Chem., 1977, vol 39, 65-70 I am currently trying to set up a FEFF file for Gd(OH)3 Sincerely yours, Nicholas

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Re: [Ifeffit] Scripting - Python
by Matt Newville 14 Jul '11

14 Jul '11

Hi Andrew, Hmm, not sure what's going on. It worked for me on one system, but I'll try this on another machine later today. I think the key is to have the folder with ifeffit_12.dll in your PATH. You say you had to edit the use_ifeffit.bat file -- did this have the incorrect paths? A reasonable workaround (and perhaps the distribution should do this) is to copy the dll to C:\Python27\DLL. The trouble with that is that many of the PGPLOT environmental variables might not be set correctly.... but that just means plotting won't work, which might be acceptaable. -Matt On Jul 14, 2011 9:59 AM, "Andrew Korinda" <a-korinda(a)northwestern.edu> wrote:

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Re: [Ifeffit] Opening SSRL data in Athena
by Scott Calvin 08 Jul '11

08 Jul '11

Actually, Athena can open binary SSRL files--I just successfully opened one of Lia's files in Athena. Here's what I did: Under Settings, choose Plugin registry. Check the SSRLB box. From there, it opened fine. Does trying that work for you, Lia? I am using Athena 0.8.061 on a Mac running OS 10.5.8. --Scott Calvin Sarah Lawrence College On Jul 7, 2011, at 6:20 PM, Wayne W Lukens Jr wrote: > Hi Lia, > > Those are binary files from SSRL, which athena cannot open. There > are a few ways that you can deal these files. > > Easiest is to use Six-Pack to work up the data. I believe it will > open SSRL binary files. Six-Pack is a GUI-driven suite of programs > analogous to Athena and Artemis. > > Slightly less easy is to convert your binary data to ascii data, > which can be done on the SSRL computer that you used to collect the > data. At this point, you will have to ask the beamline scientist to > do this for you. You can definitely open the ascii files in Six-Pack. > > Somewhat more difficult is to use EXAFSPAK to work up the data. > These are a suite of programs for EXAFS data analysis that are not > particularly easy to learn. They will open the binary files. > EXAFSPAK is easy to use once you have learned the commands. > > Six-Pack: > > http://home.comcast.net/~sam_webb/sixpack.html > > EXAFSPAK: > > http://ssrl.slac.stanford.edu/exafspak.html > > Sincerely, > > Wayne

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Re: [Ifeffit] Opening SSRL data in Athena (Abhijeet Gaur)
by Abhijeet Gaur 08 Jul '11

08 Jul '11

> Hi Julia, I have also encountered the same problem while analysing the data from SSRL. I can suggest you what I tried and got my data read by Athena. Go to the Setting pannel of the Athena window and then click on Plugin Registry. You will see all types of data format there, then you can check your data format there. Then, you can import your data. Abhijeet Gaur Research Scholar School of Studies in Physics Vikram University Ujjain, India Hello Everyone, I have a question about using Athena to analyze data taken at SSRL beam line 11-2. I can't seem to open the files, a message pops up saying it 'could not be read by ifeffit as a data file'. I have looked around these message threads and in the athena users guide but there doesn't seem to be any information on it. The users guide goes through choosing different data columns and if there is a header or not, but I can't open the data as some sort of text file to see how it is organized. I'm sure its just importing it differently or checking a box or something silly like that, but I would appreciate any guidance. Thank you very much, Lia >

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Re: [Ifeffit] Ifeffit Digest, Vol 101, Issue 7
by Eric Breynaert 08 Jul '11

08 Jul '11

Hey julia, Check the namespace of your SSRL plugins. They should be located at C:\Program Files\Ifeffit\share\perl\Ifeffit\Plugins\Filetype\Athena and they are called SSRLA.pm and SSRLB.pm. You can open the files with notepad. Check if the 1st line (package name, e.g. package Ifeffit::Plugins::Filetype::Athena::SSRLA;) reflects the plugin filename. So the last word has to be SSRLA and SSRLB for respectively SSRLA.pm and SSRLB.pm. If this is not the case , change accordingly. Hope this solves your problem. Eric On 8/07/2011 2:16, 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. Opening SSRL data in Athena (Julia M Klofas) > 2. Re: Opening SSRL data in Athena (segre(a)iit.edu) > 3. Re: Opening SSRL data in Athena (Julia M Klofas) > > Hey julia, > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 Jul 2011 16:54:38 -0700 > From: Julia M Klofas<jklofas(a)usgs.gov> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Opening SSRL data in Athena > Message-ID: > <OF693BEABF.DCFC939B-ON882578C6.0083584B-882578C6.00835860(a)usgs.gov> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL:<http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20110707/bc6…> > > ------------------------------ > > Message: 2 > Date: Thu, 07 Jul 2011 19:00:25 -0500 > From: "segre(a)iit.edu"<segre(a)agni.phys.iit.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov>, > ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Opening SSRL data in Athena > Message-ID:<fb8b7016-48d6-4d53-a330-7ed2fa9f6544(a)email.android.com> > Content-Type: text/plain; charset="utf-8" > > Hi Julia > > Could you attach the file? I think I know what it is but it would help. > > Carlo > -- Eric Breynaert Centrum voor Oppervlaktechemie en Katalyse Departement Microbiële en moleculaire systemen (M²S) Kasteelpark Arenberg 23 - bus 2461 B-3001 Leuven Tel: +3216321598 Fax: +3216321998

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Opening SSRL data in Athena
by Julia M Klofas 08 Jul '11

08 Jul '11

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request for In metal spectrum
by Brandon Reese 06 Jul '11

06 Jul '11

Hello list members, Does anyone have a scan of In metal taken at room temperature? I need the absorption edge and the EXAFS region, preferably up to 10 1/A or so. There are some potential issues with the spectra I have collected, and I would an independent measurement to compare with mine. Thanks Brandon Reese

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FEFF input files
by Bernt Johannessen 04 Jul '11

04 Jul '11

Dear All, I am looking at using Artemis ("Theory"; "New Atoms page") to create FEFF input files for Gd and Gd2O3. I believe I have got the Gd parameters right: Space group 194 a=b=3.636,c=5.7826 alpha=beta=90,gamma=120 Gd: X=Y=Z=0 And it does give me reasonable paths in the end to work with (see below FEFF.inp file) The Gd2O3 is trickier (space group 206, a=b=c=10.8(?), alpha=beta=gamma=0): How do I determine the X,Y,Z coordinates for the relevant atoms? Regards, Bernt Gd FEFF input file: * This feff6 input file was generated by Artemis 0.8.012 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu*x=1: 3.36 microns, unit edge step: 5.46 microns * specific gravity = 7.888 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00062 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * ----------------------------------------------------------------- * The following crystallographic data were used: * * title ... * space = P 63/m m c * a = 3.6360 b = 3.6360 c = 5.78260 * alpha = 90.0 beta = 90.0 gamma = 120.0 * core = Gd1 edge = L3 * atoms * ! elem x y z tag occ * Gd 0.00000 0.00000 0.00000 Gd1 1.00000 * ----------------------------------------------------------------- TITLE ... HOLE 4 1.0 * Gd L3 edge (7243.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 6.0 *CRITERIA curved plane *DEBYE temp debye-temp NLEG 4 POTENTIALS * ipot Z element 0 64 Gd 1 64 Gd ATOMS * this list contains 23 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Gd1 0.00000 0.00000 0.00000 2.89130 1 Gd1_1 2.89130 0.00000 0.00000 -2.89130 1 Gd1_1 2.89130 3.14887 1.81800 0.00000 1 Gd1_2 3.63600 -3.14887 1.81800 0.00000 1 Gd1_2 3.63600 0.00000 3.63600 0.00000 1 Gd1_2 3.63600 3.14887 -1.81800 0.00000 1 Gd1_2 3.63600 -3.14887 -1.81800 0.00000 1 Gd1_2 3.63600 0.00000 -3.63600 0.00000 1 Gd1_2 3.63600 3.14887 1.81800 2.89130 1 Gd1_3 4.64544 -3.14887 1.81800 2.89130 1 Gd1_3 4.64544 0.00000 3.63600 2.89130 1 Gd1_3 4.64544 3.14887 -1.81800 2.89130 1 Gd1_3 4.64544 -3.14887 -1.81800 2.89130 1 Gd1_3 4.64544 0.00000 -3.63600 2.89130 1 Gd1_3 4.64544 3.14887 1.81800 -2.89130 1 Gd1_3 4.64544 -3.14887 1.81800 -2.89130 1 Gd1_3 4.64544 0.00000 3.63600 -2.89130 1 Gd1_3 4.64544 3.14887 -1.81800 -2.89130 1 Gd1_3 4.64544 -3.14887 -1.81800 -2.89130 1 Gd1_3 4.64544 0.00000 -3.63600 -2.89130 1 Gd1_3 4.64544 0.00000 0.00000 5.78260 1 Gd1_4 5.78260 0.00000 0.00000 -5.78260 1 Gd1_4 5.78260 END [cid:image001.gif@01CC3A6C.C42DB2F0] Bernt Johannessen | Scientist - XAS | Australian Synchrotron p: (03) 8540 4240 | f: (03) 8540 4200 bernt.johannessen(a)synchrotron.org.au<mailto:bernt.johannessen@synchrotron.org.au> | www.synchrotron.org.au 800 Blackburn Road, Clayton, Victoria 3168 <br>This message and any attachments may contain proprietary or confidential information. If you are not the intended recipient or you received the message in error, you must not use, copy or distribute the message. Please notify the sender immediately and destroy the original message. Thank you.

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Problem with Arthemis
by Amayri, Dr. Samer 04 Jul '11

04 Jul '11

Dear colleagues, after I selected in Arthemis "write special output feff8", I had a problem to run this feff8 file (feff.inp) (see please the attached file). I get the following error: Feff 6L.02 Unknown keyword: "EDGE" at line: EDGE L3 See FEFF document for valid keywords. Fatal Error: at RDINP. Could you please help me? Thanks in advance. Samer Amayri __________________________________________________________________ Dr. Samer Amayri Institut für Kernchemie der Universität Mainz Fritz-Strassmann Weg 2 D-55128 Mainz Telefon: +496131 39-25317/25307 (Lab.) Fax-Nr. +496131 39-24510 E-mail: amayri(a)uni-mainz.de<mailto:amayri@uni-mainz.de>

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Fitting bond lengths without a known FEFF file
by Hana 01 Jul '11

01 Jul '11

Dear list experts, Here is another challenging question for me; can someone help? I have soil samples, trying to fit the first shell, I have 3 different optional bond lengths, which might give a lot of information. Now I have two questions: 1. If I do not know of specific structure (XRD implies a very amorphous material), so no specific FEFF file that I can use. what would be my way to determine the parameters for IFEFFIT (Deg, Reff, amp,...)? 2. Is there any option to fit the 3 bond lengths together (no dependency that I can think of...)? Should I fit all pairs, then accordingly assume one component; 'set' it and fit the other two as fractions of 1 (N+(1-N)? Thanks!!

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Re: [Ifeffit] E0 issues
by Scott Calvin 28 Jun '11

28 Jun '11

Hi again, > > Thanks Scott, > I think it is a mistake done by many beginners. To be confident that > I understood you well: so basically the reproducibility of E0 > between samples while fitting to FEFF files mainly depends on the > quality of my calibration. For reproducibility, yes. > Actually, if there is no clear feature in my edges and they are > different in ‘slopes’, I must have either a calibration foil, or a > known standard, measured at the same time; otherwise there is no > good way to get comparable data? Some beamlines are more stable in energy than others. Sometimes it suffices to measure a standard occasionally between measuring data. If the calibration does not drift, or drifts in a predictable way, then you're OK. But if the calibration jumps around by an eV or two, as is not uncommon, then your data inherits that uncertainty unless you measure a reference material at the same time. > Is that right, or the fitting, considering all spectra’s components > will finally lead to a good fit, even with relatively poor > calibration (I will definitely be more careful in the future; but > asking for a set of samples that were mistakenly measured for me > without a standard). This is a different question. If you are fitting to FEFF, then it doesn't matter if the E0's were defined consistently for each sample, or if the calibration drifted. You will most likely float E0 as a free parameter anyway, so the fitting process will adjust for the differences. You do lose the ability to compare the E0's of your different samples, and you lose the ability to constrain them to be the same, but the rest of the fitting process is fine. --Scott Calvin Sarah Lawrence College P.S. Also note that if ifeffit returns an E0 shift of more than about 10 eV, that's a warning sign. Check if that would correspond to an E0 still on or near the rising portion of the edge (a bit past the white line is still OK). If it's not, then the fit is not a good one. If it is, then it's best to choose a new E0 in Athena (or SixPack) that is closer to to where ifeffit wants it; FEFF loses accuracy when the E0 has to be shifted by that much.

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Re: [Ifeffit] E0 issues
by Scott Calvin 27 Jun '11

27 Jun '11

Hi Hana, On Jun 27, 2011, at 2:04 PM, Hana wrote: > I guess my question is obvious to most of you, but after some > practice and reading, the following is still unclear to me > (hopefully some other beginners will benefit): Normally I have > calibrated my spectra using a calibration foil – so energy shift > was done according to that companion standard. Doing a simple > linear combination fit, I have set all spectra to the same E0 value, > somewhere on the edge, above the first derivative maxima (was it a > good practice?). That is a good practice, in my opinion. If you're going to do a linear combination fit, it doesn't really matter how you choose E0, as long as: 1) The spectra are all aligned on the same energy scale 2) The choice of E0 is in some way consistent By using a calibration foil, you have assured #1, and then by simply making E0 the same for all spectra, you have assured #2. > Recently, I found myself actually confused about E0; since my > samples inherently have a phase difference (which is the base to my > ability to differentiate them), how a certain reference point on the > spectrum can be determined? "Reference point" is indeed the correct term. As such, it is somewhat arbitrary, and just needs to be consistent for all spectra being compared. > What can be done when I do not have the calibration foil (especially > for these heavy elements that do not have specific sharp feature)? Consistency is the only requirement. There are many ways to align consistently. If you've got really noisy reference data for some reason, you could even fit some kind of function to the edge and use that, but for reference data that's not usually necessary. > And further, now that I am starting to work on the structural model; > how actually IFEFFIT determined the energy shift when there is no > specific reference point? If you float E0 when fitting to feff files, the reported value is a shift relative to wherever you initially picked it. Thus if you change the initial choice of E0 by 2 eV upward, the shift ifeffit reports should be 2 eV less. Hope that helps... --Scott Calvin Sarah Lawrence College

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E0 issues
by Hana 27 Jun '11

27 Jun '11

I guess my question is obvious to most of you, but after some practice and reading, the following is still unclear to me (hopefully some other beginners will benefit): Normally I have calibrated my spectra using a calibration foil – so energy shift was done according to that companion standard. Doing a simple linear combination fit, I have set all spectra to the same E0 value, somewhere on the edge, above the first derivative maxima (was it a good practice?). Recently, I found myself actually confused about E0; since my samples inherently have a phase difference (which is the base to my ability to differentiate them), how a certain reference point on the spectrum can be determined? What can be done when I do not have the calibration foil (especially for these heavy elements that do not have specific sharp feature)? And further, now that I am starting to work on the structural model; how actually IFEFFIT determined the energy shift when there is no specific reference point? I would be happy to get a better insight.

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Fwd: Icosahedral cluster coordinates
by Scott Calvin 27 Jun '11

27 Jun '11

Hi Zohair, I'm posting this back to the list, because I couldn't solve the problem. I did experiment with your file for a bit; it works fine for the atoms up to 4 angstroms, but ones much past that make feff fail. Maybe someone else can suggest why feff is choking on what appears on inspection to be a valid file. (Note to others on the list: the attached feff.inp file is the one that doesn't work; the pasted one is my original, and does work.) As for atoms being able to work with icosahedral structures, that will probably never be possible. Atoms is designed to work with crystal structures, and icosahedral clusters are not crystals; i.e. they don't have translational symmetry. A separate helper application would have to be written for this kind of cluster. --Scott Calvin Sarah Lawrence College Begin forwarded message: > From: <Zohair.Hussain(a)csiro.au> > Date: June 27, 2011 1:12:06 AM PDT > To: <dr.scott.calvin(a)gmail.com> > Subject: Re: [Ifeffit] Icosahedral cluster coordinates > > Dear Scott, > > I came across an e-mail exchange from 2005 between you and Patrick > Kluth regarding icosahedral clusters and feff files as below. > > I’m trying to fit data collected at the Cu k-edge for Mg65Cu25Gd10 > bulk metallic glass(BMG). It has been reported that BMGs have an > icosahedral structure. A recent paper (attached) gives a > demonstration of that. What I’ve tried to do is to modify the feff > file you made for Patrick to my MgCuGd structure. I attach the > feff.inp file I made for that. > > The problem I’m running into is that when I try and run this > modified feff file through artemis I get an error message (file > attached). I should point out that when I run your feff file for Fe > it runs without any errors. > > I’m wondering if you can either tell me what I’m doing wrong or > guide me to make a feff file from an atoms input file for the MgCuGd > material. > > In the long run, it would be good to know how to make Feff files for > icosahedral structures starting from an atoms input file (I usually > use webatoms for this) as I would be working with various BMG > materials (Al, Ti and Mg based) that should potentially have this > structure. > > I’d be grateful for your help. > > Kind Regards, > > > > Zohair Hussain > Postdoctoral Fellow > > CPSE - CSIRO > Private Bag 33 > Clayton South MDC > Clayton VIC 3169 > Australia > e-mail: zohair.hussain(a)csiro.au > Phone +61 3 9545 7891 > Fax +61 3 9544 1128 > > > > > > [Ifeffit] Icosahedral cluster coordinates > > Scott Calvin SCalvin at slc.edu > Tue Jul 19 19:06:17 CDT 2005 > Previous message: [Ifeffit] Icosahedral cluster coordinates > Next message: [Ifeffit] Icosahedral cluster coordinates > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > Hi Patrick, > > Hopefully this will do it. A disclaimer: I never actually tested this > on an icosahedral material, and I did the coordinates by hand, so I > can't guarantee it. > > --Scott Calvin > Sarah Lawrence College > > > > > > >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). >

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system iXAFS3.0.3.dmg, cant open arthena project
by diya lee 27 Jun '11

27 Jun '11

Hi, I have a Macbook pro, and I have the iXAFS3.0.3.dmg system installed. But the artemis program could not open arthena project. when i choose open file and select the file ( arthena project), there system either does not respond or only show the first data in the entire project. How could I fix this?Thanks

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Align spectra in Athena
by Dave 24 Jun '11

24 Jun '11

Hi list, Doing my first steps in your world, I am trying to model my data. I am following Kelly's helpful review from 2008 and stuck on apparently simple issue: In order to reduce my deltaE0 (now 9.2), following her advise, I am trying to recall the theoretical spectrum from Artemis to Athena; this was produced by filtering and fitting my data according to the first shell, then fixing all parameters to their best fit, except for enot set to zero, making a sum of all paths under these conditions, saving it as a chi(k) and take it to Athena. Here, to my understanding, I suppose to introduce the 'new-made' chi(k) as a standard and align my data accordingly, save it as a chi(k) and take it back to Artemis to complete the fitting. Unfortunately I cannot make it a standard in Athena, since the whole background options are not available when a chi file is called in. Can someone give a hint? Suggest other ways to better choose E0? Best, Dave

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an error message " You have not used any memory yet"
by Mike Zhu 23 Jun '11

23 Jun '11

Hi All, I had been using Athena for couple of months and had not problem. But recently, I cannot load any new data although I am still able to open project files (*.prj) previously created. Then this error message shows up at the bottom of the Athena window. I tried to reinstall Ifeffit and to install different version of Ifeffit but all failed. I saw a message posted couple of years ago on a similar problem in this email list but it seemed no answer for it. My operating system is Window XP Professional 2000 Service Pack 3. Anyone have a clue how to fix it? Thanks. Best, Mengqiang Zhu

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Averaging of spectra for multiple configurations in Artemis
by Srinivas Tulishetti 22 Jun '11

22 Jun '11

Dear All, I am working on MD - EXAFS for ionic solvation system. I was doing MD-EXAFS for multiple configurations. Each configuration gives different spectrum. So would like get average of all spectra for those multiple configurations. Is it possible to do this in Artemis or iFEFFIT. If it is then, please give your valuable suggestions. Thanking you all. Best, Srinivas Tulishetti

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lfms1
by Francisco Garcia 21 Jun '11

21 Jun '11

Dear users, I have a question about the value lfms1 is the SCF card. What difference does it make if lfms1=0 (solid) versus lfms1=1 (molecule) for hydrated metal ion clusters? My understanding from the manual is that if the metal is the absorber and I am working with cluster, then lfms1=1. However, if the cluster is sufficiently large (radius=6 Ang--8 Ang), then should it be treated as a solid or molecule? Also, how crucial are the hydrogen atoms in the scattering process? Can the EXAFS spectra be computed with only the metal ion and oxygen positions or the hydrogen positions must be included as well? Thank you.

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Fwd: problem with horae installation on ubuntu 11.04
by Bruce Ravel 21 Jun '11

21 Jun '11

Samuel, As you can see, I am forwarding this to the mailing list. It seems to me that you do not have pgplot installed. On ubuntu this package is called "pgplot5". Have you installed it? I would have thought that the pgplot package would have been a dependency of the ifeffit package. Carlo: can you shed any light on Samuel's problem? Rgeards, B ---------- Forwarded Message ---------- Subject: problem with horae installation on ubuntu 11.04 Date: Tuesday, June 21, 2011, 08:19:46 am From: Bickel Sämi <bickels(a)student.ethz.ch> To: "bravel(a)anl.gov" <bravel(a)anl.gov> hi this is probably a stupid question but i'm quite stuck here. i need the athena software but it doesen't load. it termines with the error: > bickels@bickels-laptop:/$ athena > /usr/bin/perl: symbol lookup error: /usr/local/lib/perl/5.10.1/auto/Ifeffit/Ifeffit.so: undefined symbol: pgqndt_ > i tried compiling the ifeffit-perl but it did not work. also i don't know if i got another version of perl.. but i installed ifeffit trough synaptic. im a newbie and this is probably no big issue.. thanks and have a nice day samuel bickel ----------------------------------------- -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] SS and MS contributions to EXAFS
by Scott Calvin 18 Jun '11

18 Jun '11

Hi Francisco, Following up on Matt's comment, a FEFF calculation with default option assigns sigma2 to be 0, and that probably won't result in relative contributions between SS and MS that look much like what happens in the real material. A better strategy would be to read the calculation into Artemis, as Matt suggests, and use a Debye model for the sigma2 for the paths, trying a few different Debye temperatures to get a sense of how it affects the relative contributions. While the Debye model is not an appropriate model for quantitatively fitting most materials, at least it takes a stab at how sigma2 might depend on R, which will help with understanding how important the MS paths are to chi(k). --Scott Calvin Sarah Lawrence College On Jun 17, 2011, at 7:21 PM, Matt Newville wrote: > Hi Francisco, > > On Fri, Jun 17, 2011 at 7:34 PM, Francisco Garcia > <garcia.ff.000(a)gmail.com> wrote: >> Dear users, >> >> I would like to quantify the single scattering (SS) and multiple >> scattering (MS) contributions to the EXAFS spectra over a range of k >> values. I adopted the following approach and I would like ask >> experienced users if my approach is sound: >> >> (1) Run a regular EXAFS (default NLEG=8); I assume this includes all >> possible scattering paths. Call the chi(k) data chi.dat >> (2) Run another EXAFS but this time I set NLEG=2. I assume this is >> for >> all SS contributions. Call the chi(k) data chi_ss.dat >> (3) To obtain the MS contribution, I subtracted chi_ss.dat from >> chi.dat >> >> If my approach is faulty, can you tell me how to remedy it? >> >> Thank you. > > That approach would work under the assumption that the atomic > coordinates in the feff.inp file fully described the distribution of > atoms in the system. If, on the other hand, the feff.inp had an > idealized structure, then the approach would model the MS > contributions for that structure. For example, a feff.inp file often > assumes no static or thermal disorder in the system. In that case, > the MS contributions would have no disorder terms (eg, sigma^2) > applied to them. > > An equivalent approach that may be somewhat simpler would be to use > Artemis to run the Feff calculation with NLEG=8 (4 is probably good > enough below 6Ang in most structures), read in all the paths, and sum > the paths with NLEG>2. > > --Matt

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SS and MS contributions to EXAFS
by Francisco Garcia 18 Jun '11

18 Jun '11

Dear users, I would like to quantify the single scattering (SS) and multiple scattering (MS) contributions to the EXAFS spectra over a range of k values. I adopted the following approach and I would like ask experienced users if my approach is sound: (1) Run a regular EXAFS (default NLEG=8); I assume this includes all possible scattering paths. Call the chi(k) data chi.dat (2) Run another EXAFS but this time I set NLEG=2. I assume this is for all SS contributions. Call the chi(k) data chi_ss.dat (3) To obtain the MS contribution, I subtracted chi_ss.dat from chi.dat If my approach is faulty, can you tell me how to remedy it? Thank you.

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