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

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 07 Jul '11

07 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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