February 2012 - Ifeffit - millenia.cars.aps.anl.gov

Demeter Atoms & Vesta
by Andrew Korinda 22 Mar '12

22 Mar '12

Morning all, I finally decided to try using Demeter and this morning went to use Athena. Opening my data was all fine but importing the cif file into atoms got me in trouble. Upon selecting the file I got a pop-up saying "Choose a record from this CIF file" however there is nothing listed. If I click OK, the program crashes. This is also reproducible if I run stand-alone ATOMS. I have generated the CIF files from VESTA where I modify the crystal structure manually. This hasn't caused an issue in the past but with Demeter, perhaps there is a header I need to add? Attached is the CIF file I'm trying to use along with the error logs. Also I am using Windows 7 and the previous IFEFFIT is still installed. Thanks for the help and continued development, Andy Korinda Notestein Lab Chemical & Biological Engineering Northwestern University

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Single shell
by Anatoly I Frenkel 25 Feb '12

25 Feb '12

Dear subscribers: For your amusement, attached is a quintessential single-shell EXAFS spectrum. Second in simplicity, perhaps, after only mu_not. It is taken from a bulk metal oxide. The k-range in FT: from 2 to 15 A^-1. Can be used for teaching EXAFS basics. If anyone is interested I will send raw data. Anatoly

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AuPd CIF
by Kaiser, Julian 23 Feb '12

23 Feb '12

Dear ifeffit-list members, I'm looking for an AuPd CIF (crystal information file). I couldn't find one at the Crystallography Oben Database (www.crystallography.net<http://www.crystallography.net/>) or at the mailing-list archive. I've seen measurements at AuPd-foil published, so I think there meight also exist an CIF. Would be nice, if someone could give me a hint. Thanks for your kind help, Julian ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Corrupt .apj file
by Heinzel, John M CIV NSWCCD Philadelphia, 985 22 Feb '12

22 Feb '12

Hello, I was working on a number of different structures (Atoms pages and then FEFF input files), when one got "stuck" for some reason. While I've saved my file all the way through, the one structure that is causing an issue always makes Artemis get stuck (computer is totally fine but Artemis is unresponsive and CPU use goes to 100%) now, IF I click on it. Leave it alone and Artemis is fine, and I can work on the other theory sets. Since I cannot click on the one atoms/FEFF data set that I want to get rid of (without Artemis getting stuck, that is), is there an alternate way to edit .apj files so that I can remove the problem atoms/FEFF listing so that the file can remain functional? FYI, I'm running Artemis in iEXAFS 3.0.3 on OSX 10.7, if that helps. Thanks, John Heinzel

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Re: [Ifeffit] Ifeffit Digest, Vol 108, Issue 17
by 陈娟 15 Feb '12

15 Feb '12

Dear Bruce Thanks a lot for your suggestion. Yes, I did according your suggestion. I did the self-absorption correction and got the perfect spectrum as shown below. However, for the pure standards without dilution by BN, How to do the self-absorption correction? For example, I try one, but cannot get the credible spectra. ForDibenzyl Disulfide, the formula should be (C14H14S2)0.5435(BN)0, no dilution. I put (C14H14S2)0.5435(BN)0 in, but the spectrum I got is So can you tell me how to do the pure standards self-absorption correction using Athena? Much appreciated. Warm regards Juan Chen At 2012-02-15 02:00:01,ifeffit-request@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: fitting sulphur using standards by Athena (Bruce Ravel) > 2. Re: fitting sulphur using standards by Athena (Matthew Marcus) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 14 Feb 2012 09:07:45 -0500 >From: Bruce Ravel <bravel(a)bnl.gov> >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] fitting sulphur using standards by Athena >Message-ID: <201202140907.45529.bravel(a)bnl.gov> >Content-Type: Text/Plain; charset="utf-8" > >On Tuesday, February 14, 2012 07:55:54 am ?? wrote: >> As I known, the spectra for standard diluted with BN and non-diluted are >> different. The peak of the non-diluted is low due to self-absorption, as >> shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur >> to about 3%. For dilution, the position of the peak is also changed. >> Therefore the non-diluted s1 spectra isnot the real spectra of >> dibenzothiophene. The question is what percentage should I dilute the >> standard to get the credible spectra for the standards?and how to explain >> the peak position change? > >Although this sort of thing can be approximated from tables of >absorption coefficients, the advice I usually give to my users is to >prepare a series of samples of diminishing concetrations and measure >then. > >Having a good intuition for sample preparation and the effects of poor >sample preparation is always important and even more so for low energy >edges. The best way to develop that intuition is by doing the >experiment yourself. > >> Can I use Athena to counteract the self-absorption and get the >> credible spectra for sdandards? > >Yes it can -- in principle. Doing a good job of self absorption >correction requires a lot of knowledge about your sample and its >matrix -- often more than one has. > >The use of the self absorption tool is explained in the Athena >document. I have also written a lecture on this topic. Go to > > https://github.com/bruceravel/XAS-Education/downloads > >and download the "selfabs.pdf" file. > >B > > >-- > > 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/ifeffit/Demeter > > > >------------------------------ > >Message: 2 >Date: Tue, 14 Feb 2012 07:33:38 -0800 >From: "Matthew Marcus" <mamarcus(a)lbl.gov> >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] fitting sulphur using standards by Athena >Message-ID: <03B21711433A40B4AA45C3DE3410452A(a)als.lbl.gov> >Content-Type: text/plain; format=flowed; charset="utf-8"; > reply-type=original > >To reiterate a point which is often not understood - dilution won't fix overabsorption if the particles of the concentrated material >which are mixed in with the diluent are too big. For concentrated S compounds, "too big" is in the low microns. >When I run a S standard, I do it in total electron yield to avoid this problem. When I fit a S spectrum, I use a crude >oveabsorption model with a single parameter which is treated as an unknown fitting parameter, with the assumption >that the reference spectra were collected in a way which avoids overabsorption. > mam >----- Original Message ----- >From: "Bruce Ravel" <bravel(a)bnl.gov> >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Sent: Tuesday, February 14, 2012 6:07 AM >Subject: Re: [Ifeffit] fitting sulphur using standards by Athena > > >> On Tuesday, February 14, 2012 07:55:54 am ?? wrote: >>> As I known, the spectra for standard diluted with BN and non-diluted are >>> different. The peak of the non-diluted is low due to self-absorption, as >>> shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur >>> to about 3%. For dilution, the position of the peak is also changed. >>> Therefore the non-diluted s1 spectra isnot the real spectra of >>> dibenzothiophene. The question is what percentage should I dilute the >>> standard to get the credible spectra for the standards?and how to explain >>> the peak position change? >> >> Although this sort of thing can be approximated from tables of >> absorption coefficients, the advice I usually give to my users is to >> prepare a series of samples of diminishing concetrations and measure >> then. >> >> Having a good intuition for sample preparation and the effects of poor >> sample preparation is always important and even more so for low energy >> edges. The best way to develop that intuition is by doing the >> experiment yourself. >> >>> Can I use Athena to counteract the self-absorption and get the >>> credible spectra for sdandards? >> >> Yes it can -- in principle. Doing a good job of self absorption >> correction requires a lot of knowledge about your sample and its >> matrix -- often more than one has. >> >> The use of the self absorption tool is explained in the Athena >> document. I have also written a lecture on this topic. Go to >> >> https://github.com/bruceravel/XAS-Education/downloads >> >> and download the "selfabs.pdf" file. >> >> B >> >> >> -- >> >> 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/ifeffit/Demeter >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 108, Issue 17 >****************************************

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fitting sulphur using standards by Athena
by 陈娟 14 Feb '12

14 Feb '12

Dear Sir, I face one quite confusing question. Hope to get your help about using Athena to do the fitting. What I am concerning is sulphur species in my char sample. However, I cannot get the good fitting results due to the standards i used. Please see the following figure. S1 in the figure means the dibenzothiophene standard, c26 is my char sample. I intend to fit the char sample by using the standards such as dibenzothiophene, dibenzyl disulfide, sulphate and so on, to get the sulphur species. However, because of the self-absorption, the pure standard spectra intensity is even lower than our char sample as shown in fig. 1. If I do like this, the fraction is higher than 1 in my sample, I cannot get the reasonable fitting data. So how to do the fitting? As I known, the spectra for standard diluted with BN and non-diluted are different. The peak of the non-diluted is low due to self-absorption, as shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur to about 3%. For dilution, the position of the peak is also changed. Therefore the non-diluted s1 spectra isnot the real spectra of dibenzothiophene. The question is what percentage should I dilute the standard to get the credible spectra for the standards?and how to explain the peak position change? Can I use Athena to counteract the self-absorption and get the credible spectra for sdandards? Waiting for your reply. Thank you very much. Best regards Juan Chen

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SCF convergence
by Christopher Patridge 13 Feb '12

13 Feb '12

Dear All, I recently starting using FEFF9 for XANES and I am trying to calculate LiCoO2 structure with deintercalation. The SCF iteration fails to converge at the 3rd iteration and I do not understand what setting I have used which is causing this hang up. I tried several different SCF radii in the attached feff input file and read in the manual that a cluster of about 30 atoms should be enough for a solid to reach convergence. Thank you in advance for any help, buena salud, Chris -- Christopher J. Patridge PhD. Contact: (315)-529-0501

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CLnorm Background - Possible Bug?
by Ashley Norris 10 Feb '12

10 Feb '12

Dear All, I was going to post this directly to Bruce, but the website asks for feedback to be directed to the list, so here it is. I'm a novice Athena user, but so far have found it to work very well for my needs. What I am writing about is that I have a problem with the CLnorm background routine: when there is a pre-edge peak present the edge is assigned to this peak position, instead of to the true edge position. I have attached a sample spectrum that shows exactly what I mean. Is there any way to work around this? Is it a limitation of the software or a bug? Is it even a problem? ...see, novice! :) It is particularly surprising to me because the marker (orange circle) shows the E0 position correctly, but the CLnorm routine is ignoring this...which is why I'm suspicious that it could be a bug. If CLnorm used this E0 position for its edge then everything would be well. I'm not jumping up and down in despair here as AutoBK will serve my immediate needs for now, but for what I want to do I am suspecting that CLnorm will be better*. Thanks again for a great program and all of the development work that has gone into it, Ash *open to suggestions as to why I am wrong about this. -- --- Ashley Norris Experimental Petrology Department of Earth Sciences Oxford University, UK --- ashley.norris(a)earth.ox.ac.uk --- +44 1865 272 051 ---

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Re Iffeffit LCF
by fred.mosselmans＠diamond.ac.uk 09 Feb '12

09 Feb '12

Dear Niken, I have had a look and i am afraid there are some problems, so what follows is not very positive. I am not sure your normalisation of the dilute samples is very good i ended up treating each spectrum slightly individually using a post-edge range of about 40-90 and adjusting the pre-edge range depending on the curviness of the pre-edge background. This is not ideal for linear combination fitting but i got spectra that looked like they had an edge step of 1. So That's fixable. But as you noticed the thiophene-10 and thiophene spectra are quite different. (you call it disulfide in your email but there are two thiophene and 1 disulfide spectra in the project. Ignoring self absorption which might give some relative peak intensity changes, i think this means they aren't the same thing Preparing your dilute samples some surface oxidation may have occurred in thiophene-10 there's a lump at 2481 or so that is bigger and displaced from the pure thiophene sample, this lump is quite reminiscent of some sulfate being present - this may be trace surface amounts, but the experiment will be sampling only about 10 microns worth of real sample so can be very important. This unfortunately is i think pretty unrecoverable. If the samples weren't well enough mixed and i mentioned earlier you are looking at only about 10 microns worth of powder in the post edge, then of course the sample you looked at is actually an unknown and not a standard, so a good fit in LCF might be the correct answer. Regards Fred BTW please use Dear Fred, dear professor fred just seems ridiculous to me. Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK T 00 44 1235 778568 M 00 44 7785510211 E fred.mosselmans(a)diamond.ac.uk F 00 44 1235 778448 Never mind the W it's the tax that counts -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Re Iffeffit LCF
by fred.mosselmans＠diamond.ac.uk 09 Feb '12

09 Feb '12

Dear Niken, To my untutored eye your normalisation and fitting look OK so thus it comes down to the data or whether the treatment is valid: Did you collect the data in fluorescence mode? Two possible problems occur to me. As thiophene is a liquid at RT unless you did the experiment cryogenically I think 2 is unlikely. 1) Most probably there is an inherent self-absorption problem with S XANES LCF which was written about by G. Almkvist, K. Boye and I. Persson J. Synchrotron Rad. (2010). 17, 683-688 [ doi:10.1107/S0909049510022946 ] K-edge XANES analysis of sulfur compounds: an investigation of the relative intensities using internal calibration. The self-absorption seen can affect the results of simple LCF data quite alot. 2) the samples were not well enough mixed, hence the data collected does not reflect the real mixture but a fraction that is more like the values you obtain by the LCF. S K-edge measurements don't sample much sample (sorry for that) so mixing solid standards is not necessarily trivial but for liquids/solutions this should not apply. Cheers Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK T 00 44 1235 778568 M 00 44 7785510211 E fred.mosselmans(a)diamond.ac.uk F 00 44 1235 778448 Never mind the W it's the tax that counts -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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