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

Artemis fitting k-weight
by George Sterbinsky 20 Sep '11

20 Sep '11

Hello, When fitting data in Artemis with the "other k weight" box checked and the kw = 1, 2, or 3 boxes unchecked, I find that the log file lists "k-weight = 1, kw", where kw is the value I entered into the "other k weight" text box. If I choose 0 as the other k weight, then the log file lists "k-weight = 1". Is it possible to run a fit in Artemis using only a k-weight of something other than 1, 2, or 3? Thank you, George

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Re: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon
by Anatoly I Frenkel 20 Sep '11

20 Sep '11

Ru oxidizes easily. Since you fixed CN in bulk Ru as total 12 in the fit to hcp Ru it probably gave you a small amplitude factor for the foil. Thus when you transferred that small amplitude factor to fit NP Ru it resulted in large CN. We use freshly made Ru powders as standards. What amplitude factor have you got from the foil? Anatoly Sent from my mobile phone, please forgive typos. -----Original message----- From: Anatoly I Frenkel <afrenke2(a)yu.edu> To: Dreher Marian <Marian.Dreher(a)psi.ch>, "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue, Sep 20, 2011 18:27:57 GMT+00:00 Subject: Re: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon You have to be careful using Ru foil. Sent from my mobile phone, please forgive typos. -----Original message----- From: Dreher Marian <Marian.Dreher(a)psi.ch> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue, Sep 20, 2011 18:00:15 GMT+00:00 Subject: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon Dear Ifeffit Community, I am currently trying to extract the particle size of Ru supported on carbon from EXAFS data. I also recorded spectra of a Ru foil as a bulk reference sample. So, my approach is to fit the first coordination shell of my bulk reference, setting CN to 12. From that I get a value for s02. I'm then using this value in the first shell fit for the Ru nanoparticles in order to get the coordination number. However, the fit suggests that CN is still pretty much 12. What is changing drastically, though, is sigma^2 which usually doubles in value compared to the bulk sample. That makes sense, I guess, since there might be higher disorder in the nanoparticles. Obviously, there is a chance that my nanoparticles are rather big, in which case CN would be close to 12. However, STEM and HRTEM pictures suggest that the Ru particles are between 1 and 2 nm in diameter. I'm just starting to get into EXAFS analysis and pretty clueless right now about how to approach this. Happy about any input, many thanks, Marian.

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Re: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon
by Anatoly I Frenkel 20 Sep '11

20 Sep '11

You have to be careful using Ru foil. Sent from my mobile phone, please forgive typos. -----Original message----- From: Dreher Marian <Marian.Dreher(a)psi.ch> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue, Sep 20, 2011 18:00:15 GMT+00:00 Subject: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon Dear Ifeffit Community, I am currently trying to extract the particle size of Ru supported on carbon from EXAFS data. I also recorded spectra of a Ru foil as a bulk reference sample. So, my approach is to fit the first coordination shell of my bulk reference, setting CN to 12. From that I get a value for s02. I'm then using this value in the first shell fit for the Ru nanoparticles in order to get the coordination number. However, the fit suggests that CN is still pretty much 12. What is changing drastically, though, is sigma^2 which usually doubles in value compared to the bulk sample. That makes sense, I guess, since there might be higher disorder in the nanoparticles. Obviously, there is a chance that my nanoparticles are rather big, in which case CN would be close to 12. However, STEM and HRTEM pictures suggest that the Ru particles are between 1 and 2 nm in diameter. I'm just starting to get into EXAFS analysis and pretty clueless right now about how to approach this. Happy about any input, many thanks, Marian.

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Re: [Ifeffit] Spline range?
by Matt Newville 19 Sep '11

19 Sep '11

Wei, On Sun, Sep 18, 2011 at 9:10 AM, Wei Li <weili(a)udel.edu> wrote: > Dear all, > > I am wondering about what range should be chosen in Athena? Some literature > says from 1 to the end; some says from 0.5 to the end. What literature says this? Do you mean to imply that someone is saying it should be 0.5 or 1.0, and *not* some other value? In principle, the background should start at k=0, and one should use k-weight=1, as Integral_E=E0^E=infinity chi(E) dE = 0 Integral_k=0^k=infinity chi(k) * k * dk = 0 In practice, that is nearly useless beyond the suggestion that the integral (which is to say, the DC component), *should* be zero. Using kmin between 0 and 1 and k-weight between 0 and 2 usually "work best", especially in the sense of "stable". In my experience, the value of E0 is much more important than kmin, and it is hard to predict whether k-weight = 1 or 2 works better. My advice is to not over-think or spend too much time worrying about background subtraction. --Matt

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Spline range?
by Wei Li 18 Sep '11

18 Sep '11

Dear all, I am wondering about what range should be chosen in Athena? Some literature says from 1 to the end; some says from 0.5 to the end. Wei -- Wei Li Postdoc researcher Environmental Soil Chemistry Group Delaware Environmental Institute University of Delaware, Newark,19713 Tel:631-949-0663 http://ag.udel.edu/soilchem/li.html <http://ag.udel.edu/soilchem/>

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Re: [Ifeffit] Negative Sigma^2
by pierre.lecante＠cemes.fr 14 Sep '11

14 Sep '11

one big issue is if your frequency terms are right when the amplitude ones are wrong, i.e. if you have computed and experimental chi functions reasonnably in phase while keep a not too high deltaE0 value; if so, as Scott said it sounds like a correlation between amplitude terms, which is fairly common; maybe an incorrect amplitude reduction factor, but more likely something wrong in the model: neighbours too light, or with a wrong multiplicity; if not, even worse and hard to say; my two cents, Pierre ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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. Negative Sigma^2 (Palomino, Robert) > 2. Re: Negative Sigma^2 (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 13 Sep 2011 13:32:46 -0400 > From: "Palomino, Robert" <rpalomino(a)bnl.gov> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Negative Sigma^2 > Message-ID: > <B32CD18BE9D42745B75847F981879A3602D1BF05(a)exchangemb3.bnl.gov> > Content-Type: text/plain; charset="us-ascii" > > I am trying to fit data I recently collected and occasionally I am > getting negative sigma squared values. Could anyone tell me what this is > indicative of: am I using the wrong model or are my initial guesses of > some parameters way off? > > > > Robert > >

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Negative Sigma^2
by Palomino, Robert 13 Sep '11

13 Sep '11

I am trying to fit data I recently collected and occasionally I am getting negative sigma squared values. Could anyone tell me what this is indicative of: am I using the wrong model or are my initial guesses of some parameters way off? Robert

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Re: [Ifeffit] Ifeffit Digest, Vol 103, Issue 9
by Mikutta Christian 11 Sep '11

11 Sep '11

Hi Marc, Forgot another illuminative paper: Van Schaik J.W.J. et al. (2008) EXAFS study on the reactions between iron and fulvic acid in acid aqeous solutions. Environ. Sci. Technol. 42, 2367-2373. Cheers, C. -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, September 08, 2011 7:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 103, Issue 9 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 on Athena (Niken Wijaya) 2. Re: Fitting on Athena (Bruce Ravel) 3. Re: Fitting on Athena (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Thu, 08 Sep 2011 09:52:38 +1000 From: Niken Wijaya <niken.wijaya(a)monash.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Fitting on Athena Message-ID: <4E6803C6.9070407(a)monash.edu> Content-Type: text/plain; charset="iso-8859-15"; Format="flowed" On 7/09/2011 7:24 AM, Bruce Ravel wrote: > On Sunday, September 04, 2011 08:52:30 pm Niken Wijaya wrote: >> 1. As you can see on the figure (i.e. filename: ifeffitlist-sample1 >> fitting), the intensity of the fitting spectra is higher than the >> actual sample. This is I believe due to the higher intensity of the >> individual standard compounds when compared to the spectra of my samples (i.e. >> filename: ifeffitlist-intensity). This is the case for every fitting >> I did for my sample so I am just not sure with the fitting results. > Well, there are a lot of problems contributing to your confusion. > > One thing that probably doesn't help, but which certainly isn't the > central problem, is that you have extremely large values for the > y-axis offset parameter of several of the standards. This makes it > difficult to plot normalized spectra in an unconfusing way. > > Your central problem is that, for most of the data groups, the values > of parameters for the pre-edge and normalization lines are not well > chosen. It would seem that you trusted the default values without > checking them. See > > > http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/norm.htm > l > > In your case, the default values resulted in unusably short ranges for > thepre-edge line or the post-edge line or both. The moral of this > story is to plot the data with its pre- and post-edge lines to verify > that the values result in sensible normalization. See > > > http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/plot/tabs.ht > ml > > You also had a problem that some of your data were somehow imported as > normalized mu(E) rather than as mu(E) or xanes(E). See > > > http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/colum > ns.html#datatypesandenergyunits > > This is usually not a good idea as it tells Athena that your data are > already reliably normalized and should not be further processed. > Those data, however, were not unit edge-step normalized, which is what > the LCF utility requires. The way to fix that in an existing Athena > project file is explained just a little further down on that same > page. > > Once I fixed the datatype for all of your groups and performed a > sensible normalization for your data, I got the LCF fit shown in the > attached image. Not great, but not the ridiculous result you were > getting with so many things done wrongly in your project file. > > I think that the underlying problem is that you expected Athena to > magically do the right thing with your data without verifying its > results. Or, perhaps, you plowed forward without fully understanding > how to use the program. The documentation isn't exactly exciting > reading, but it doesn't completely suck. You might want to bookmark > its URL. > > >> 2. If we see figure "ifeffitlist-sample39", we can see that the >> spectra has different slopes on the pre and post-edge region. When I >> used MBACK for background removal, the normalized spectra is weird, >> illustrated in "sample39-fig-norm.pdf". What is the best way to fix >> this issue? I have >> 5 samples with this feature that I cannot process due to the weird >> normalized spectra. > Well, MBACk isn't my thing, so I can only comment on it in general > terms. I suspect that you would get better results if you severely > truncated your data, say from about 2455 to 2515. Something wonky > happens in that spectrum at the beginning and the end. I suspect that > MBACK is having trouble figuring out what part of the data is actually > the edge step. > >> 3. Regarding the self-absorption correction, I was not aware that >> Athena has this function. I will have a look at the manual again. >> Thank you for letting me know. > > http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/process/sa.h > tml > > Again, not exciting ... doesn't suck ... bookmark. > > Here's a talk I gave at the University of Ghent last January on the > topic of self-absortion corrections. It may be of some help to you: > > http://cars9.uchicago.edu/~ravel/misc/selfabs.pdf > >> 4. With the 3rd derivative spectrum, I did indeed derive it from the >> normalized values. As you can see from the file I attached earlier, >> from the experts points of view, do you think I should go on with the >> Nth derivative spectra or due to the very low signal-to-noise ratio >> of the spectra, I should just focus on the absorption spectra? > I don't really have an opinion one way or the other about the 3rd > derivative. The folks from Stanford and CLS who do a lot of sulfur > work have made extensive use of the 3rd derivative and they are really > smart people. I haven't done a lot of S work in my own career and > none of Athena's users have ever asked for a 3rd derivative option, so > Athena doesn't currently do that. > > B > > PS: Doesn't it just blow your mind how there is a strong correlation > between quality and clarity of the question and specificity of the > answer? Amazing...! > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Hi Bruce, I think I have to clarify that I used MBACK to do the normalization instead of ATHENA. This might as well explain why I got such a high value of y-axis offset, why you think I did not choose the right parameters for the "pre-edge" and "normalization range" and also why I imported the data as normalized mu(E) rather than mu(E). As mentioned in the manual, doing normalization in Athena is very subjective, tiny difference in the point chosen for both the "pre-edge region" and "normalization range" will result in different normalized spectra. Due to lack of experience in processing XAFS spectra and noisy spectra obtained, I was planning to eliminate this problem by using MBACK. My initial plan was to combine the benefit I can get from both ATHENA and MBACK. So, I did the normalization using MBACK, then do the self-absorption correction and fit the normalized spectra in ATHENA. However, looking at your comment, LCF in ATHENA requires edge-step normalization, by saying that, does it mean that I cannot normalized my spectra using MBACK then fit them in ATHENA? Thanks, Niken

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XAFS of poly-metals contaminated soil samples
by Xia Bing 09 Sep '11

09 Sep '11

Dear members of the mailing list: This year we have applied the synchrotron radiation and get the chance to Beijing Synchrotron Radiation Facility at beamline 1W1B-XAFS. It is the first time to use this equipment to measure our samples. We communicate with the beamline staff for some guideline and help, but they also do not have much experience on soil samples. Would you like give us some suggestions? If you could, can you supply me some resources like sample preparation or others? Now I try to use synchrotron radiation to elucidate some phenomenons of heavy metals in mining area soil. In my soil sample, the Zn is about 498ppm and the Cu is about 562ppm, the first step I focus on Zn but the copper concentration is higher than Cu. Will copper interfere zinc If I use XAFS to measure the Zn? I plan to use fluorescence detection. The Fe in the sample is at high concentrations (85g/kg), from some literature that might be an issue. Would you like to give me some suggestions in the sample preparation and measurement? Table 1. Characterization of the soil (mean ± SD, n = 3) > > TOC > > g·kg-1 > > TN g·kg-1 > > Available phosphorus > > mg·kg-1 > > Available potassium > > mg·kg-1 > > CEC > > cmol·kg-1 > > Trace metals mg·kg-1 > > Pb > > Zn > > Cu > > Cd > > Mine soil > > 3.69 > > 0.16 > > 0.9 > > 4.1 > > 5.27 > > 1368.2±244.76 > > 497.74±90.27 > > 562.2±94.36 > > 6.48±0.36 > *Not detected Thank you very much. Best Regards Xia Bing -- Department of Environmental Engineering, Room D-614, 6/F, Geography and Environmental Sciences Building, Sun Yat-sen University, Guangzhou, Guangdong, 510275 Cellphone: +86 150 1301 6565 Personal Website:http://sweetblues.cn

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Fwd: Re: XAFS and feffit
by Bruce Ravel 09 Sep '11

09 Sep '11

Hi everyone, This fellow clearly did not take my hint that he should ask his question on the Ifeffit mailing list, so I am taking the liberty of forwarding his questions along. As for his first question: http://cars9.uchicago.edu/ifeffit/FAQ/RunningFeff#crystal The second question is rather too broad and open ended for me to know what to do with it, but perhaps someone else will want to take a stab. B ---------- Forwarded Message ---------- Subject: Re: XAFS and feffit Date: Friday, September 09, 2011, 08:53:12 am From: samrath ninama <samrathn(a)gmail.com> To: Bruce Ravel <bravel(a)bnl.gov> Hello Sir, I have some question about Artemis Software. 1.How can we get crystal structure's file for operating this software. 2.suppose we have doped ferrites with transition metal so what is required doping % of Cu/Co/Ni/Ti in all samples %. please give me the answer any way as soon as possible. SAMRATH NINAMA (EXAFS Reaearch) SOP, DAVV ,INDORE [MP],INDIA On Mon, Jul 25, 2011 at 5:39 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > http://cars9.uchicago.edu/ifeffit/BruceRavel/FormLetters/HelpRequest > > > > On Sunday, July 24, 2011 07:51:05 am you wrote: > > Hello sir, > > > > My self *Samrath Ninama* Research Scholar SOP,DAVV ,*Indore* [mp] > > *INDIA*.My field of work is related to XAFS of some transition metal > > comlexes and feffit data analysis.I was attending *AWX 2011* ASEAN > > WORKSHOP ON X-RAY ABSORPTION SPECTROSCOPY ON 20-22 JUNE 2011 held AT > > *NAKHON RATCHASIMA ,THAILAND**,at There I was also meet with Dr.Matt > > Newvill**(USA*) and *Dr. Grant Bunker**(USA*). They have presented their > > lecture on Athena and Artimis software.But I want to learn more about to > > FEFFIT software .so how i get more knwoledge about these soaftware by > > analyzing data. i wiil waiting for your answer in soon future on my > mail. > > > > your siencerly > > *Samrath Ninama* > > *Email : samrathn(a)gmail.com* > > SOP,DAVV ,*Indore* [mp] *INDIA* > > -- > > 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/ > ----------------------------------------- -- 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

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