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

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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More for dealing the LCF
by Hana 09 Sep '11

09 Sep '11

I would be happy to get advices for LCF of EXAFS spectra, at the following context: 1. Constraining the sum of components fractions to one – - when to apply? - Which factors should be considered at this context while working with soil samples? - How would you suggest dealing the penalty when sum of components is different than one in these heterogeneous soil samples (with unknown composition and probably high effect of disorder)? 2. Any reason not to constrain all fractions to be positive? Thanks, Hana

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Request on behalf of V. Petkov
by Anatoly I Frenkel 08 Sep '11

08 Sep '11

Dear members of the mailing list, I am forwarding to you a request from Valeri Petkov, an organizer of a workshop on nanomaterials at the Denver X-ray conference: ***** We need an instructor for a workshop at the X-ray conference in Denver, Colorado at the first week of August, 2012, who can give an intro (45 mins) to EXAFS basics as applied to study nanoparticles and then provide training/demo (another 45 mins) on EXAFS data analysis using some of the freely available software packages. ***** Perhaps, some of you are available to contribute to this effort. In that case, please contact Valeri directly: petkov(a)phy.cmich.edu] Thank you, Anatoly

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Fitting on Athena
by Niken Wijaya 08 Sep '11

08 Sep '11

Hi Everyone, I am facing a lot of problems when I am trying to fit my sample's spectra with my standards one. Initially, I used Athena to do the background subtraction, but the fitting results are just too "funny". The fitting does not really fit the actual spectra. Since I am analyzing Sulphur and many papers has reported how it is prone to self-absorption effect, I thought, probably if I am using a better background subtraction such as MBACK, I would get a better results. So I decided to use it for the normalization and unlike in Athena, the normalized intensity of the spectra does not equal to 1. By saying this, the intensity of my standard models is way higher than the actual samples. Hence, when I use Athena to fit my real spectra, I would not get a good results. I have also tried using the 3rd derivative of my absorption spectra, but the fitting results are even worse. The intensity of the "fit" spectra is way higher than the actual spectra of my samples that I am trying to fit it with. In fact, when I stack the spectra from the standards and the sample together, the 3rd derivative peak of the samples is almost completely flat due to the very high intensity of the standards themselves. What did I do wrong? and what can I do to fix it? I have also attached my samples and standards spectra. Thank you very much for the assistance. Niken

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Re: [Ifeffit] Ifeffit Digest, Vol 103, Issue 7
by Rajesh Kumar 06 Sep '11

06 Sep '11

Dear Matt, Thanks for your mail. I moved with your advice with PGPLOT a couple of weeks back. After that I could install PGPLOT. Then I installed ATHENA, ARTEMIS and there were some error messages when I was trying to run FIT in ARTEMIS. I tried to resolve them, but then I thought of testing the installation of PGPLOT and then I found that the demos were not working. Since at that time I had tried to install different versions of IFEFFIT, ATHENA and DEMETER, my system got cluttered. So I cleaned the system. Removed all the programs. I installed PGPLOT, HORAE though ubuntu afresh. Then I started to run the demos of PGPLOT. with advice from Pawel, I was able to run compile and execute the .f programs. with "I am not able to run the demo programs" meant that at that time I was not able to run the PGPLOT demos. As I mentioned running PGPLOT demos was just a check, my goal is to use IFEFFIT, ATHENA and now I would be moving to that. With regards Rajesh On 6 September 2011 22:30, <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: Regarding the execution of Demos in PGPLOT (Matt Newville) > 2. Re: Looking for reviewers for data reduction chapter (Wei Li) > 3. Re: Question on GaN Artemis fit (esp. So2 factor) (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 6 Sep 2011 09:03:55 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Regarding the execution of Demos in PGPLOT > Message-ID: > <CA+7ESbqeQ87-wy8OvdDn_unfWXQtzg6DUVR-Os-TJf+v_rEmkg(a)mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > Rajesh, > > > On Tue, Sep 6, 2011 at 7:52 AM, Rajesh Kumar <rajesh.sdc(a)gmail.com> wrote: > > I recently installed > > 1. PGPLOT 5 (ver: 5.2.2-15) through Synaptic Package Manager from ubuntu > - > > MOTU-Developers (Mathematics, Multiverse) > > 2. IFEFFIT from Carlo Segre < segre(a)debian.org>, (version > > 2:1.2.11d-6~lucid0 ) and > > 3. Horae-07-1 through Synaptic Package Manager from ubuntu - developers > > (Science, Multiverse) > > I am not able to run the demo programs. So I started running demo > programs > > for PGPLOT first. > > My examples are in directory: > > /usr/share/doc/pgplot5/examples/pgdemo2.f.gz > > When I compile the program "depgplot10.f" and executed the file, the > > interaction on the console is attached in the file attached herewith. > > I need help in this regard and I am very very new to "xafs" as well as > > ubuntu. > > As far as I can tell from the message you attached, you ran a PGPLOT > demo program that requires a cursor for user input, selected a device > that does not support user input, and got a message saying so. That > seems reasonable to me... you might try selecting the /XW device. > > But, is running the PGPLOT demos your goal? What does that have to do > with Ifeffit? If running Ifeffit is the goal, what happens when you > try to run the programs ifeffit or athena? What does "I am not able > to run the demo programs" mean? > > --Matt > > > ------------------------------ > > Message: 2 > Date: Tue, 6 Sep 2011 10:57:43 -0400 > From: Wei Li <weili(a)udel.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Looking for reviewers for data reduction > chapter > Message-ID: > <CAG_WZxfBDkd4Vbr7GTSEV0n=-CT=FZ=9OrOMVoCt4OoM83AXxA(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, Scott, > > I am also glad to read the chapter. > > Wei > > On Sat, Sep 3, 2011 at 7:13 PM, Lachlan MacLean < > Lachlan.MacLean(a)lightsource.ca> wrote: > > > Hi Scott > > > > I'm in! > > > > Cheers > > Lachlan > > ________________________________________ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ > > ifeffit-bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin [ > > scalvin(a)sarahlawrence.edu] > > Sent: September 3, 2011 3:16 PM > > To: XAFS Analysis using Ifeffit > > Subject: [Ifeffit] Looking for reviewers for data reduction chapter > > > > Hi all, > > > > Once again, I have a draft of a chapter of my textbook ready for review. > > This chapter is on data reduction, including normalization, background > > subtraction, and Fourier transforms. This will be Chapter 4 in the book, > so > > it should be suitable for near-beginners as well as those with more > > experience. This is also a chapter where I had to make a lot of decisions > on > > nomenclature and presentation, so experts might be interested as well, > > particularly if you have strong opinions on that kind of thing! It is a > bit > > more than 40 pages long, which makes it the longest so far. > > > > If you are interested in reviewing the chapter and can get feedback to me > > by 29 September, please contact me directly at SCalvin(a)slc.edu . As > > always, repeat reviewers are welcome! > > > > --Scott Calvin > > Sarah Lawrence College > > _______________________________________________ > > 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 > > > > > > -- > 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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Question on GaN Artemis fit (esp. So2 factor)
by Alejandro X Levander 06 Sep '11

06 Sep '11

Dear ifeffit community; I am working on modeling the local structure of amorphous GaN(1-x)As(x) alloys. After helpful learning experiences at the SSRL XAS Summer School and reading Scott Calvin's doped material help page, I was able to model all of the data for the As K edge I had collected. However, I am now having issues modeling the Ga K edge spectra despite using similar methods. I expect the Ga to be tetrahedrally coordinated and bonded to a mixture of As and N based on the previously determined overall composition. To determine the SO2 parameters for the Ga K edge I am using data collected in fluorescence mode of a thin film (690 nm) of GaN on a sapphire (Al2O3 - 500um) substrate as a reference sample. I have fixed the first and second shell amplitudes in order to determine SO2. The SO2 parameter for the nitrogen shell appears too low to be physically correct (~0.5). When I use these values for SO2 to try and model my amorphous films, I get highly unexpected coordination values much larger than four when summed for As and N bonding since the model is compensating for the low SO2. I am concerned there may be an issue with the data processing in Athena (e.g. self-absorption or deglitching) or multiple-scattering, but cannot pin down the problem. I have attached the GaN (sample code sn281) Athena and Artemis files and an example of trying to fit the Ga K edge of amorphous GaN(0.55)As(0.45) material in Artemis (sample code sn404). The amorphous thin film was 220 nm thick on a 500um pyrex glass substrate measured in fluorescence mode. As a side note, I have also been having trouble with using ATOMS for the wurtzite crystal structure. Despite trying multiple appropriate .cif files from ICSD and making sure to use 1/3 instead of 0.33334 when I run ATOMS, there appear to be rounding errors that turn one coordination into three. Thus I have been manually changing the feff input. Any help is greatly appreciated, Alejandro

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Looking for reviewers for data reduction chapter
by Scott Calvin 06 Sep '11

06 Sep '11

Hi all, Once again, I have a draft of a chapter of my textbook ready for review. This chapter is on data reduction, including normalization, background subtraction, and Fourier transforms. This will be Chapter 4 in the book, so it should be suitable for near-beginners as well as those with more experience. This is also a chapter where I had to make a lot of decisions on nomenclature and presentation, so experts might be interested as well, particularly if you have strong opinions on that kind of thing! It is a bit more than 40 pages long, which makes it the longest so far. If you are interested in reviewing the chapter and can get feedback to me by 29 September, please contact me directly at SCalvin(a)slc.edu . As always, repeat reviewers are welcome! --Scott Calvin Sarah Lawrence College

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Regarding the execution of Demos in PGPLOT
by Rajesh Kumar 06 Sep '11

06 Sep '11

I recently installed 1. PGPLOT 5 (ver: 5.2.2-15) through Synaptic Package Manager from ubuntu - MOTU-Developers (Mathematics, Multiverse) 2. IFEFFIT from Carlo Segre < segre(a)debian.org>, (version 2:1.2.11d-6~lucid0 ) and 3. Horae-07-1 through Synaptic Package Manager from ubuntu - developers (Science, Multiverse) I am not able to run the demo programs. So I started running demo programs for PGPLOT first. My examples are in directory: /usr/share/doc/pgplot5/examples/pgdemo2.f.gz When I compile the program "depgplot10.f" and executed the file, the interaction on the console is attached in the file attached herewith. I need help in this regard and I am very very new to "xafs" as well as ubuntu. Wishing you best of life and time, With regards Rajesh Kumar

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Worm in SixPack
by Abhijeet Gaur 05 Sep '11

05 Sep '11

Hi all, I have been encountering this problem each time when I run SIXPACK on my sytem. Every time I run SIXPACK it shows the infection due to a worm* * * SIXPACK\MULTIARRAY.PYD,WORM.Z040709.0486.9.* * * Thus, after some time SIXPACK stops running and I have to download it again. I am sorry if I am asking a question already asked on this list but I had searched this on ifeffit mail archieve, but unable to find a similar problem. Kindly help. With thanks Abhijeet Gaur

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Re: [Ifeffit] settings tab in Artemis
by Matt Newville 05 Sep '11

05 Sep '11

Hi Morgan, Sorry, somehow your legitimate message got lost in the spam box. > From: Morgan Scott <msco001(a)aucklanduni.ac.nz> > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Mon, 5 Sep 2011 12:04:45 +1200 > Subject: settings tab in Artemis > Hello; > > I have changed some settings in my plot display (legend position, gridlines) in Athena. > I wish to do the same thing in Artemis, but there is no settings tab in the menu. > Is it possible to change the display in Artemis? > If so how? > > regards; > -- > Morgan Scott > Ph.D. candidate > School of Chemical Sciences > University of Auckland Yes, these preferences can be set, it's just in a different place. Use Edit -> Edit Preferences (at very bottom) which will bring up a panel to set and save such options. --Matt

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LCF with different scales
by Hana 03 Sep '11

03 Sep '11

Hi list, I'm looking for a way to make LCF with standards that were measured at different occasions and beam-lines. I did read previous comments regarding this issue, but still need to clarify: 1. Does limiting the range to the smallest range help in this case (if spectra were measured with the same steps size, and a calibration standard was used)? 2. For harder situation; when different steps were used - I found that sixpack (according to its manual) interpolating all spectra to the same energy grid - does this solve the problem? I will be happy to be advised. Thanks, Hana

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A simple question regardng the 'chi' in the xmu.dat file (FEFF8)
by Deok-Yong Cho 02 Sep '11

02 Sep '11

Dear Ifeffit users: Hello, I have a simple question regarding the 'chi' in the xmu.dat, an output file of FEFF8. I wish I could get helps from you to resolve this. As far as I know... in the xmu.dat file from Feff6, mu=mu0*(1+'chi') as it should be, but in the xmu.dat file from Feff 8, the 'chi' written in the xmu.dat is a rescaled one by mu0/(mu0 at edge+tens eV) so that mu should be equal to mu0+'chi'. I checked up for FEFF8.4 by turning on and off the FMS card, and found that with the FMS card, mu = mu0+'chi', while without the FMS card, mu is quite close to or same as mu0*(1+'chi') instead of mu0+'chi'. Please help me to find which one is correct. Attached are the Feff.inp and the resultant xmu.dat for ZnO. Thank you all. Best Regards, Deok-Yong Cho Post-doctoral researcher at RWTH Aachen, Germany

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Athena in Demeter
by Amitava D Roy 30 Aug '11

30 Aug '11

Bruce, Is it possible to put back the "negate" button into the Demeter version of Athena? You have it in the classic version. The button is very useful. Thanks very much, Amitava Roy Amitava Roy J. Bennett, Sr., Center for Advanced Microstructures and Devices 6980 Jefferson Highway Louisiana State University Baton Rouge, LA 70806 225-578-6706 (O) 225-578-6954 (Fax)

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Re: [Ifeffit] Regarding Demeter
by Bruce Ravel 29 Aug '11

29 Aug '11

On Monday, August 29, 2011 03:48:26 pm you wrote: > Dear Bruce, > I have been struggling to install the any of the demeter or horae. I have > tried so many things but not able to install. > I have installed PGPLOT, IFEFTIT already on my computer (Ubuntu 10.04, > intel i686). > There are so many different version available and I have tried many of > them. > I need your help and word of guidance. Let me know the more straight > forward way of doing it. > I would be using it in my research on edge spectroscopy. Rajesh, I am CCing this to the Ifeffit mailing list, which is the proper venue for a question of this sort. If you are not subscribed to the Ifeffit mailing list, here is the info: http://cars9.uchicago.edu/mailman/listinfo/ifeffit In the future, please make use of the list. First off, you should know that "horae" is the version of the codes that has been out for years. "Demeter" is the new version which is under development. Demeter is better than horae in almost every way, but, like all software under development, it's not guaranteed to work as advertised. That said, I use Demeter for all my own work and many others have begun using it. If something stable is more to your liking, Carlo Segre has built installation packages for horae. Use your package manager to install it. If a search for "horae" turns up nothing, add the appropriate repository (I think 10.04 == Lucid) from: http://debian-xray.iit.edu/ to your package manager. If you have never done this before, consult https://help.ubuntu.com/community/Repositories/Ubuntu Once you have done that, you should be able to simply install "horae" and have all the dependencies met. If you want to use the newer, fancier, but not-yet-stable code, follow the instructions at: http://cars9.uchicago.edu/ifeffit/Demeter/InstallDemeterOnUnixWithGit Follow these instructions to the letter. Don't improvise unless you know what you are doing. It will take you a while to get all the dependencies built. Be patient -- once you are set up, updating is quick and easy. 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

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Job Vacancy in UK
by fred.mosselmans＠diamond.ac.uk 26 Aug '11

26 Aug '11

Because of an internal promotion, there is now a vacancy for a beamline scientist on the microfocus spectroscopy beamline at Diamond. The details can be found at http://www.diamond.ac.uk/Home/Jobs/Current/DIA0638-TH.html Thanks Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK -- 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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PhD position in Lausanne/Villigen (Switzerland)
by Chergui Majed 26 Aug '11

26 Aug '11

PHD POSITION IN ULTRAFAST X-RAY ABSORPTION SPECTROSCOPY A PhD position is available in the group of Professor M. Chergui to carry out steady-state and time resolved (ps/fs) X-ray absorption spectroscopy studies on metalloproteins in physiological solutions. The experiments involve the use of ultrashort pulse lasers to excite the sample, while the probing is done by the pulsed X-rays from a synchrotron. Involvement with experiments at the X-ray Free Electron Laser at LCLS-Stanford is also envisioned. The research is carried out in collaboration with the Swiss Light Source (Paul-Scherrer Institut, Villigen) and the candidate will be based there. For more information about the methodology and results, see: Picosecond and femtosecond X-ray absorption spectroscopy of molecular systems M. Chergui, Acta Crystallografica A66 (2010) 229-239 Light-induced spin crossover in Fe(II)-based complexes: the full photocycle unravelled by ultrafast optical and X-ray spectroscopies A. Cannizzo et al, Coordination Chemistry Reviews 254 (2010) 2677-2686 experiments on chemical and biological systems in solution F. A. Lima, et al, Review of Scientific Instruments 82 (2011) 063111 Probing the transition from hydrophilic to hydrophobic solvation with atomic scale resolution V.-T. Pham, et al, Journal of the American Chemical Society, 2011, 133, 12740-12748 For information and applications (letter of motivation, recommendations, CV and list of publications, if any), please contact: Dr. Chris Milne Chergui Group Swiss Light Source, PSI CH-5232 Villigen PSI Tel: +41 (0)56 310 5477 Fax: +41 (0)56 310 4413 Email: chris.milne(a)psi.ch<mailto:chris.milne@psi.ch> Or Professor Majed CHERGUI Ecole Polytechnique Fédérale de Lausanne Laboratoire de Spectroscopie Ultrarapide ISIC, Faculté des Sciences de Base Station 6 CH-1015 Lausanne, Switzerland tel: xx 41 21 6930447 / 0457 fax: xx 41 21 6930365 email: Majed.Chergui(a)epfl.ch<mailto:Majed.Chergui@epfl.ch> http://lsu.epfl.ch/ P<http://lsu.epfl.ch/P> Please consider the environment before printing this email - Considérez svp l'environnement avant d'imprimer ce courriel

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dementer Artemis crashing on XP
by Christopher Patridge 22 Aug '11

22 Aug '11

Hello all, I recently (yesterday) installed the new Dementer package with Strawberry perl on a freshly installed XP Pro SP3. I have tried to open a couple different old Artemis projects (.apj) and once chosen, (D) Artemis shuts down immediately with no warnings messages. The message line reads something like - "converting data to Dementer fit serialization" and then everything disappears. I have attached one of the projects I attempted to open. I can open data from previous Athena projects with no problem. Any help would be appreciated. buena salud, Chris Patridge

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New software being developed
by Bruce Ravel 18 Aug '11

18 Aug '11

Hi everyone, I suppose I should say a few words about this Demeter thing that got mentioned a couple of times today. As some of you may know, I have been working on replacements for Athena, Artemis, and Hephaestus for a while now. The new programs involve better and prettier GUIs, improved plotting capabilities, 100% re-written source code, and lots of new fitting capabilities. I expect that the new codes will be better in almost every way than what we are all currently using. I am getting very close to releasing the new codes for everybody to use. A couple months ago, I asked a small group of people to try out the new programs and to help me find bugs and other problems. This small-scale beta-testing period has been very productive and I have made good progress towards the day when I can begin transitioning everyone from the musty old software to the shiny new software. If beta-testing buggy software sounds like something you might want to try, you can find information about Demeter -- including installation instructions, documentation, source code, and other goodies -- at http://cars9.uchicago.edu/ifeffit/Demeter Be mindful that this is new software. It continues to need testing and it remains likely to crash. If that sounds like fun to you, great! But you then need to be responsible about sending me prompt and useful bug reports. If that sounds like hell to you, you should probably wait for the first stable release. Regards, 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

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LCF E0
by Pieter-Jan Sabbe 18 Aug '11

18 Aug '11

Dear All I am trying to do a linear combination fit with Athena. To do that i want to first prepare my standard spectra. My unknown sample is (I presume) a combination of Cu and Cu(I)O (cuprite) and Cu(II)O (tenorite). I started with calibrating the Cu to 8979 eV as how the Athena manual say how to do it (I use the zero crossing point at the second derivative). This provided me an E0 and Eshift. I am doubting now for what I should do next: Cuprite and Tenorite have different oxidation states, meanin that the binding energies of the inner electrons will shift and in that way shifting the absorption edge of the compound. Should I look somewhere in a database (does that exist, or articles) for the absorption edge of cuprite and tenorite and set it like that or should I use the same E0 as i did for Cu? Another important thing for me, I have found some old data with some standard reference (powder spectra) measured in fluorescence mode, but my guess they are from different beamtimes, can I use data from different beamtimes/beamlines as standards in a linear combination fit? thank you in advance Pieter-Jan

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Athena: problems with LCF
by Nina Siebers 15 Aug '11

15 Aug '11

Dear All, I acquired Cd L3-edge spectra of some binary and ternary mixtures in varying proportions and for the individual components. The mixtures were created on Cd-mass basis. Then, I tried to fit the reference spectra to the spectra of the mixtures using linear combination fitting of Athena to get their abundance. However, the results were disappointing despite all spectra were carefully energy calibrated and normalized, so I decided to create simple mathematical binary and ternary mixtures by summing up the spectra of the individual reference spectra. After that I did an edge-step normalization in excel and imported the normalized calculated mixtures into Athena. Then, I tried the fitting again to exclude mixing-failures and check sensitivity of LCF with the idealized spectra. Even though the results of the LCF of the mathematical mixtures were better compared to the real mixtures, LCF was also not able to reliable deconvolute these spectra into the individual reference spectra. Does anybody have an explanation for that? It would be nice if somebody could give me information about the mathematical fitting algorithm implemented in Athena. Attached is a data file of three mixtures (two ternary and one binary mixture) including the mathematical mixture created in excel (named calculated at the end). Mixing ratios are named 1to1to1 (meaning 1:1:1 of the components in the same order). For the 1:1:1 ternary mathematical mixture the deconvolution was very good, but the others need improvement. I hope I made my problem clear this time. Thanks a lot! Wishes, Nina

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