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

demeter on xp access for all users
by fred.mosselmans＠diamond.ac.uk 02 Feb '12

02 Feb '12

Hi I am sure this has probably been posted before but I couldn't find it on a rudimentary search of the mailing list archive- I think Bruce fixed it in a previous release after the course he gave at Diamond. I'd recommend it when the video comes out soon But having installed the latest Demeter release on my xp windows pc's on the beamline, I can use it fine but my users who log in to these pc's as themselves with few rights in the windows world cant. If they try to start the program the old dos window shows for milliseconds and that's it. I am sure it is a permissions issue for a log file or something so I have made the strawberry pearl directory full control for anyone but obviously I need to do something else as well. Ta Fred Prof JFW Mosselmans Principal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell campus Chilton Didcot OX11 0DE E fred.mosselmans(a)diamond.ac.uk<mailto:fred.mosselmans@diamond.ac.uk> P 00 44 1235778568 M 00 44 7785510211 -- 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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Au-foil (fcc) splitted peak
by grant bunker 29 Jan '12

29 Jan '12

Julian - the scattering amplitudes of all elements have structure in them that are connected to electron scattering (Ramsauer-Townsend) resonances within the backscattering atom. For light elements (e.g. O, S, Fe) they occur at energies that are lower than the typical transform range, so they usually are ignored. For heavier scatterers like Au there are strong minima and maxima in the Au scattering amplitude over the transform range. From a signal processing point of view, these amplitude modulations look like beats, which normally are due to different distances interfering. In the case of Au back scatterers, even if there is only one physical distance, you will get multiple peaks (perhaps overlapping). Mathematically the fourier transform is the distance distribution convoluted with the fourier transform of the amplitude. So, how do you deal with it? First, if you know what's going on that may be enough. Alternatively, if all the scatterers are the same, it's not difficult to divide out the scattering amplitude and subtract out the scattering phase before the transform to obtain an "optical transform", which eliminates the effect you're seeing. I don't know if that is supported by ifeffit but it's not hard to do. This approach is less useful if you have multiple types of scatterers (e.g. Au, S) because if you do the compensation for one type of scatterer it screws it up for the others. Techniques like regularization are probably better in that case. hope that helps grant bunker

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HELP! EXAFS calculation for "+2" charged molecule
by YOON Zin Seok 17 Jan '12

17 Jan '12

Dear FEFF users, Hi, I am using FEFF9. I would like to calculate EXAFS spectrum of +2 charged molecule. According to the manual feff90_users_guide.pdf, in pages 33-34, I thought maybe I ccould use ION card. In page 34, in ION 1 0.2, what do 1 and 0.2 mean? Can you help me? Thank you. Zin

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(no subject)
by JeongEunSuk 13 Jan '12

13 Jan '12

Hello all I want to understand EO(edge-energy), precisely. (In Artemis, EO is writed as Enor) Generally, EO is energy when electrons start to go out from core atom in XAFS. As you know, the experiments show that to find EO is not easy in XAFS. To remove background, sometimes I chose EO, the value of the maximum derivative in Athena. and when fitting, the E0 is correted by theoritical FEFF. This is my question. The attached file is the figure of Pt foil(Pt L3 edge measurement). I think edge-enegy has to be in range between A and C because electrons start to move to continum state in that range. However, fitted E0 is shifted to C (about 11573eV). and then when removing background I chose E0=11563eV(This is Pt L3 edge). Fitted E0 is overestimated value, compared with whit line(B). That means the calculated EO obtained from FEFF8.0 (using auto-self consistency field potential) is larger than that of experiment. Do I need to change SCF potential in FEFF8.0? ---------------------------------------------------------------------------------------------------------------------------- This is fitting parameters and results(in my case, I used Linux version) To remove background k -range = 2.5 ~ 15, EO=11563eV, Rbkg=1.3, kweight =1 To fit data k -range = 3.0~13.5, R -range =2.3~13.5 1. fitting parameters set macc = 0.0 set so2 = 0.89 // reduction factor guess ePt = 0.0 // energy shift set npt1=1.0 // the number of Pt (1.0 means 12 Pt atoms around core Pt) guess dpt1 = 0.0042 // effective bonding length guess sigpt1=0.005100 //Debye waller factor 2. fitting results fit results, goodness of fit, and error analysis: independent points in data = 8.152 number of variables in fit = 3 degrees of freedom in fit = 5.152 r-factor of fit = 0.002700 chi-square = 1267.097168 reduced chi-square = 245.926361 feffit found the following values for the variables: variable best fit value uncertainty initial guess ept = 10.758198 0.860494 4.000000 dpt1 = 0.006462 0.002930 0.004200 sigpt1 = 0.005114 0.000098 0.005100 correlation between variables variable #1 variable #2 correlation ept dpt1 0.926524 all other correlations are less than 0.25000 --------------------------------------------------------------------------------------------- Because the correlation between E0 and effective bonding length is big, I checked the fit as set bonding and the rest of parameters is variables, and then the result is not changed. That means EO still is big.

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Find R-factor for linear combination sums?
by Scott Calvin 09 Jan '12

09 Jan '12

Hi all, Is there a way to get Athena (or Ifeffit) to report an R-factor for a linear combination sum, as opposed to a fit? Artemis does that for FEFF fitting, and Athena will do a linear combination sum ("plot data + sum" with weights entered into the LCF standards boxes), but I don't see a way to get it to report the statistics. Here's the reason I'd like to be able to do this: when I run LCF fits, I often do one fit for XANES and another on chi(k) for EXAFS (and perhaps another using the derivative of XANES, just for good measure). The fits unsurprisingly usually give somewhat different weights to each fraction. So suppose XANES tells me my sample is 0.22 A and 0.78 B, and EXAFS tells me its 0.28 A and 0.72 B. I'd like to be able to force the EXAFS to 0.22 A and 0.78 B (i.e. the results of the XANES fit), and have it give me an R-factor for that sum. Then I could apply something like a Hamilton test to decide if they're actually consistent. If it's not currently a feature, it's one I'd like to see. It's not that high a priority--I can just export the spectra and calculate it in Excel. But it would be nice. --Scott Calvin Sarah Lawrence College

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ifeffit on Mac OSX 10.7 (Lion)?
by Peggy O'Day 09 Jan '12

09 Jan '12

Hi, Does anyone know if there is a version of ifeffit that works on the new Mac OSX 10.7 (Lion)? iXAFS on Snow Leopard was great… but doesn't work on Lion (at least not obviously). thanks, Peggy ********************************************************* Peggy O'Day Professor & Founding Faculty School of Natural Sciences University of California, Merced 5200 North Lake Road Merced, CA 95343 (209) 228-4338 poday(a)ucmerced.edu

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star parser to be installed for Horae
by denis testemale 05 Jan '12

05 Jan '12

Dear Carlo, dear members of the list, I just wanted to share something about a problem with horae I just solved. I don't know if it is related to the debian and debian-like builds of horae or something else. Here is the context: - I run ubuntu - I use the last versions of horae package, but I had the same problem for years... - I could not import a .cif file in Artemis (error trapped) and had to enter the data manually. I decided to take the time to solve this small but annoying problem and it appeared to be easily done: the error message said that I could not import a cif file because the STAR::Parser was not installed. By installing libstar-parser-perl I solved the problem. In an old message, Carlo you said that you had built the packages which included (among other things) this libstar-parser-perl package: http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg00256.html but for some reasons it did not install even if I used your horae packages on your repositories. If that helps someone... Cheers denis

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Extracting "raw values" from ATHENA and ARTEMIS plots
by Tony Kelly 04 Jan '12

04 Jan '12

Hello All, I am attempting to essentially extract the numbers behind the graphical outputs of ARTEMIS and ATHENA. Currently, the only way I have been able to do this is to save a plot, then use third party software to click points on the graph and extract the information, which I can then analyze further and plot in ROOT. I suppose I could try to abandon the GUI interface and write command line scripts, writing out the arrays into text files as I go along... but I'd rather not have to go that far under the hood if possible. Does anyone know how I might extra this information from the GUI? An ATHENA example, say I plot the background subtracted signal in k-space, is there a way of then finding the numbers that went into forming this plot? Thanks much, Tony Kelly -- Tony Kelly, M.Sc. DTRA PhD Student Air Force Institute of Technology Nuclear Physics and Engineering

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Re: [Ifeffit] Deconvolution of K-edge of lanthanides
by Eugenio Otal 04 Jan '12

04 Jan '12

Hi Bruce, thanks for the help. Looks not so straightforward like L edges. The information has a price. I also found this software: http://www.cells.es/Beamlines/CLAESS/software/xanda.html Kind Regards, euG 2012/1/3 <ifeffit-request(a)millenia.cars.aps.anl.gov> > 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. tutorial + data athena and sixpack (Pieter-Jan Sabbe) > 2. Re: tutorial + data athena and sixpack (Scott Calvin) > 3. Re: tutorial + data athena and sixpack (Bruce Ravel) > 4. Deconvolution of K-edge of lanthanides (Eugenio Otal) > 5. Re: Deconvolution of K-edge of lanthanides (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 02 Jan 2012 22:54:12 +0100 > From: "Pieter-Jan Sabbe" <PieterJan.Sabbe(a)ugent.be> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] tutorial + data athena and sixpack > Message-ID: <20120102225412.20801zllz36q8zgk(a)webmail.ugent.be> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear all, > > This spring I need to supervise some undergraduate students during a > 4-week project in my research group. I would like to introduce them > into the world of data processing with athena and sixpack. I would > like to find a tutorial for sixpack and some test data on principal > component analysis and linear combination fitting before giving them > some of my own data. Can anybody help me ? Or anybody else had to > teach something similar, any idea would help! > > Thank you very much in advance, > > Have a great 2012 > > PJ Sabbe > > -- > Met Vriendelijke groeten, > Pieter-Jan Sabbe > > > Pieter-Jan Sabbe > Vakgroep Analytische Chemie > Universiteit Gent > Krijgslaan 281 S12 > B-9000 Gent > Tel +32 (0)9/264 48 20 > E-mail: pieterjan.sabbe(a)ugent.be > > > > > ------------------------------ > > Message: 2 > Date: Mon, 2 Jan 2012 17:05:24 -0500 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] tutorial + data athena and sixpack > Message-ID: <D9F45019-20AC-4D45-923B-261BBFEE1877(a)slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Pieter-Jan, > > The "EXAFS Divination Set" should work as test data, although I haven't > tried PCA on it: http://www.xafs.org/EXAFS_Divination_Set > > Feel free to contact me for follow-up if you'd like to know more about > that set, etc.. > > --Scott Calvin > Sarah Lawrence College > > On Jan 2, 2012, at 1:54 PM, Pieter-Jan Sabbe wrote: > > > Dear all, > > > > This spring I need to supervise some undergraduate students during a > > 4-week project in my research group. I would like to introduce them > > into the world of data processing with athena and sixpack. I would > > like to find a tutorial for sixpack and some test data on principal > > component analysis and linear combination fitting before giving them > > some of my own data. Can anybody help me ? Or anybody else had to > > teach something similar, any idea would help! > > > > Thank you very much in advance, > > > > Have a great 2012 > > > > PJ Sabbe > > > > > ------------------------------ > > Message: 3 > Date: Tue, 3 Jan 2012 10:48:45 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] tutorial + data athena and sixpack > Message-ID: <201201031048.46156.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Monday, January 02, 2012 04:54:12 pm Pieter-Jan Sabbe wrote: > > Dear all, > > > > This spring I need to supervise some undergraduate students during a > > 4-week project in my research group. I would like to introduce them > > into the world of data processing with athena and sixpack. I would > > like to find a tutorial for sixpack and some test data on principal > > component analysis and linear combination fitting before giving them > > some of my own data. Can anybody help me ? Or anybody else had to > > teach something similar, any idea would help! > > Pieter-Jan, > > There is a ton of useful stuff and useful links at > http://xafs.org/Tutorials, including much written by folks whose > names you'll recognize from this mailing list. > > 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: 4 > Date: Tue, 3 Jan 2012 17:10:58 +0100 > From: Eugenio Otal <eugenioh(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Deconvolution of K-edge of lanthanides > Message-ID: > <CAKUU9GSiBC2sNz4ow9g_C3_X=07kTQFW9Kh77Aw4VfCH1JAJTA(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I am dealing with some spectra of Er and Yb in the K-edge. > Does somebody was doing the deconvolution of the spectra in these energies? > I will appreciate all the help to treat the spectra in this high energy > regions. > Kind regards, euG >

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Deconvolution of K-edge of lanthanides
by Eugenio Otal 03 Jan '12

03 Jan '12

Hi all, I am dealing with some spectra of Er and Yb in the K-edge. Does somebody was doing the deconvolution of the spectra in these energies? I will appreciate all the help to treat the spectra in this high energy regions. Kind regards, euG

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