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

Artemis: How to treat Neglected? DS path
by Takahide Yamaguchi 03 Feb '12

03 Feb '12

Dear all, I have been analyzing some EXAFS data based on crystal structure by Artemis. The model construction and analysis within the First shell had come along OK. And I would like to refine the analysis of higher shell including multiple scattering. But the problem about "How to treat the MS path(especially DS)" is existing in the way to goal. Generally, Considering triangle arrangement (A-B-C; A is Absorber, B is nearest neighbor, C is the next neighbor) offers the possibility of two double scattering paths. Stated another way, the following two type can be readily considerable. "Type I: A-->B-->C-->A and Type II; A-->C-->B-->A" By calculation of FEFF on Artemis, a number of DS is computed and listed, of course on my computer. However, I could find JUST ONLY type II double scatter, no type I. In this case, should I simply multiply the amplitude by two? Or, are there reasonable answer to neglected type I path? I will be glad with your help. Best regards, Takahide

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Re: [Ifeffit] Sudden Difficulty with Importing Data into Athena
by Tony Kelly 02 Feb '12

02 Feb '12

1. I made sure to check the data files for strange behavior, definitely a good idea. I know when I use other software such as ROOT, file structure and pat names can become problems. This didn't fix the problem, however :-/ 2. I then ran Athena from the command line as was suggested, and it seems that there is a major problem there: bash-3.2$ athena Can't load '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle' for module Ifeffit: dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle, 1): Library not loaded: libifeffit.so Referenced from: /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle Reason: image not found at /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm line 204. at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67 Compilation failed in require at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67. BEGIN failed--compilation aborted at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67. 3. Then I became more curious and attempted ifeffit itself: bash-3.2$ ifeffit dyld: Library not loaded: libpgplot.dylib Referenced from: /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit Reason: image not found Trace/BPT trap I am using Max OSX 10.6.8. Intel Core i5. Any other Mac users out there have ideas? Thanks much, Tony Kelly Air Force Institute of Technology Nuclear Physics and Engineering

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Sudden Difficulty with Importing Data into Athena
by Tony Kelly 02 Feb '12

02 Feb '12

Hi Bruce, Thank you for the quick reply. I tried uninstalling and reinstalling twice, though I suppose I could try a different version. I have also made sure that my x11/xquartz software was up to date, though I have not changed or added software or updates between the last time it worked and now. It literally worked last night, then it no longer worked this morning. I've never had antivirus software on my macs, but I could download one and do a scan to see what that gives me. If I find a clear solution to what may have happened, I'll be sure to reply again to share the answer. Tony Kelly Air Force Institute of Technology Nuclear Physics and Engineering

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Sudden Difficulty with Importing Data into Athena
by Tony Kelly 02 Feb '12

02 Feb '12

Hopefully this is not long winded, but I want to be as detailed with the problem as I can be. In the past, I have never had difficulty importing data into Athena, given it was formatted properly. It was working as recently as last night, but suddenly I have a problem today. 1. I open Athena 2. I go to File->Open Files 3. I click on the data file to bring me to the window where I choose Energy, Numerator, Denominator for the data and any reference spectra, etc 4. I choose the Energy, Numerator and Denominator This is when the first moment of "oddness" happens... I don't get a plot. Normally, I would get a plot of the spectra I am about to import to know if I selected the correct columns with the correct sign (and whether a Log is needed). 5. Confused, I continue anyway and import my choices. 6. I then get the following error from Athena: The following problems were found for group "Fe.060" 1 : The edge energy is unset 2 : The kmin for the forward transfer is negative (-2) You should fix these values before continuing analysis of these data. Note 1: I was trying with some old data that I have analyzed in the past from Athena through Artemis and know to be okay for analysis. Note 2: I then tried studying some MnO spectra by importing that data taken during the 2011 XAFS Summer School in Chicago taken from APS. I know these text files to work, as we looked at them AT the summer school. Note 3: As a last resort, I tried downloading the Fe example from the Athena website (as you can see above from Fe.060), but it can't even read this in. Note 4: Athena CAN open old projects where the data was already imported without problems... it just seems I can't start a new project and import data into it successfully. I have tried searching all through the internet for anyone who had the error above or my difficulties to no avail. I have tried making sure the line breaks were correct by resaving data into new files through textwrangler and even going through vim in a terminal, to no avail. Note 5: As a last resort, I reinstalled iXAFS, but this hasn't fixed the problem. Anyone have any suggestions? Am I suddenly forgetting a step in the data import process? Thanks, Tony Kelly Air Force Institute of Technology Nuclear Physics and Engineering

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Re: [Ifeffit] Ifeffit Digest, Vol 107, Issue 16
by Carmelo Prestipino 02 Feb '12

02 Feb '12

Hi I have also some problems to start demeter ..... My computer is equipped with Vista Demeter is installed on C:\strawberry If I digit "C:\strawberry\perl\site\bin\datoms.bat" on the dos windows no output come out. Here bellow the text in file DATOMS.log Can't locate Demeter.pm in @INC (@INC contains: /usr/lib/perl5/5.8/msys /usr/lib/perl5/5.8 /usr/lib/perl5/site_perl/5.8/msys /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/vendor_perl/5.8/msys /usr/lib/perl5/vendor_perl/5.8 /usr/lib/perl5/vendor_perl/5.8 .) at ./datoms.bat line 31. BEGIN failed--compilation aborted at ./datoms.bat line 31. DARTHEMIS.log Can't locate Demeter/Here.pm in @INC (@INC contains: /usr/lib/perl5/5.8/msys /usr/lib/perl5/5.8 /usr/lib/perl5/site_perl/5.8/msys /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/vendor_perl/5.8/msys /usr/lib/perl5/vendor_perl/5.8 /usr/lib/perl5/vendor_perl/5.8 .) at ./C:\strawberry\perl\site\bin\dartemis.bat line 16. BEGIN failed--compilation aborted at ./C:\strawberry\perl\site\bin\dartemis.bat line 16. Thanks Again Carmelo -- Carmelo Prestipino Sciences Chimiques de Rennes UMR 6226 Solid State and Materials Chemistry group (CSM) Campus de Beaulieu, Bât 10B, bureau 122 F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959 >

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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 08 Jan '12

08 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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