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

How to use "OVERLAP" card?
by Jun Lin 09 May '07

09 May '07

I have read some references of Kelly Shelly, and I have got some idea of how to construct a structure without difinite crystalline structure. But when I try to apply to my own question, meet some difficulties. In my case, four nitrogen atoms is surrounding a iron atom. So I use OVERLAP and SS card as to define such system as described in the FEFF manual: -------------------------------------------------- POTENTIALS * ipot Z element 0 26 Fe 1 7 N * Determine approximate overlap for central and 1st nn in Cu OVERLAP 0 *determine overlap for central atom of Fe *iphovr novr rovr * ipot, number in shell, distance 1 4 2.15 OVERLAP 1 *determine approximate overlap for 1st shell N *iphovr novr rovr * ipot, number in shell, distance 0 1 2.15 *SS index ipot deg rss SS 1 1 4 2.15 -------------------------------------------------- but feff8 stopped and said: Absorbing atom coords not specified. Cannot find multiple scattering paths. since the OVERLAP does't need ATOMES card, where can I define the coordination of absorbing atom? Is there any other CARD needed for such situation? ========================================= Hi Jun, That keyword is explained here: http://feff.phys.washington.edu/feff/wiki/index.php?title=OVERLAP I think the problem is that you have not specified the SS keyword: http://feff.phys.washington.edu/feff/wiki/index.php?title=SS I use the overlap/ss thing in feff very infrequently. My preference is to start from a known structure that is somehow similar to the material I am investigating. For example, if I were to look at amorphous germanium, I would use crystalline germanium as my starting point. I would then construct the model in such a way that I parameterize the differences between the starting structure and what I expect to find in the data. I'd recommend reading papers by Scott Calvin or Anatoly Frenkel on nanoparticles or by Shelly Kelly on uranium in biogeochemical systems for excellent examples of how that sort of analysis is done. Hope that helps, B -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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How to use "OVERLAP" card?
by Jun Lin 08 May '07

08 May '07

Hi everybody: It is the first time I send mail to this list. I wanna use OVERLAP of Feff8.4 to design a structure for my analysis, but the program give error message as followed: > Feff 8.40 > OVERLAP: > Expert option, please read documentation carefully and check your results. > OVERLAP: > Expert option, please read documentation carefully and check your results. > My test for OVERLAP > Absorbing atom coords not specified. > Cannot find multiple scattering paths. > RDINP > STOP statement executed in my feff.inp, I wrote like this: TITLE My test for OVERLAP * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 POTENTIALS * ipot Z element * l_scmt l_fms stoichiometry 0 26 Fe 1 7 N OVERLAP 0 0 1 0.00 1 4 1.15 END Is there anyone give me some suggestion? Thanks! Lin Jun -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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Ru input file - a question and a problem
by Vivek Murthi 02 May '07

02 May '07

Hi Bruce/Matt/Scott I am trying to fit some Ru based catalysts using Ifeffit - 0.8.007. 1. Does anyone have an atoms input file for Ruthenium that they can share with me? _ The problem:_ 1. I got the crystallographic data for Ru from "database.iem.ac.ru/*mincryst*/" which I used inside atoms to generate FEFF a input file. However, FEFF returns an error saying that my atoms list might be wrong and that two atoms are separated by less than an 0.93 angstroms. I also checked the 5 digit precision in the input file to make sure that wasn't creating the problem. The FEFF input file generated by atoms definitely has atoms bizarrely close to each other. I do not understand why a standard crystallographic data would give such results. I have attached the "Ru.inp" input file I used and the error buffer from FEFF below for your convenience. 2. So I tried playing around with the atoms input file. I set all the xyz co-ordinates to 0, then the FEFF runs without any error but that however gives me 2 Ru paths with two separate R eff ( 2.14 and 2.70 A) but very close to each other in the first shell. Is this a possible scenario? Thank you for your time/comments/solutions. Vivek # Artemis version 0.8.007 # This file created at 16:41:31 on 2 May, 2007 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.9 # IFEFFIT_DIR is C:\Program Files\Ifeffit # Workspace: C:\Program Files\Ifeffit\horae\stash\artemis.project.1\ Feff 6L.02 WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 1 2 1 0.00000 0.00000 0.00000 2 0.00000 0.00018 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 3 9 3 -1.56108 0.00014 2.14100 9 -1.56116 0.00009 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 4 5 4 0.78066 -1.35186 2.14100 5 0.78058 -1.35191 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 6 10 6 -1.56108 0.00014 -2.14100 10 -1.56116 0.00009 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 7 8 7 0.78066 -1.35186 -2.14100 8 0.78058 -1.35191 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 11 13 11 0.78058 1.35209 2.14100 13 0.78066 1.35214 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 12 14 12 0.78058 1.35209 -2.14100 14 0.78066 1.35214 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 15 23 15 0.00000 -2.70382 0.00000 23 0.00000 -2.70400 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 16 21 16 2.34173 -1.35182 0.00000 21 2.34173 -1.35200 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 17 22 17 -2.34173 -1.35182 0.00000 22 -2.34173 -1.35200 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 18 24 18 2.34173 1.35200 0.00000 24 2.34173 1.35218 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 19 25 19 -2.34173 1.35200 0.00000 25 -2.34173 1.35218 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 20 26 20 0.00000 2.70400 0.00000 26 0.00000 2.70418 0.00000 Run continues... ... Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 muffin tin radii and interstitial parameters phase shifts for unique potential 0 This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg). This may be due to the presence of hydrogen atoms in your feff.inp file, in which case this is an innocuous warning and may be ignored. However, this may indicate a problem constructing the Atoms list. The most common cause of this problem is a mistake in the crystallographic data used on the Atoms page. You may have incorrect values for lattice constants or angles or incorrect values for site coordinates. You may need a shift vector to move the lattice into its standard setting. Please be aware that Atoms works with 5 digits of precision. Thus, if you have a site with a coordinate of 1/3, you should use either "1/3" or "0.33333" on the Atoms page. Using insufficient precision, say "0.333" is a common cause of this error message. Artemis has continued on the possibility that the warning is caused by hydrogen atoms, but be warned that the feff.inp may require your attention. ! This atoms input file was generated by Artemis 0.8.007 ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = ... space = P63/MMC a = 2.7040 b = 2.7040 c = 4.2820 alpha = 90.0 beta = 90.0 gamma = 120.0 core = Ru edge = K rmax = 3.0 shift 0.00000 0.00000 0.00000 atoms ! elem x y z tag occ. Ru 0.33330 0.66670 0.25000 Ru 1.00000

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large Eo's and neg. D-W factors
by Richard Mayes 02 May '07

02 May '07

Greetings! I have inherited a vanadium EXAFS data set (due to a group member graduating - lucky dog!) that is giving me major fits. I am getting consistent numbers with all my fits which visually look fantastic, that is until I look at the numbers...one Debye-Waller factor is negative (a V-O path) and the Eo's are large, the V-Cl path is on the order of -20 eV, the V=O path is on the order of 17 eV, and the V-O path falling at -11 eV. ARe there any "tricks" outside of restraints or constraints that I can attempt to get more realistic values? (I understand that a large Eo can be realistic, but a negative Debye-Waller factor doesn't make sense.) I can restrain the V-O Debye-Waller factor and get a positive value, but then the V=O D-W factor is negative. If I restrain both D-W factors, the fit falls apart, suggesting something else is wrong that I just can't find. Another issue I'm having involves something in Artemis that's confusing me. Sometimes after a fit, the Artemis Pallet shows the V=O feature as the one at 1.8 Angstroms and the V-O feature at 1.6 Angstroms, completely reversed to the FEFF model. I have seen this when I separated the chlorides as well (I attempted to model the Cl at different distances as reported by Deguns, et. al. (attached) due to the immediate environment around the V in our sample being similar to the one they report in scheme 1-(I), p5008). Attached is a text file that shows an Artemis Pallet output illustrating what I'm trying to describe for the V=O and V-O paths. The Artemis project that generated the output is also attached. At this point, I'm wandering what I'm missing. Any help is greatly appreciated!! Many thanks in advance! Rich Mayes Barnes Group 450/452 Buehler Hall Dept. of Chemistry Univ. of Tennessee Knoxville, TN 37996 Project title : Fitting SA_162deglitch-merge.chi Comment : Fit #1 Prepared by : Contact : Started : 15:46:44 on 17 April, 2007 This fit at : 15:58:01 on 18 April, 2007 Environment : Artemis 0.8.007 using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.9 Figure of merit : 3 ============================================================ Independent points = 14.027343750 Number of variables = 9.000000000 Chi-square = 45.640992098 Reduced Chi-square = 9.078550099 R-factor = 0.012557807 Measurement uncertainty (k) = 0.000687372 Measurement uncertainty (R) = 0.023895029 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): enot = 17.1999060 +/- 3.4058600 (0.0000) delr = 0.1588460 +/- 0.0081480 (0.0000) ss = -0.0022720 +/- 0.0007180 (0.0030) enot_O2 = -11.0384940 +/- 9.8688920 (guessed as enot) delr_O2 = -0.2214820 +/- 0.0356500 (0.0000) ss_O2 = 0.0027560 +/- 0.0021290 (0.0030) enot_Cl = -16.0026700 +/- 3.5982940 (guessed as enot) delr_Cl = -0.0118230 +/- 0.0104780 (0.0000) ss_Cl = 0.0016470 +/- 0.0004220 (0.0030) Set parameters: amp = 0.93 CN_O1 = 1 CN_O2 = 1 CN_Cl = 2 Correlations between variables: enot_Cl and delr_Cl --> 0.9479 enot_O2 and delr_O2 --> 0.9104 enot and enot_Cl --> 0.8766 enot and enot_O2 --> -0.8755 ss and delr_Cl --> 0.8737 delr_O2 and enot_Cl --> -0.8655 ss and enot_Cl --> 0.8469 enot_O2 and enot_Cl --> -0.8220 ss and delr_O2 --> -0.8025 enot and delr_Cl --> 0.7864 enot and delr_O2 --> -0.7825 delr_O2 and delr_Cl --> -0.7817 enot_O2 and ss_O2 --> 0.7535 delr_O2 and ss_O2 --> 0.7259 enot_O2 and delr_Cl --> -0.7080 ss and enot_O2 --> -0.6872 enot and ss --> 0.6795 delr_O2 and ss_Cl --> -0.6271 delr and ss_Cl --> -0.6217 ss_O2 and enot_Cl --> -0.6173 ss and ss_Cl --> 0.5740 ss_O2 and ss_Cl --> -0.5640 enot and ss_O2 --> -0.5314 enot_Cl and ss_Cl --> 0.5264 ss and ss_O2 --> -0.5084 enot_O2 and ss_Cl --> -0.4750 ss_O2 and delr_Cl --> -0.4747 delr_Cl and ss_Cl --> 0.4701 delr and ss_O2 --> 0.4134 enot and delr --> 0.3090 enot and ss_Cl --> 0.2693 All other correlations are below 0.25 ===== Data set >>SA 162deglitch-merge<< ======================================== file: C:\Program Files\Ifeffit\horae\stash\artemis.project.2\chi_data\SA_162deglitch-merge.chi title lines: Self absorption correction of 162deglitch-merge using method of Troger et al. + V K edge + Formula=H24.75 C8.25 O21.48 Si12.125 Cl4.7 V1.48 Merge in e space of: ** D:/200600603/Barnes-lab/EXAFS/NSLS/EXAFS/MYL-JULY-2006/all-VOCl3/162-Me2SiCl2+V5/162.001 ** D:/200600603/Barnes-lab/EXAFS/NSLS/EXAFS/MYL-JULY-2006/all-VOCl3/162-Me2SiCl2+V5/162.002 ** D:/200600603/Barnes-lab/EXAFS/NSLS/EXAFS/MYL-JULY-2006/all-VOCl3/162-Me2SiCl2+V5/162.003 k-range = 2.388 - 15.000 dk = 2.000 k-window = hanning k-weight = 2 R-range = 1.200 - 3.000 dR = 0.200 R-window = hanning fitting space = R background function = none phase correction = none R-factor for this data set = 0.01256 ===== Paths used to fit SA 162deglitch-merge FEFF1: Path 1: [O] .. feff = C:\Program Files\Ifeffit\horae\stash\artemis.project.2\data0.feff1\feff0001.dat id = reff= 1.6819, nlegs= 2, path= V<->O label = r = 1.840746 degen = 1.000000 s02 = 0.930000 e0 = 17.199906 dr = 0.158846 ss2 = -0.002272 3rd = 0.000000 4th = 0.000000 ei = 0.000000 FEFF1: Path 2: [O] .. feff = C:\Program Files\Ifeffit\horae\stash\artemis.project.2\data0.feff1\feff0002.dat id = reff= 1.8269, nlegs= 2, path= V<->O label = r = 1.605418 degen = 1.000000 s02 = 0.930000 e0 = -11.038494 dr = -0.221482 ss2 = 0.002756 3rd = 0.000000 4th = 0.000000 ei = 0.000000 FEFF1: Path 3: [Cl] .. feff = C:\Program Files\Ifeffit\horae\stash\artemis.project.2\data0.feff1\feff0003.dat id = reff= 2.1121, nlegs= 2, path= V<->Cl label = r = 2.100277 degen = 1.000000 s02 = 1.860000 e0 = -16.002670 dr = -0.011823 ss2 = 0.001647 3rd = 0.000000 4th = 0.000000 ei = 0.000000

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Athena and Artemis reference
by IONESCU, Mihail 02 May '07

02 May '07

Dear Bruce, What reference we can give in our papers for using Athena and Artemis packages, which you guys have been provided so generously to the user community? Thanks, Mihail ----------------------------------------------------------------- Dr Mihail Ionescu Senior Research Scientist Ion Beam Accelerator Applications Australian Nuclear Science and Technology Organisation ANSTO Bld. 53, New Illawarra Rd, Lucas Heights, NSW 2234 Australia PMB1, Menai, NSW 2234 Ph: +612 9717 3301 Fax: +612 9717 3257 -----------------------------------------------------------------

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Potential Postdoctoral Position in XAFS
by Bare, Simon R 30 Apr '07

30 Apr '07

POSTDOCTORAL POSITION in XAFS and XRD UOP LLC There is a potential opening for a postdoctoral position in synchrotron radiation research of catalysts and adsorbents with UOP LLC. The successful candidate with work with UOP LLC research scientists and will support UOP LLC exploratory and fundamental industrial research activities primarily at the Advanced Photon Source (APS) at Argonne National Laboratory. UOP LLC, a Honeywell Company, located in northwest suburban Chicago, is an international leader in technology, products, and services for the petroleum processing and separation industries (www.uop.com <http://www.uop.com/> ). The successful candidate will participate in all aspects of experiments related to operating a beamline, collecting, analyzing and interpreting the data. This position requires expertise in techniques of XAFS (preferably with knowledge of Athena/Artemis or Iffeffit software) and XRD, together with hands-on experience with electronic control and measuring equipment and beamline components. A CV with publications list, and the names and addresses of two references, should be sent via e-mail to Dr. Simon Bare at: simon.bare(a)uop.com.

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sum path NAN?
by Mauro Rovezzi 27 Apr '07

27 Apr '07

Dear all, Do you have any idea of what means NAN (Not A Number?) in "sum path" Ifeffit output during the fit? I've already posted this issue in a post dated 2006/10/04 and Bruce asked to me to give him something to reproduce this issue on his computer but this behavior is very unstable and I don't understand how to exactly reproduce it. I would like to know in your opinion what could bring a variable during the minimization process to NAN. In addition, what exactly means the four numbers visible in the "sum path #1 #2 #3 #4" output? It seems to me that, for each path, #2 = delr and #3 = sigma2, isn't it? M. -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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mailing list downtime
by Matt Newville 20 Apr '07

20 Apr '07

Hi Folks, Sorry to bother you with non-XAFS related mail, but I wanted to let you know that the Ifeffit mailing list, web pages (everything on http://cars9.uchicgo.edu, http://millenia.cars.aps.anl.gov, and http://xafs.org) will be unavailable tomorrow (Apr 21), starting around 6am Central Daylight Time (11am UTC) and lasting for around 12 hours. This is due to a scheduled complete power outage to the building housing the server and network equipment. I assume the network equipment and server will come back from the power outage just fine, but will be watching for signs of life. Mail sent to the mailing list during the down time should queue up until the server is back up, but I wouldn't want to guarantee that mail won't get bounced over the weekend. Sorry for the inconvenience, --Matt

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Several Questions
by Edward L. Kunkes 20 Apr '07

20 Apr '07

Hello everyone, I am currently using IFEFFIT to fit LIII edge data collected for Pt, Re and PtRe bi-metallic Nan particles supported on carbon, and I have several questions: 1. I get an So2 value of 0.54 from a first coordination shell fit on Re-foil (this So2 value also seems to work when fitting NH4ReO4-) Has anyone ever worked with Re before and gotten a similar value for So2 ? 2. I model the path for the a single coordination shell as 6 octahedrally arranged nearest neighbor atoms surrounding the absorber atom at a distance equal to that of inter -atomic spacing in the metal. When comparing the IFEFFIT predicted EXAFS for this model to one that is generated by using the first path from a crystallographic model, the two seem slightly different. The nanoparticles are very small (amorphous to XRD), and probably consist of a disordered phase, so I cannot assign a crystal structure. What should I do in this case? 3. I often get high correlations the coordination number and ss, or delEo and dR (the correlations are ~0.8). Using multiple k-weights doesn’t decrease the correlations. What is an acceptable value for these correlations? Thank you very much for taking the time to answer my questions -Ed Kunkes

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Re: [Ifeffit] Structures with multiple crystallographic sites
by Vadim G Palshin 20 Apr '07

20 Apr '07

Matt, Bruce - thank you! I believe I found the problem - Artemis does seem to choke even on 200 paths, especially with the "fit background" option on. At least it does on my office PC - relatively old and weak machine, will start begging for a new one shortly. Sometimes it would generate a long error message starting with "use of uninitialized value in abs at artemis line 12984."; sometimes there is no error message but results would look really strange. Had me so confused that I started to doubt my fitting method. I have since trimmed down the number of paths and variables to a minimum (didn't need that many anyway), and the problem seems to be solved. Thanks again for your responses, gentlemen! Vadim.

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