If you trust that the calibration did not change between when the nanoparticles and the Fe foils were run, then all you need to do is to align the spectra so that the edge for Fe comes out at the same place as it did for the references. The tricky bit is that if you have references from somewhere else, you may not know what the energy basis was. Some people take the Fe K-edge to be at 7112eV, some at 7110.75 (Kraft's paper), etc. If all reference spectra came from the same source, it may be reasonable to assume that they all had the same energy reference, so you could do your LCF with an e0 shift as an additional parameter. Now, suppose you don't trust the calibration. There may be a monochromator glitch at a convenient energy. These tend not to move very much, so if you have the raw data for Fe foil, you can back out the energy of the glitch, then use that to calibrate the unknown, provided the data for it was taken at the same beamline as the Fe, and not too long before or after. We have a set of reference spectra, most of which were collected at 10.3.2, and done with consistent calibration: http://xraysweb.lbl.gov/uxas/Databases/Overview.htm . mam On 5/24/2010 2:39 PM, Monson, Todd wrote:

I have XAFS data from several Fe nanoparticle samples as well as some Fe and Fe oxide standards collected during two different months. I would like to fit the Fe nanoparticle data using LCF and the Fe & Fe oxide standards. Data collected from Fe foil during the two months have been calibrated in energy. What is the best way to calibrate or align the other nanoparticle samples and standards collected during both of these sessions prior to doing LCF?

Thanks,

Todd

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: Saturday, May 22, 2010 11:00 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 87, Issue 28

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Today's Topics:

1. XANES and DOS calculations (Joanna Czapla)

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Message: 1 Date: Sat, 22 May 2010 17:21:41 +0200 From: Joanna Czapla To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] XANES and DOS calculations Message-ID: Content-Type: text/plain; charset=windows-1252

Dear Feff Users, first of all I must admit that I am a total beginner and probably there are some things which I don?t understand very well. I need to make XANES and DOS calculations for K-edge of sulfur and then compare them with experiment. I use feff 8.4. First, I started from inorganic compounds such as CdS. I generated feff.inp file in ATOMS and first run feff with default values (generated by ATOMS). The fit wasn?t perfect so I started to change parameters-FMS and SCF but there was so significant improvement. I can only add that others fit are even worse. My question is which parameter I should change or which card should I add to make XANES calculations better? Maybe you can recommend any paper?

The second question is about DOS calculations. I took the pDOS functions for each atom, set Fermi level from ldosNN files, but the main peaks are below this level and I don?t have any correspondence with XANES spectrum. For other compounds I have the same problem. Should I add any extra shift?

I will be grateful for your advice.

Regards Joanna Czapla

I add the original feff.inp file generated by ATOMS: * This feff8 input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) * Atoms written by and copyright (c) Bruce Ravel, 1998-2001

TITLE name: CdS (greenockite) (cubic zinc sulfide structure) TITLE formula: CdS TITLE sites: Cd1,S1 TITLE refer1: wyckoff 1,III,110 TITLE refer2: TITLE schoen: TITLE notes1: cubic zinc sulfide structure

* S K edge energy = 2472.0 eV EDGE K S02 1.0

* pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0

*** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0

*** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0

*** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0

*** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 5.54240 0

*** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1

*** for EXAFS: RMAX 8.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20

POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 16 S 2 2 0.001 1 48 Cd 3 3 4 2 16 S 2 2 4

ATOMS * this list contains 87 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 S1 0.00000 0 -1.45450 1.45450 1.45450 1 Cd1 2.51927 1 1.45450 -1.45450 1.45450 1 Cd1 2.51927 2 1.45450 1.45450 -1.45450 1 Cd1 2.51927 3 -1.45450 -1.45450 -1.45450 1 Cd1 2.51927 4 2.90900 2.90900 0.00000 2 S1 4.11395 5 -2.90900 2.90900 0.00000 2 S1 4.11395 6 2.90900 -2.90900 0.00000 2 S1 4.11395 7 -2.90900 -2.90900 0.00000 2 S1 4.11395 8 2.90900 0.00000 2.90900 2 S1 4.11395 9 -2.90900 0.00000 2.90900 2 S1 4.11395 10 0.00000 2.90900 2.90900 2 S1 4.11395 11 0.00000 -2.90900 2.90900 2 S1 4.11395 12 2.90900 0.00000 -2.90900 2 S1 4.11395 13 -2.90900 0.00000 -2.90900 2 S1 4.11395 14 0.00000 2.90900 -2.90900 2 S1 4.11395 15 0.00000 -2.90900 -2.90900 2 S1 4.11395 16 4.36350 1.45450 1.45450 1 Cd1 4.82403 17 1.45450 4.36350 1.45450 1 Cd1 4.82403 18 -4.36350 -1.45450 1.45450 1 Cd1 4.82403 19 -1.45450 -4.36350 1.45450 1 Cd1 4.82403 20 1.45450 1.45450 4.36350 1 Cd1 4.82403 21 -1.45450 -1.45450 4.36350 1 Cd1 4.82403 22 -4.36350 1.45450 -1.45450 1 Cd1 4.82403 23 -1.45450 4.36350 -1.45450 1 Cd1 4.82403 24 4.36350 -1.45450 -1.45450 1 Cd1 4.82403 25 1.45450 -4.36350 -1.45450 1 Cd1 4.82403 26 -1.45450 1.45450 -4.36350 1 Cd1 4.82403 27 1.45450 -1.45450 -4.36350 1 Cd1 4.82403 28 5.81800 0.00000 0.00000 2 S1 5.81800 29 -5.81800 0.00000 0.00000 2 S1 5.81800 30 0.00000 5.81800 0.00000 2 S1 5.81800 31 0.00000 -5.81800 0.00000 2 S1 5.81800 32 0.00000 0.00000 5.81800 2 S1 5.81800 33 0.00000 0.00000 -5.81800 2 S1 5.81800 34 -4.36350 4.36350 1.45450 1 Cd1 6.34002 35 4.36350 -4.36350 1.45450 1 Cd1 6.34002 36 -4.36350 1.45450 4.36350 1 Cd1 6.34002 37 -1.45450 4.36350 4.36350 1 Cd1 6.34002 38 4.36350 -1.45450 4.36350 1 Cd1 6.34002 39 1.45450 -4.36350 4.36350 1 Cd1 6.34002 40 4.36350 4.36350 -1.45450 1 Cd1 6.34002 41 -4.36350 -4.36350 -1.45450 1 Cd1 6.34002 42 4.36350 1.45450 -4.36350 1 Cd1 6.34002 43 1.45450 4.36350 -4.36350 1 Cd1 6.34002 44 -4.36350 -1.45450 -4.36350 1 Cd1 6.34002 45 -1.45450 -4.36350 -4.36350 1 Cd1 6.34002 46 5.81800 2.90900 2.90900 2 S1 7.12557 47 -5.81800 2.90900 2.90900 2 S1 7.12557 48 2.90900 5.81800 2.90900 2 S1 7.12557 49 -2.90900 5.81800 2.90900 2 S1 7.12557 50 5.81800 -2.90900 2.90900 2 S1 7.12557 51 -5.81800 -2.90900 2.90900 2 S1 7.12557 52 2.90900 -5.81800 2.90900 2 S1 7.12557 53 -2.90900 -5.81800 2.90900 2 S1 7.12557 54 2.90900 2.90900 5.81800 2 S1 7.12557 55 -2.90900 2.90900 5.81800 2 S1 7.12557 56 2.90900 -2.90900 5.81800 2 S1 7.12557 57 -2.90900 -2.90900 5.81800 2 S1 7.12557 58 5.81800 2.90900 -2.90900 2 S1 7.12557 59 -5.81800 2.90900 -2.90900 2 S1 7.12557 60 2.90900 5.81800 -2.90900 2 S1 7.12557 61 -2.90900 5.81800 -2.90900 2 S1 7.12557 62 5.81800 -2.90900 -2.90900 2 S1 7.12557 63 -5.81800 -2.90900 -2.90900 2 S1 7.12557 64 2.90900 -5.81800 -2.90900 2 S1 7.12557 65 -2.90900 -5.81800 -2.90900 2 S1 7.12557 66 2.90900 2.90900 -5.81800 2 S1 7.12557 67 -2.90900 2.90900 -5.81800 2 S1 7.12557 68 2.90900 -2.90900 -5.81800 2 S1 7.12557 69 -2.90900 -2.90900 -5.81800 2 S1 7.12557 70 -7.27250 1.45450 1.45450 1 Cd1 7.55780 71 -1.45450 7.27250 1.45450 1 Cd1 7.55780 72 7.27250 -1.45450 1.45450 1 Cd1 7.55780 73 1.45450 -7.27250 1.45450 1 Cd1 7.55780 74 4.36350 4.36350 4.36350 1 Cd1 7.55780 75 -4.36350 -4.36350 4.36350 1 Cd1 7.55780 76 -1.45450 1.45450 7.27250 1 Cd1 7.55780 77 1.45450 -1.45450 7.27250 1 Cd1 7.55780 78 7.27250 1.45450 -1.45450 1 Cd1 7.55780 79 1.45450 7.27250 -1.45450 1 Cd1 7.55780 80 -7.27250 -1.45450 -1.45450 1 Cd1 7.55780 81 -1.45450 -7.27250 -1.45450 1 Cd1 7.55780 82 -4.36350 4.36350 -4.36350 1 Cd1 7.55780 83 4.36350 -4.36350 -4.36350 1 Cd1 7.55780 84 1.45450 1.45450 -7.27250 1 Cd1 7.55780 85 -1.45450 -1.45450 -7.27250 1 Cd1 7.55780 86 END

2010/5/21 :

...

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When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..."

Today's Topics:

? 1. fitting (mohamed sobhy) ? 2. update error in Windows 7 (pkraal@geo.uu.nl) ? 3. Re: update error in Windows 7 (Laurent Menard) ? 4. Re: update error in Windows 7 (Bryan Gauntt)

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Message: 1 Date: Thu, 20 May 2010 14:14:18 -0700 (PDT) From: mohamed sobhy To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] fitting Message-ID: <725080.73390.qm@web50302.mail.re2.yahoo.com> Content-Type: text/plain; charset="us-ascii"

Dear all thanks for your help and explanation about the background I fitted my data after removing the background and in the attached file I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. So how can I get the right coordination number? How to improve the fitting of second shell? thanks

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Message: 2 Date: Fri, 21 May 2010 12:09:24 +0200 From: pkraal@geo.uu.nl To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] update error in Windows 7 Message-ID: ? ? ? ?<3ded096a7acb18ecc34d49196967ce21.squirrel@webmail.geo.uu.nl> Content-Type: text/plain;charset=iso-8859-1

Dear sir or madam,

I am using IFEFFIT on a Windows 7 system. When the runner informs that updates are available, I select to download and install them. Then, the first package is downloaded, but during expanding and installation of this package the update basically stops and the runner gives an error associated with access to bin/athena.exe. Windows 7 (like Vista pretty easily stressed when you try to change software) does not inform me that a program is trying to change the system or whatever, so I don't know what to do. Is there anybody out there with similar problems and maybe, even better, a solution?

Regards and many thanks,

Peter Kraal.

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Message: 3 Date: Fri, 21 May 2010 09:23:38 -0400 From: "Laurent Menard" To: "'XAFS Analysis using Ifeffit'" ? ? ? ? Subject: Re: [Ifeffit] update error in Windows 7 Message-ID: <01cb01caf8e8$d2cc0e90$78642bb0$@unc.edu> Content-Type: text/plain; ? ? ? charset="US-ASCII"

Peter,

You need to make sure you have permission in Windows to write to the IFEFFIT folder. ?If I remember correctly all you have to do is right click on the IFEFFIT folder, select Properties. ?Go to the Security Tab and then select the Edit button. ?Make sure that under Users all of the "allow" boxes are checked then click OK. ?IFEFFIT should install the updates the next time it checks for updates.

Regards, Laurent

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of pkraal@geo.uu.nl Sent: Friday, May 21, 2010 6:09 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] update error in Windows 7

Dear sir or madam,

I am using IFEFFIT on a Windows 7 system. When the runner informs that updates are available, I select to download and install them. Then, the first package is downloaded, but during expanding and installation of this package the update basically stops and the runner gives an error associated with access to bin/athena.exe. Windows 7 (like Vista pretty easily stressed when you try to change software) does not inform me that a program is trying to change the system or whatever, so I don't know what to do. Is there anybody out there with similar problems and maybe, even better, a solution?

Regards and many thanks,

Peter Kraal.

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Message: 4 Date: Fri, 21 May 2010 09:26:01 -0400 From: Bryan Gauntt To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] update error in Windows 7 Message-ID: ? ? ? ? Content-Type: text/plain; charset=ISO-8859-1

Dear Peter, I found that setting both Artemis and Athena to run in compatibility mode (XP Service Pack 3) did the trick for me. ?You can do this by locating the executables in the start menu and right clicking them. Select "properties" and then the "compatibility" tab. Under "compatibility mode" select the box next to "Run this program in compatibility mode," and then select Windows XP (Service Pack 3) from the drop-down list.

Best of luck, Bryan Gauntt

On Fri, May 21, 2010 at 6:09 AM, ? wrote:

...

Dear sir or madam,

I am using IFEFFIT on a Windows 7 system. When the runner informs that updates are available, I select to download and install them. Then, the first package is downloaded, but during expanding and installation of this package the update basically stops and the runner gives an error associated with access to bin/athena.exe. Windows 7 (like Vista pretty easily stressed when you try to change software) does not inform me that a program is trying to change the system or whatever, so I don't know what to do. Is there anybody out there with similar problems and maybe, even better, a solution?

Regards and many thanks,

Peter Kraal.

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Bryan D. Gauntt

PhD Candidate Department of Materials Science and Engineering 274 Materials Research Lab Penn State University (814) 574-2751

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