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

Exporting derivative data
by Paul Bingham 31 May '10

31 May '10

Hi, I wonder if you can help: I'm using Athena to process some XANES data and wish to export the derivative data so that I can use a package such as Excel to prepare the data for publication. However, the derivative data that is presented visually in the graphics window is a much cleaner, smoother data set than the one I get when I export it in either deriv Mu(E) or deriv Norm(E). I tried the smoothing option in Data-Smooth mu(E) with 3 iterations and again with 10 iterations on the interpolative smoothing. Both gave far noisier data than the data shown in the Graphics window. Please can you tell me how to get exported derivative data that will be (more or less) the same as that shown in the graphics window? Basically I' hoping for WYSIWYG if that's possible? Any thoughts or suggestions would be very welcome and thanks for your time. -- Dr. Paul Bingham Postdoctoral Research Associate Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham(a)sheffield.ac.uk Direct Line: (0114) 2225473

4 3

the use of constraints
by Kellie Aldi 28 May '10

28 May '10

Hi, I have a question on the use of constraints and restraints in EXAFS data fitting. I am using SixPack to build a model for the EXAFS of some synthetic layered transition metal (TM) oxides with relatively large amounts of layer vacancies. I am refining the occupancy of the layer TM site, from which I can determine the amount of layer vacancies. I want to include a parameter in this model that refines the number of these vacancies that are capped by interlayer TM (something that can happen in these structures), but I am having difficulty in deciding a responsible way to define the parameters of this variable. I am modifying the intensity of the interlayer TM scattering paths with a parameter fcap = (1-focc)*percap where focc is the refined occupancy of the layer TM site, and percap is the percentage of vacancies, "1-focc", that are capped by interlayer TM. However, just letting percap float, the value goes greater that 1... which, as a percentage, does not make much sense physically in my model. So I want to keep the value of this between 0 and 1. I have tried what was suggested on the IFEFFIT frequently asked questions page regarding constraints and restraints. I don't feel comfortable simply using a constraint and forcing the value to be between 0 and 1 using the suggested min/max idiom. I like better the idea of penalizing a fit when percap is outside of a defined range and thus "encouraging" the fit to settle percap somewhere inside this range. But in trying to use the restraint idea, including the fix suggested by Matt Newville for only penalizing the fit outside of the min/max range, percap still goes slightly above 1 (about 1.02) and in my results I get a value for the "penalty" that I am unsure how to interpret. Can this value be used to understand why the restraint still allows the value of percap to be outside of the defined "ideal" range? I am trying to understand how the restraint that Matt Newville defined in the link in the restraints/constraints FAQ works, but I am relatively new to EXAFS modeling and thus shaky on my skills at defining these parameters and knowing how certain math functions can be used. Are there any other help sections or guides that might address the use of such restraints? Or any suggestions on how to re-define this restraint? I would greatly appreciate any suggestions/input! Thanks, Kellie Aldi

3 2

athena an widows 7
by Matthias Bauer 28 May '10

28 May '10

Dear all, i have a problem with running athena on windows 7. I can open the program, but when I try to open a file, just by clicking "open" the interfaces closes and only the graph window remains open. Does anyone encounter the same problem or even has a solution? Many thanks, matthias Dr. Matthias Bauer Inst. f. Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) - Campus Süd Engesserstrasse 18 76131 Karlsruhe email: matthias.bauer(a)kit.edu phone: +49 721 608 4320

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athena an windows 7
by Matthias Bauer 28 May '10

28 May '10

Dear all, i have a problem with running athena on windows 7. I can open the program, but when I try to open a file, just by clicking "open" the interfaces closes and only the graph window remains open. Does anyone encounter the same problem or even has a solution? Many thanks, matthias Dr. Matthias Bauer Karlsruhe Institute of Technologie - Campus Süd Inst. für Technische Chemie und Polymerchemie Engesserstrasse 18 76128 Karlsruhe email: matthias.bauer(a)kit.edu phone: 0049 721 608 4320

1 0

fitting
by mohamed sobhy 26 May '10

26 May '10

----- Forwarded Message ---- From: mohamed sobhy <bakhshwan1981(a)yahoo.com> To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Thu, May 20, 2010 4:14:18 PM Subject: [Ifeffit] fitting 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 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

co-ordination number for given shell
by Jatinkumar Rana 25 May '10

25 May '10

Dear Ifeffit users, I am working on EXAFS analysis of a mineral Arrojadite. It has very very complicated crystal structure. I have measured EXAFS in fluoresence mode on Mn and Fe edge. The mineral contains Mn and Fe as divalent cations distributed over 7 different atomic positions e.g. 3 different Mn atomic position (Mn1, Mn2 and Mn3) and 4 different Fe position (Fe4, Fe5, Fe6, Fe7). My question is : How do i know that How many paths should i take into consideration to fit 1st shell, 2nd shell and 3rd shell.. ?? I have rough idea that the first shell is octahedral Oxygen ions. I tried fitting first shell taking into account first 6 Oxygen paths and it gave reasonably good fit to first shell. But the confusion is how to consider paths for 2nd Shell, 3rd shell....etc. Your feedback is highly appreciated. P.S. I have attached artemis file (both Fe and Mn edge) with this mail for your reference. Best regards, Jatin

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Re: [Ifeffit] calibrating and aligning samples for LCF
by Monson, Todd 24 May '10

24 May '10

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(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: Saturday, May 22, 2010 11:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 87, Issue 28 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. XANES and DOS calculations (Joanna Czapla) ---------------------------------------------------------------------- Message: 1 Date: Sat, 22 May 2010 17:21:41 +0200 From: Joanna Czapla <czapla.asia(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] XANES and DOS calculations Message-ID: <AANLkTimVJVPZoDKuU0NW8GEr9wdrrOI7OyfaAeOxSzMN(a)mail.gmail.com> 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 <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. fitting (mohamed sobhy) > ? 2. update error in Windows 7 (pkraal(a)geo.uu.nl) ? 3. Re: update > error in Windows 7 (Laurent Menard) ? 4. Re: update error in Windows 7 > (Bryan Gauntt) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 May 2010 14:14:18 -0700 (PDT) > From: mohamed sobhy <bakhshwan1981(a)yahoo.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] fitting > Message-ID: <725080.73390.qm(a)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 > > > > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201005 > 20/4d94da82/attachment.html> > > ------------------------------ > > Message: 2 > Date: Fri, 21 May 2010 12:09:24 +0200 > From: pkraal(a)geo.uu.nl > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] update error in Windows 7 > Message-ID: > ? ? ? ?<3ded096a7acb18ecc34d49196967ce21.squirrel(a)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. > > > > ------------------------------ > > Message: 3 > Date: Fri, 21 May 2010 09:23:38 -0400 > From: "Laurent Menard" <menard(a)email.unc.edu> > To: "'XAFS Analysis using Ifeffit'" > ? ? ? ?<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] update error in Windows 7 > Message-ID: <01cb01caf8e8$d2cc0e90$78642bb0$(a)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(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > pkraal(a)geo.uu.nl > Sent: Friday, May 21, 2010 6:09 AM > To: ifeffit(a)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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 4 > Date: Fri, 21 May 2010 09:26:01 -0400 > From: Bryan Gauntt <bdg160(a)psu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] update error in Windows 7 > Message-ID: > ? ? ? ?<AANLkTikFXm8cspcd65cHnFcT7R9MN78Gf8gjwBAY6oWB(a)mail.gmail.com> > 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, ?<pkraal(a)geo.uu.nl> 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(a)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 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 87, Issue 27 > *************************************** > ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 87, Issue 28 ***************************************

2 1

XANES and DOS calculations
by Joanna Czapla 22 May '10

22 May '10

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 <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. fitting (mohamed sobhy) > 2. update error in Windows 7 (pkraal(a)geo.uu.nl) > 3. Re: update error in Windows 7 (Laurent Menard) > 4. Re: update error in Windows 7 (Bryan Gauntt) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 May 2010 14:14:18 -0700 (PDT) > From: mohamed sobhy <bakhshwan1981(a)yahoo.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] fitting > Message-ID: <725080.73390.qm(a)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 > > > >

1 0

update error in Windows 7
by pkraal＠geo.uu.nl 21 May '10

21 May '10

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.

3 2

fitting
by mohamed sobhy 20 May '10

20 May '10

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

1 0