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

orbital configuration (FEFF8)
by Dream Dream 01 Jul '09

01 Jul '09

Hi everyone,I would like to calculate K-edge of oxygen XANES spectrum for CdO film. I attached my feff.inp file to this e-mail. When I check log1.dat file I observe next information: "... Electronic configuration iph il N_el 0 0 1.953 //comment: 0-centr.atom (O) 0 1 5.159 0 2 0.040 0 3 0.000 1 0 0.723 //comment: 1-Cd 1 1 0.711 1 2 10.149 1 3 0.000 2 0 1.921 //comment: 2-O 2 1 4.443 2 2 0.052 2 3 0.000 mu_new= -5.168 Charge transfer: iph charge(iph) 0 -0.152 1 0.417 2 -0.417 Done with module 1: potentials." As is well known, orbital configuration for Cd and O is: 4d10 5s2 and 1s2 2s2 2p4, respectively. I think that obtained results for Cd differ much according to presented orbital configuration (s,p). So, my question is: do there exist some possibilities to change something in my feff.inp file to improve the results? Best regards, Iraida.

1 0

problem with Athena's E0 !
by Arezki, Bahia 01 Jul '09

01 Jul '09

Hi all, I am using Athena (version: 08.058) to study the changes in the XANES profiles as a function of temperature of an organometallic compound containing Fe. I have a problem with the E0 value suggested by Athena : I noticed that it is not taking the same maximum in the first derivative. I am sending 2 examples of xanes taken at RT ( E0 guessed is 1722.8 eV ) and 10 K (1727.3 eV !), can any one help me please to solve this problem ? should I force athena to take the first maximum at 1722 eV ? I tough that my spectra have been properly calibrated: I first calibrated the iron foil -reference channel (E0=1712 eV) of a sample xanes and then I aligned the rest of the reference channels to that one. I though this was enough to calibrate my data. can you please tell me if my data processing is correct? I need to be sure about the E0 value in order to know the correct shift of the different xanes features as a function of temperature. Also, with a wrong E0 the normalization is not correct...did I miss an important step? I am having hard time with these basic questions...before using linear combination analysis and peak fitting analysis. Of course I have already looked in the IFFEFIT archive, but I did not find such problem. I only found a question about a wrong E0 because taken before the edge which is not my case. Thanks so much for your time, Bahia

4 7

Re: [Ifeffit] plotting anotation
by Bruce Ravel 30 Jun '09

30 Jun '09

Hi Dr. Matsuura, I am answering CCing this email to the Ifeffit Mailing List http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ which is the most appropriate forum for asking questions about the software. If you have not yet joined the mailing list, we encourage you to do so. I have also taken the liberty of converting the image file you attached into a format that everyone will be able to view. On Tuesday 30 June 2009 02:49:51 am you wrote: > Dear Bruce Ravel > > I'm a beginner of IFEFFIT. I'm pleased if you could ask following > questions about plotting in Artemis. > > 1) In a plotted figure as attached, annotation shows "2/path #". What > does it mean letter" 2". Presumably, you have more than one Feff calculation in your Artemis project, one of which still has its default name of "Feff2". To save horizontal space in the legend of the plot, I have Artemis drop the ltters "Feff". So, that legend entry means "Path N from Feff calculation 2". > 2) In the plotted figure attached, the sum of each path constituent is > not equal to fitting data. The reason of why. In Ifeffit, we use a complex Fourier transform to convert chi(k) to chi(R), thus chi(R) is a complex function. When the fit is evaluated, the real part of the theoretical chi(R) is compared to the real part of the data chi(R) and the imaginary part is compared to the imaginary part. You have plotted the magnitude of this complex function. You should not expect the sum of the moduli of the paths to equal the modulus of the sum of the paths. For a complex function, summation and mudulus are not commutative operations. B > > > > *************************************************************************** >* ****************** > > Metallic Glass Inorganic Materials Joinning Technology Development > > Institute for Materials Research, Tohoku University,Sendai, 980-8577,Japan > > Dr. Makoto Matsuura > > e-mail:m_matsuura@imr.tohoku.ac.jp > > *************************************************************************** >* ******************* -- 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/~ravel/software/exafs/

1 0

Fwd: Follow-up on your Athena issue
by Bruce Ravel 24 Jun '09

24 Jun '09

Gautier, First off: USE THE MAILING LIST! That's what it's there for. Why ask two people for help when you can ask hundreds? As you say, you are not the first to see this behavior, but I am not among those who have witnessed this. It is, of course, hard for me to troubleshoot a problem that I have never seen and don't know how to reproduce. The only helpful thing that comes to mind is to ask if there are any non-lower-ascii characters in the path either to the folder where Ifeffit is installed or to the folder where your data lives. At some point in the last couple years, I thought I had fixed the issues with nono-lower-ascii characters -- but who knows? Perhaps you keep your data in folder called "données" or "データ". If so, try installing Ifeffit in a place with only lower-ascii characters and do the same with your data. No guarantees, but it is something to try. B ---------- Forwarded Message ---------- Subject: Follow-up on your Athena issue Date: Wednesday 24 June 2009 From: Gautier Landrot <landrot(a)udel.edu> To: n.thammajak(a)gmail.com Dear Dr. Thammajak: I noticed on the Ifeffit email list that you posted last year a message about a problem you had on Athena. I currently do have the same problem with my athena, the symptoms I have are the same than those described in your post: 1) Any single XAFS spectrum, which could be opened with Athena before the problem occurred, cannot be opened anymore. Only a message saying "you have not used any memory yet" appears at the bottom of the Athena Window. Oddly, old saved project files can still be opened. Then, when the data is opened from these old projects, new project cannot be saved (nothing happens when I try to save a project). Data files are not corrupted or have strange format, since the files could be opened before the problem occurred. Also I can open the data with Athena installed on other PCs without any problem. 2) The main Athena window won't close. The only way to close that window is to force quit the program. 3) I checked the command rpompt window, and ran Athena, as Bruce Ravel suggested in his reply. A message says "Ifeffit checked for updates recently. Your version of Ifeffit is up to date". That's it. No error message obviously... 4) I reinstalled both Athena and Windows XP, but the problem still occurs. I don't think anybody from the Ifeffit email list found the source of your issue. Is your Athena working now? If yes, have you figured what was the problem? Thanks a lot, Gautier ----------- Gautier Landrot graduate student University of Delaware Plant and Soil Sc. Dept. Environmental Soil Chemistry Group 152 Townsend Hall Newark, DE 19711 (302)831-1230 http://ag.udel.edu/SoilChem/landrot.html ------------------------------------------------------- -- 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/~ravel/software/exafs/

1 0

Artemis multiple edge refinement problem
by alessandro di domenico 24 Jun '09

24 Jun '09

Hello to everyone; I'm a master thesist student in physics and I'mdoing a XAS analysis on bimetallic nanoparticles. my problem is that when I try to do a refinement on two different edges (K-Pd and L3-Au) Artemis changes one of the experimental data-set. Say that I have the data set for the K-edge of Pd and L3-edge of Au (which are plotted correctly); after the fit one of the two data set are plotted different. it seems that experimental data have been modified.... I don't know what to do about it; maybe I'm doing something wrong but unfortunately there isn't a complete guide to artemis . On the internet i have found some pdf which deals with the argument but don't focus on the procedure that one has to do in the program. Has someone ever had this problem, and if not can someone suggest me a "tutorial" on multiple edge refinement with artemis that I can follow step by step? Thank you alessandro

2 2

Re: [Ifeffit] Edge step
by Eugenio Otal 24 Jun '09

24 Jun '09

Bruce, I supposed the answer would be a little inconvenient truth. I will follow your wise words. Thanks, euG Eugenio, I am afraid that the question, as posed, is somewhat unanswerable. Careful alignment (preferably to a reference) is essential and you should take care to use the same parameters for every data set. I don't know how to advise you about "rightness", but consistency is certainly a must-do. If you are looking at subtle changes in the XANES features, you might consider turning off the "flattening" display trick that Athena uses for displaying XANES data. HTH, B

1 0

Re: [Ifeffit] Interpolating in feff - the Lead Titanate example
by Matt Newville 22 Jun '09

22 Jun '09

Hi Joseph, On Mon, Jun 22, 2009 at 8:15 PM, joseph washington<jswashin(a)ncsu.edu> wrote: > Hi Matt, > Thanks for your reply. I actually did not diliberately modify the > intermediate FEFF files. I think you should probably post the input file. > Up to this point, I beleive that I've been > following Bruce's example consistently. Its only when I noticed that the > path lengths were showing up differently that I started opening feff files. Which example is that? > Furthermore, it may be that this is just a bug because if I import the > "misbehaving" path into the list of paths for fitting in Artemis, it then > shows the correct path length there. So wierd - it says it is 5.9211 in > feff2019.dat but it says its 5.9179 when you import it for fitting. Yeah, I agree...that looks like a problem. --Matt

1 0

Re: [Ifeffit] Primitive unit cell from .cif file
by joshua jason kas 22 Jun '09

22 Jun '09

Thanks everyone for your suggestions! I have tried the following things. I used atoms (webATOMS) to generate a p1.inp file using diamond as an example, but this gives me the conventional cell with 8 atoms in it instead of the 2 atom primitive cell. Am I doing something wrong? The input file came from the atoms database and the output is as follows: * * "F d -3 m" appears in the International Tables with * multiple choices of origin. If the atoms list seems wrong, you * should use a shift vector of: * -0.125, -0.125, -0.125 * * ! This p1.inp file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = name: diamond title = formula: C title = sites: C1 title = refer1: Kittel, ISSP title = refer2: title = schoen: title = notes1: diamond structure space p 1 ! original space group: F d -3 m a = 3.5670 b = 3.5670 c = 3.5670 alpha = 90.0 beta = 90.0 gamma = 90.0 core = C1_1 edge = K rmax = 6.0 atoms ! elem x y z tag occ C 0.12500 0.12500 0.12500 C1_1 1 C 0.12500 0.62500 0.62500 C1_2 1 C 0.62500 0.12500 0.62500 C1_3 1 C 0.62500 0.62500 0.12500 C1_4 1 C 0.87500 0.37500 0.37500 C1_5 1 C 0.87500 0.87500 0.87500 C1_6 1 C 0.37500 0.37500 0.87500 C1_7 1 C 0.37500 0.87500 0.37500 C1_8 1 I also tried the Mercury demo, but all editing features are disabled. I will try Diamond now. Just to give some motivation here, I am working with abinit (along with feff) to produce optical spectra. If I use a conventional cell, the calculations become much more time consuming, so ideally I want to use a primitive cell. Thanks again for all your help! Josh > Hi Josh, > You may try Diamond Demo version which is free. > > http://www.crystalimpact.com/diamond/download.htm I will give this a try. > > Hi Josh, > > If I understand your question, I think that Atoms does what you want. Running the command line tool as "atoms -p" turns the attached cif file into the attached "p1.inp" file. You can do the same thing inside of Artemis using "write special output" in the Theory menu. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at Brookhaven National Laboratory > Building 535A > Upton NY, 11973 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of joshua jason kas > Sent: Wed 6/17/2009 2:16 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Primitive unit cell from .cif file > > Hi everyone, > I was wondering if there is a simple (free) utility for producing a > primitive cell (not conventional) from an asymmetric cell and space group. > Basically, I want to be able to easily go from a crystallographic > information file to a primitive unit cell. I know that there are ways to > do this within applications like material studio, but these are expensive. > Any help would be appreciated. > Thanks, > Josh Kas > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

4 3

Edge step
by Eugenio Otal 22 Jun '09

22 Jun '09

Hi, I am looking for some small differences in XANES spectra and want to know how to set the edge step to a "right" value. The differences are around 2 eV shift and a change in the edge step is critical. Thanks euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

2 1

problem with E0 (enot) parameters
by Zajac, Dariusz A. 22 Jun '09

22 Jun '09

Hi all, can anybody help me and send some link about problems with enot in Artemis? in google, tutorials I couldn't find any help. Of course are few posts about delr or ss parameters, but enot is somehow omited (or I can not find it...) the problem is with fiting K4W(CN)8*2H2O at W:L3 edge. fit and others parameters looks ok, except enot for C and N, where both are around 12 and don't want to fit to other values... thanks darek ------------------------------------------------------------------------ dr. Zajac Dariusz A. Deutsches Elektronen-Synchrotron -Hasylab phone: +49-40-8998-2932 Notkestr. 85 fax: +49-40-8998-2787 22607 Hamburg e-mail: dariusz.zajac(a)desy.de Germany ------------------------------------------------------------------------

6 15