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

RE: [Ifeffit] N K-edge XANES, normalization parameters
by Barton, David (DG) 14 Nov '05

14 Nov '05

Peter, ATHENA is mainly written for EXAFS analysis, however...it is still quite useful for XANES analysis as well. I opened your project that you sent and there were a couple of obvious challenges with this dataset. First of all, you should read the section regarding Normalization in the ATHENA help POD if you haven't already. One useful feature in ATHENA is the ability to turn ON the Pre-edge and Post-edge plots. After looking at your two Plots in the file you sent it is obvious that the choice of the Post-edge region is quite poor for the dataset "merge21to27". The "Flattening" Normalization routine in Athena uses a Linear function for the pre-edge (Pre-edge Region) and a quadratic for the post-edge (Normalization Region). Flattening is the process of subtracting these two functions from your experimental dataset (subtracting pre-edge function at energies below Eo and subtracting the post-edge function above Eo) and then scaling the dataset to unity over the normalization range. Your dataset is a bit challenging because the pre-edge region has a limited range so that a when you fit a linear function to it, it crosses over your data set indicating that it is not a good representation of the sample background. I can't think of a quick workaround for this, but you may want to consider manually subtracting a linear function with a smaller slope from your raw dataset prior to opening in ATHENA and then adding a couple of points to the begin of the dataset that could be used for the pre-edge region in ATHENA to force a zero slope. Then you could look closer at your post-edge region (Normalization Range) to ensure the shape of the quadratic is reasonably fitting your dataset. At this point ATHENA only allows a linear pre-edge and a quadratic post-edge, however it does looks like Matt and Bruce are working on adding additional fitting functions to IFEFFIT and ATHENA. So if you cannot get a sufficient background normalization fitting with these functions! you will have to try some other tool. Finally, ATHENA likes to work in eV so you should adjust your energy scale, especially if you want to attempt to use CLNORM background subtraction. Hope this helps, Dave > -----Original Message----- > From: Peter Leinweber [mailto:peter.leinweber@uni-rostock.de] > Sent: Monday, November 14, 2005 3:25 PM > To: ATHENA Userlist > Cc: fan.walley(a)usask.ca > Subject: [Ifeffit] N K-edge XANES, normalization parameters > > > dear all, > i am a new XANES and ATHENA user. i didi N K-edge XANES of > soil samples. while feeling very good with data import, > deglitching, truncation, merging etc. i am insecure about > parameters for normalization. > in the attached project i did truncation of data before > 395900 (it is milli-eV), because these seem to be invalid, > and i set an E-shift of -900 sinc the beamline had -9.9 eV > off compared to the N K-edge of N2 gas. in this way i should > be right back on scale ? the i did set the pre-edge > parameters manually at start of the curve, and around 397000 > since non of the previously measured N standard substances > had edge steps below this value. > however, then i am insecure how to set the other parameters > for normalization properly. depending on how i play with the > parameters sometimes i get normalized spectra which look > pretty reasonable, sometimes the curves disappear completely > from the graphics window, and sometimes i get curves of a > shape never senn in the literature. is there easily > understandable advice for the setting of the normalization > parameters available; or can anybody more experienced check > my project and give me recommendations. thanks, peter > > Prof. Dr. Peter Leinweber > Institute for Land Use > Universitaet Rostock > D-18051 Rostock > > Present address: > Department of Soil Science > University of Saskatchewan > 51 Campus Drive > SK S7N 5A8 > Canada > > phone: 001-306-966-6866 > fax: 001-306-966-6881 >

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N K-edge XANES, normalization parameters
by Peter Leinweber 14 Nov '05

14 Nov '05

dear all, i am a new XANES and ATHENA user. i didi N K-edge XANES of soil samples. while feeling very good with data import, deglitching, truncation, merging etc. i am insecure about parameters for normalization. in the attached project i did truncation of data before 395900 (it is milli-eV), because these seem to be invalid, and i set an E-shift of -900 sinc the beamline had -9.9 eV off compared to the N K-edge of N2 gas. in this way i should be right back on scale ? the i did set the pre-edge parameters manually at start of the curve, and around 397000 since non of the previously measured N standard substances had edge steps below this value. however, then i am insecure how to set the other parameters for normalization properly. depending on how i play with the parameters sometimes i get normalized spectra which look pretty reasonable, sometimes the curves disappear completely from the graphics window, and sometimes i get curves of a shape never senn in the literature. is there easily understandable advice for the setting of the normalization parameters available; or can anybody more experienced check my project and give me recommendations. thanks, peter Prof. Dr. Peter Leinweber Institute for Land Use Universitaet Rostock D-18051 Rostock Present address: Department of Soil Science University of Saskatchewan 51 Campus Drive SK S7N 5A8 Canada phone: 001-306-966-6866 fax: 001-306-966-6881

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atoms and the alloys
by Mauro Rovezzi 13 Nov '05

13 Nov '05

Hi to all, I have noticed that Atoms fails to generate a correct "feff.inp" file in the case of alloys. For example, let's take the Ni_xCu_{1-x}, x=0.5, an fcc substitutional. If I put Ni as central atom and give 0.5 occupancy on the shared Cu-Ni site (0,0,0.5) the result is a normal Ni fcc without Cu. At the moment I modify my feff.inp by hand to simulate alloys, but maybe I'm just not using Atoms properly. If this is the case, it could be useful to insert your answer in the FAQ. Cheers, Mauro

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Re: [Ifeffit] doubts
by Feng Wang 12 Nov '05

12 Nov '05

Dear Bruce and Scott, I am a beginner of IFEFFIT, trying to follow Scott's example. In the ZnO DEMO PART 1, everything went well before doing the fit, however when I click the green button "Fit", I was told by the message: This parameter uses a name which has special meaning in Ifeffit: dr You must change this parameter name before attempting to fit. One common example of this sort is a variable named "dr1", which should be changed to something like "dr_1" or "drone". Could you or anyone direct me? I would appreciate that. Best regards, Feng > > I could write on and on about this topic, but I think it would be > fruitful for you to follow the example that Scott Calvin wrote up. > Look at: > > http://cars9.uchicago.edu/~ravel/software/contrib.html > > And download the ZnO example. This consists of a series of Artemis > project files. Scott wrote comments in the journals of each project > to walk you through the process of using Artemis to fit real data. I > think that it would be helpful to you to work through this example > carefully. I suspect that doing so will help to clear up some of your > confusion. > > If, after working through Scott's example, you still have questions -- > we on the mailing list will be glad to help you out. > > B >

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Re: [Ifeffit] doubts
by Feng Wang 09 Nov '05

09 Nov '05

Hi Carlo. Thanks a lot for the solution, it works. Best regards, Feng > On Wed, 9 Nov 2005, Feng Wang wrote: > > > Dear Bruce and Scott, > > > > I am a beginner of IFEFFIT, trying to follow Scott's example. In the ZnO DEMO > > PART 1, everything went well before doing the fit, however when I click the > > green button "Fit", I was told by the message: > > > > This parameter uses a name which has special meaning in Ifeffit: > > dr > > You must change this parameter name before attempting to fit. > > One common example of this sort is a variable named "dr1", which > > should be changed to something like "dr_1" or "drone". > > > > Could you or anyone direct me? I would appreciate that. > > > Dear Feng: > > Click to the Interpretation tab and select "Guess, Def, Set" in the > middle pane. YOu should see all the variables that are defined. My guess > is that you have "dr" instead of something like "delr". Change the name > to "delr" and then click on the individual paths and change any occurence > of "dr" to "delr". > > If you are working on Scott's example for ZnO, I am not sure how you got > "dr" as he uses "delr" in evrything as far as I recall. In fact, I just > looked at the tutorial myself and if I follow all the instructions, I get > the following variables in the "Guess, Def, Set" > amp > enot > delr > ss > > note that Scott's instructions are for an older version of Artemis and > there is not menu entry for loading a FEFF calculation, instead you need > to Open File, go into the FEFF subdirectory and select "feff.inp". > Artemis is smart enough to know that this is a calculation and asks how > many paths to import. > > hope this helps, > > Carlo > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Special Projects, Graduate College > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > Carlo.Segre(a)iit.edu http://www.iit.edu/~segre ================================== Feng Wang fwang(a)phys.ualberta.ca CW182 (Tel 492-5599) Electron Microscopy Group Department of Physics =========================================================

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doubts
by Marcos Eleoterio 09 Nov '05

09 Nov '05

good afternooon, My name is Marcos Eleotério, i am undergraduate in physics and i have a scholarship at Brazilian Synchroton Light Laboratory, nearly one month ago i start using the software Athena and Artemis, to analyse some X-ray absorption data that i have, to make my problem more easy to you understand i list below the steps that i use in those programs: 1) After a normalization of the data, i put the data in "Athena" turn on the options: "pre-edge line", "post-edge line" and then "normalized" (in fact i usually turn the option "flatten" on, in dispite of the fact that i don´t know what that means, what that means?), i save using the option "Save chi(k)" in "file". 2)Then i open the program "Artemis" and insert the data saved in the step "1)" in the column of the middle i click with the right button of the mouse and select the option "theory", "atoms" and insert the spatial group, unit cell parameter, and atomic location (here its important to say that the compound that i'm studying is LaCaMnRuO6 the measure of x-ray absorption was performed in the K-edge of the Mn, we are interested in Mn-O ligands so in "Artemis" i only put the data of the Mn and O, right?) 3)I click in the option "run atoms" for each atoms that i inserted the information, choosing 10 paths in each step, i click the in the option "run feff" for each atom that i inserted the information (again), after that, i click in "Fit" then appears in the screem the advise: "there is something wrong with your math expressions" (or something like that) i ignore that advise and go on, but the big problem is that the fit appears very poor! I have to say that the information that i use to insert the atomic position, unit cell parameters, was obtained from a Riteveld refinament, that i performed with the data from a cooper x-ray tube, do i need a data from a beam line, at synchroton? Do you have some idea of my problem? Have i make the correct steps? I'm sorry for my english, i will be very thankful if you answer my e-mail or give to me someone who can do it! REGARDS

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Re: [Ifeffit] Question with FL Database
by Marco Alsina 08 Nov '05

08 Nov '05

El Martes, 8 de Noviembre de 2005 13:14, Matt Newville escribió: > Yes, there are a few different formats of data in the Lytle > database. As far as I can tell, the files with > 'CUEDGE START STOP BEG FSCTS: ...' > do not include a "known" d-spacing or steps-per-degree, but > tend to use Si(111) (dspace = 1.9202). You didn't include the > rest of the file or say which file you're trying to use, so it's > impossible to tell what problem you're having. Well actually what I was trying to do was to obtain a meanigful value for motor step 168620 (CUEDGE, which I included in the header), and with d-space set to 1.92017 and step-per-degree equal to 8000 you get CUEDGE =8977 eV, so set(dspace=1.92017, stpdeg=8000) fixed my problem For further files what I needed was possible values for stpdeg, which you already give me. Thanks Matt and the community,and also thanks for the macro too! Regards, Marco

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new release of my codes (horae-057)
by Bruce Ravel 08 Nov '05

08 Nov '05

Hi folks, This morning I made a new release of the source code tarball for my codes as well as a new Windows updater. Matt and I finally have the update system organized well enough that I can actually release the source and the windows update on the same day. Yay! New tarballs are at SourceForge and on my web site. The Windows updater should run the next time you fire up one of the programs. Artemis and Hephaestus are unchanged. All the new stuff is in Athena (new version is 0.8.045). See http://cars9.uchicago.edu/iffwiki/HoraeVersion057 for details. Most of the work was on the linear combination fitting tool and some improvements to the scheme for importing data in unusual file formats. There are a few other new tidbits and several bug fixes as well. One change which will be immediately obvious is that I split the controls for background removal parameters into two groups. The division is more or less between the more and less often used parameters. There are buttons for switching the display between the two groups of parameters. You'll see what I mean when you fire up Athena. The linear combination fitting has several fixes for bugs that people mentioned after the last release as well as a few new features. The scheme for importing data in unusual formats merits its own page on the wiki, which I'll post soon. Enjoy, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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ATHENA: Encoder option missing?
by Norbert Weiher 05 Nov '05

05 Nov '05

Bruce, I just updated to the latest version of A&A. When I open a file it seems that the "encoder" option in the energy units is missing... Regards, Norbert -- Dr. rer. nat. Norbert Weiher (norbert.weiher(a)manchester.ac.uk) School of Chemical Engineering and Analytical Science Sackville Street, Manchester, M60 1QD - Phone: +44 161 306 4468

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WG: [Ifeffit] hephaestus
by Peter Leinweber 02 Nov '05

02 Nov '05

hello bruce, i am a new user of your software. when i load the programm the following shows up lower right: Emin -200 and Emax 800. when i load data they are plotted with proper x-axis. but when i did any modification the scaling of x-axis changes to invalid or in-comfortable values. i can fix it by modifying Emin and Emax but to get an axis of 395 to 410 eV i have to type Emin -400 and Emax 18000. is that o.k. ? another question: will you or will someone of your group attend the CLS user meeting here in saskatoon in november. there is interest of other newcomers like me to get introduced into ATHENA. perhaps some arrangement such as coverage of additional hotel costst for staying a day longer or so could be made. kind greetings, peter Prof. Dr. Peter Leinweber Institute for Land Use Universitaet Rostock D-18051 Rostock Present address: Department of Soil Science University of Saskatchewan 51 Campus Drive SK S7N 5A8 Canada phone: 001-306-966-6866 fax: 001-306-966-6881 ----- Originalnachricht ----- Von: Bruce Ravel <bravel(a)anl.gov> Datum: Mittwoch, November 2, 2005 5:31 pm Betreff: [Ifeffit] hephaestus > > > Hi all, > > Today, in a conversation that Carlo, Matt, and I have been having, > Matt said the following: > > > I know some beamlines (PNC-CAT, for example) don't install > > Ifeffit/hephaestus on data collection machines because it uses too > > much memory (~40Mb+ on Win32). > > In fact, the only thing for which hephaestus uses Ifeffit is the f'/f" > utility. None of the other tools in hephaestus make use of ifeffit in > any way. > > Would there be some interest in a "hephaestus-lite"? That is, a > version of hephaestus that does not include the f'/f" utility. > Such a > thing would have a much smaller footprint on the computer -- just > whatever the perl interpreter requires, maybe 4 or 5 meg. > > If enough people express inetrest, I can inlcude thas in the > distribution. I can even make a stand-alone distribution that > installs only hephaestus-lite and the external files it needs to do > its thing. That would be a much smaller beast (both in disk space and > memory footprints) than the full ifeffit install. > > B > > > -- > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > Molecular Environmental Science Group, Building 203, Room E-165 > MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 > > Argonne National Laboratory phone and voice mail: (1) 630 > 252 5033 > Argonne IL 60439, USA fax: (1) 630 > 252 9793 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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