March 2005 - Ifeffit - millenia.cars.aps.anl.gov

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

9 21

Re: sigma squared
by Bruce Ravel 01 Apr '05

01 Apr '05

Hi Karla, These are excellent questions for the mailing list, so I am taking the liberty of CCing my answers to the list. That way, other people can have a chance to answer your excellent questions. On Thursday 31 March 2005 14:10, you wrote: > Hello, > I am fairly new to EXAFS data analysis. I am currently working on > data that I collected from 10-ID at the APS. Aha! My new home! I just collected my first spectra from that beamline a couple of weeks ago. ;-) > I have a couple of questions. First, in Artemis, when I click on > the "x" buttons to select my k- and r-ranges, the window never seems > to correspond to where I clicked. Is this a bug? Probably not. The default in Artemis is use a Kaiser-Bessel window. The various strange words to describe FT windows ("Kaiser-Bessel", "Hanning", "Welch", and so on) refer to different functional forms for the window. None of the functional forms will be 0 at the specified boundary -- instead they all have window sills that extend a bit below the boundary. Thus, if you use the Kaiser-Bessel window, set kmin=2, and dk=1, the window will become non-zero at about 1.5. In short, it's not a bug. It's an unexpected (for you, at least ;-) feature of the functional form of the window. Try setting dk or dr to 0 then replotting. The FT may not look good, but the window plotted by Artemis will be what I think you were expecting. > Second, why does Artemis allow a physical parameter like sigma > squared to be negative? There are a few ways I could answer this question. I could talk about how Artemis allows arbitrarily sophisticated fitting models where the sophisticated user needs complete freedom to specify the fitting model. But that's a little abstract, so let's consider a slightly more concrete example. Suppose that your sample has some kind of oxygen-coordinated iron atom and you have reason to believe that there is a high level of disorder in the first coordination shell. So you choose to run Feff using some model compound that itself has much disorder in the first shell. You then use the first shell paths that came from the Feff calculation to model your unknown data. In this case a negative sigma^2 might be telling you that your unknown has *less* disorder than you model compound. In more general terms, the negative sigma^2 is probably trying to tell you something. You should remember that sigma^2 is correlated to other terms in the fit, most importantly to the various amplitude terms, such as coordination number and S02. If sigma^2 is negative, then the fitten value for amplitude is probably to small. A negative sigma^2 will puff up the signal to compensate for the amplitude term being rather too small. If Artemis did not allow sigma^2 to go negative, you might never know about this kind of problem. So I would say that this too is a feature of the program and not a bug. > Lastly, I have had a hard time figuring out these math expressions > despite reading over the mailing lists. Can you use the ">" sign so > that sigma squared is always greater than 0? How else can I write a > math expression so that the fitting never gives me a sigma squared > that is less than 0? Any help would be greatly appreciated! Using ">" won't work. ">" is not a symbol in Ifeffit's math parser. This is a topic that has come up many times over the past few years on the mailing list. In fact, I think that someone should write a FAQ entry on this topic. Here are a few suggestions: 1. Guess a parameter like this: "guess ss 0.003", then use it on the sigma^2 line of the path page like this: "abs(ss)". 2. A very similar approach is to use the max function. In the sigma^2 line of the path page, say this: "min(ss, 0)". This can be improved slightly. Doing this: "min(ss, 0.001)" constrains the sigma^2 for the path to be no smaller than 0.001. 3. If you start reading the mailing list archives here: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-February/001650.html you will find a conversation between Matt and Scott about a way to impose a penalty for a sigma^2 being too small rather than forcing to be above a hard boundary. Matt's scheme is kind of involved... If you use any of these approaches, I would encourage you to do so with hesitation. As I mentioned above, the negative sigma^2 is not a short coming of Ifeffit or Artemis. Much more likely, it is useful information that you should heed and use to figure out what shortcoming in your fitting model is leading that to happen. HTH, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

9 16

installation of horae in fedora2
by ynliu＠eps.mcgill.ca 22 Mar '05

22 Mar '05

Hello,all We finally succeeded in installing horae-048 in Fedora 2! It took us a long time to figure out why Tk could not be detected, but it turned out that the right version of Tk is the key. We found Tk-804.027 working in our Fedora2 system. The right order of installation is also important. We had to restart everything in installing horae after we set up Tk.If you are using this Tk-804.027, you don't need to look for unix folder as said on some web,just simply gunzip tar -xvf finename.tar (enter the new folder Tk-804.027) make make install(after this,you can make test if you want) And then the installation of horae will jsut go fluently following the instructions! To use athena or artemis, you need to enter the fold where athena.pl and artemis.pl are,and then "perl athena.pl". cheers Yanan ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

4 5

file causing trouble creating chis
by Daniel Carter 15 Mar '05

15 Mar '05

Ok Matt, I thought you might have a general idea for how I could gather more info for you about the problem. I did mention previously this weekend to you that I am using windows XP. I also had thought I'd posted a file, but I'd just sent it to Adam. From now on I will send a file every time I have a problem. This is with athena version 8.034. Matts theory that there is not enough of a Mu(E) range sounds good to me so far. --Dan

3 3

Re: [Ifeffit] file causing trouble creating chis
by Adam Webb 15 Mar '05

15 Mar '05

Hi, I looked at the file. But as with your first file, I have no trouble saving chi files. I used athena 0.8.34 on Windows 2000. You should not have any trouble with XP. BTW the file you sent says it was created with Athena 0.8.30. I think it should still work but it might indicate a problem with your installation. You could try unistalling and re-install and get the updates when the updater runs. I hope this helps, Adam > Ok Matt, > > I thought you might have a general idea for how I could > gather more info for you about the problem. I did mention previously > this weekend to you that I am using windows XP. I also had thought > I'd posted a file, but I'd just sent it to Adam. From now on I will > send a file every time I have a problem. This is with athena version > 8.034. Matts theory that there is not enough of a Mu(E) range sounds > good to me so far. > > --Dan ------------------------------------------------------ M. Adam Webb Ph.D., MCIC Alberta Synchrotron Institute (http://www.asi-cls.ca/) 8308 - 114 Street, Suite 2080 Edmonton, Alberta, T6G 2E1, Canada Phone: (780)492-5464 Fax: (780)492-6160 Email: adam.webb(a)asi-cls.ca

1 0

blank chi files still
by Daniel Carter 15 Mar '05

15 Mar '05

Bruce, Matt, Adam, others, I'm still having this problem with Athena where I try to save data as a chi file and the file is created, but empty. The chi files should be several killobytes large, but mine are 0 KB. I've just upgraded to the newest version of Athena 8.037. I wonder, is it my data or my operating system? No one else seems to be having these sorts of problems. --Dan

2 1

Athena functionality report
by Raul Barrea 14 Mar '05

14 Mar '05

Hi Bruce, I found a difference in functionality in Athena when I tried to use "open file" or "open many files" in the main menu . When using the many files option I found this message: Athena trapped a warning! The following message was trapped by Athena: Athena0.8.034warnC:\Program Files\Ifeffit\horae\stash\ATHENA.TRAPCODE(0x21a5d800 ) at athena line 1363 main::__ANON__('Tk::Error: Can\'t call method "lower" without a package or objec...') called at blib\lib\Tk.pm (autosplit into blib\lib\auto\Tk\Error.al ) line 402 Tk::Error('MainWindow=HASH(0x21072a84)', 'Can\'t call method "lower" wit hout a package or object reference...', '[\&main::read_file,1]', '(menu invoke)' ) called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at athena line 1419 When I opened the same file alone using the "open file" option , Athena says the file is not monotonically sorted and it cannot be opened. So, that's the problem with the file. Then, Athena offers to sort the data and continue loading the file. Why this message is not shown when I opened multiple files? I tried to open only one file (the one that is not monotonically sorted) using the "open many files" option and the message was the same as the "open file"option. When using the "many files" option with many files, Athena does not show that message window and stays partially inactive (menu options are active but plot options are not active). A few sample file are atached. Thanks, Raul -- Raul Barrea, Ph.D. Assistant Research Professor of Physics, Associate Director Biophysics Collaborative Access Team (BioCAT) CSRRI, Dept. BCPS, Illinois Institute of Technology BioCAT/APS/435B/Sector 18 Argonne National Laboratory 9700 South Cass Avenue, Argonne, IL 60439 Tel.: (630) 252-0541 Fax: (630) 252-0545 Email: barrea(a)bio.aps.anl.gov Email: barrea(a)iit.edu pager: barrea-pager(a)bio.aps.anl.gov # File header: # Date and time: Sun Feb 20 23:25:41 2005 # Original name of the file: whiteCuscan.154 # Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -74.0000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 431984.40375 132525.96670 241.67263 8779.18220 435848.70000 132897.63333 141.66667 8779.82148 436557.03333 134347.63333 225.00000 8780.77597 435390.36667 132805.96667 150.00000 8781.72001 436465.36667 133330.96667 200.00000 8782.66579 437065.36667 133889.30000 183.33333 8783.61330 438248.70000 134264.30000 241.66667 8784.55950 437082.03333 134222.63333 141.66667 8785.50438 437123.70000 133539.30000 150.00000 8786.44947 437282.03333 134014.30000 150.00000 8787.39629 436107.03333 133122.63333 108.33333 8788.34332 434823.70000 133097.63333 166.66667 8789.29057 434557.03333 132589.30000 191.66667 8790.23802 433707.03333 132772.63333 183.33333 8791.18568 422148.70000 129089.30000 150.00000 8792.13508 429932.03333 131405.96667 158.33333 8793.08316 437498.70000 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Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.7000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 432284.41115 133059.31319 158.33724 8779.18524 434157.03333 132955.96667 241.66667 8779.82756 437123.70000 133730.96667 250.00000 8780.78358 436932.03333 133655.96667 191.66667 8781.72915 436957.03333 133989.30000 183.33333 8782.67341 437665.36667 133889.30000 216.66667 8783.61939 438032.03333 134189.30000 183.33333 8784.56559 436982.03333 134022.63333 150.00000 8785.51047 437232.03333 133439.30000 250.00000 8786.45709 436223.70000 133564.30000 150.00000 8787.40544 437707.03333 133880.96667 175.00000 8788.35095 436365.36667 134472.63333 266.66667 8789.29667 434840.36667 132680.96667 241.66667 8790.24565 431982.03333 132805.96667 275.00000 8791.19331 420565.36667 128739.30000 141.66667 8792.13966 429857.03333 131897.63333 158.33333 8793.08622 438582.03333 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Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.8000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 433951.11893 132784.30641 183.33786 8779.17763 436815.36667 133447.63333 141.66667 8779.81082 439482.03333 134747.63333 216.66667 8780.76531 440382.03333 134464.30000 141.66667 8781.71088 438232.03333 134530.96667 216.66667 8782.65665 440173.70000 134480.96667 225.00000 8783.60264 440082.03333 134664.30000 208.33333 8784.54883 441157.03333 135155.96667 216.66667 8785.49371 438932.03333 134080.96667 200.00000 8786.43880 439473.70000 134630.96667 208.33333 8787.38714 438398.70000 133797.63333 200.00000 8788.33417 438715.36667 134355.96667 183.33333 8789.27989 437207.03333 133639.30000 191.66667 8790.22734 437015.36667 134147.63333 241.66667 8791.17653 424165.36667 129697.63333 216.66667 8792.12439 433532.03333 132714.30000 208.33333 8793.07095 439940.36667 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Original name of the file: whiteCuscan.153 # Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.9000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 433634.44445 133059.31319 166.67078 8779.17459 437473.70000 133564.30000 191.66667 8779.80625 440073.70000 134939.30000 266.66667 8780.76227 440582.03333 134755.96667 175.00000 8781.70631 439757.03333 134755.96667 150.00000 8782.65056 438990.36667 134322.63333 191.66667 8783.59807 439523.70000 134147.63333 191.66667 8784.54426 439682.03333 134864.30000 158.33333 8785.48914 439732.03333 134214.30000 225.00000 8786.43575 438548.70000 134097.63333 175.00000 8787.38257 439715.36667 134189.30000 266.66667 8788.32807 437440.36667 133664.30000 208.33333 8789.27531 437715.36667 134005.96667 241.66667 8790.22276 435532.03333 133222.63333 158.33333 8791.17042 424065.36667 130064.30000 158.33333 8792.11982 431790.36667 131622.63333 233.33333 8793.06637 439115.36667 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Original name of the file: whiteCuscan.150 # Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.6000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 432592.75209 132475.96547 175.00432 8779.20655 435715.36667 133297.63333 233.33333 8779.86866 436465.36667 133597.63333 183.33333 8780.82316 437198.70000 133547.63333 233.33333 8781.76874 438007.03333 134439.30000 175.00000 8782.71301 437823.70000 133214.30000 66.66667 8783.66053 438132.03333 134872.63333 183.33333 8784.60826 437873.70000 133439.30000 125.00000 8785.55315 437923.70000 134372.63333 141.66667 8786.49825 437890.36667 133622.63333 191.66667 8787.44509 436590.36667 133614.30000 208.33333 8788.39213 435848.70000 133114.30000 166.66667 8789.33938 436748.70000 133489.30000 158.33333 8790.28685 434573.70000 133222.63333 141.66667 8791.23452 420948.70000 128247.63333 183.33333 8792.18240 431765.36667 132214.30000 183.33333 8793.12897 437840.36667 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Residual
by yetao＠chem.uga.edu 11 Mar '05

11 Mar '05

Hi, Is there anyone who can tell me how to view the residual in Artemis? Every time I checked the residual, only got the data curve. Best, Ye

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back to work....
by Bruce Ravel 10 Mar '05

10 Mar '05

Hi everyone! I am back from vacation and (on March 7th) started my new position here in Argonne's Environmental Research Division. I had a splendid vacation and am very excited about my new position. For those of you who are APS users, I'll be spending a good fraction of my time at sector 10 (MR-CAT). Stop by and say hi -- especially those of you that I have met in person! I have to confess that I have not been following the discussions on the mailing list very closely in the last several weeks, but I see that there have been a number of bug reports and other problems that people have encountered with the software. I am still settling into my new job and my new home, but I hope to get back to work on the codes real soon. And I will certainly resume active participation in the discussions on the list. Regards, Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Environmental Research Division, Bldg 203, Room E165 Argonne National Laboratory phone: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Re: [Ifeffit] Athena Chi file created, but nothing there
by Adam Webb 08 Mar '05

08 Mar '05

Dan, I think the problem was when you first imported the data. When you import the data, Athena tries to figure out what type it is. In your case the first file is very short and Athena probably selected XANES data. This disables the k,q etc since they don't apply. Re-import your data but be sure to select mu(E) as the Data Type in the import window. The rest of your problems should go away. Cheers, Adam > Dear mailing list -- > > I'm having difficulty creating a chi file. First off I cannot > plot my data files in k, q , etc. The files can only be plotted in E > or merged and plotted in k, q, etc. > > Second, when I go to the file menu to create a chi(k) from the > marked original text file, Athena won't let me. That is to say the > only option is create to Save Mu(E) and when I do that a file is > created with nothing in it. > > When I merge 2 data files and create a chi(k) file from that, > again, a file is created and named, but nothing is there. Is there > something wrong with my data files? I don't see any error messages. > Let me know if you need more info. > > I'll also attach my athena file. > > Thanks, Dan ------------------------------------------------------ M. Adam Webb Ph.D., MCIC Alberta Synchrotron Institute (http://www.asi-cls.ca/) 8308 - 114 Street, Suite 2080 Edmonton, Alberta, T6G 2E1, Canada Phone: (780)492-5464 Fax: (780)492-6160 Email: adam.webb(a)asi-cls.ca

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