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

consultation
by 康明亮 27 Jan '10

27 Jan '10

Dear Bruce, I want to sonsult a question about using Linear Combination fitting. I normalized all the standards (measured in transmission mode) and samples (fuorescence mode) with Athena, and then wish to use LCF to quantify each unique component in the samples. But I noted that the normalized samples spectra are lower than any references, thus the fit results are also high than the original spectra. I do not know why? Wish to obtain guidance from you. Thanks! In addition, I wish to use Artemis to do some fitting for XAFS data(processed by Athena firstly). It is my first time to perform such work, is there an helpful manual avaible online for freshman? Thanks! Best wishes Mingliang

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Re: [Ifeffit] iXAFS for OS X 10.6
by フォンスポール 27 Jan '10

27 Jan '10

Hi Jeff, (A somewhat belated) happy new year. I was at the APS recently and it so happened that Bruce was using sector 20 right before me. I was curious about the version of ixafs for snow leopard and if there was any way that I might be of some help to you (Bruce mentioned your surgery). I also noticed your note (just now) on the ifeffit list about wanting to run a beta. I would be glad to help out in this regard (I have been postponing the upgrade to snow leopard up to this point as ixafs is a must have for me. Thanks for your efforts. Sincerely, Paul

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Re: [Ifeffit] SIXPack How to plot the data
by Abhijeet Gaur 27 Jan '10

27 Jan '10

"Vijay, I have used SixPack sometimes. The programming is a little less forgiving than Athena and Artemis for inputting of data. What I would try if I were you is first importing your data into Athena. I've only used this program for PCA and LCF so I don't know if this will work for the other types of analysis but this is what I do to get my data working. 1) Import the data into Athena (which requires that you specify your mu0, muE) 2) Click on the checkbox for the individual file that you want to make "ready" for SixPack 3) Go to file -> saved marked group to file as -> mu(E) .. (( if you want to export it as normalized that is fine but make sure you do your background subtraction, I still save it as a .mu in that case anyhow but I just choose norm(E) instead of mu(E) )) 4) Then Athena prompts you with "marked".. What you need to do is to save it as a .mu file ((or .chi if you're doing EXAFS analysis, but I have not done that so you're going to have to figure out how to do that if that's what you're needing it for)).. So an example file name is one.mu.. (don't put numbers in your file name, the compiler doesn't like it, i.e. cu2ostd.mu is a bad file name) 5) I prefer to remove the header files from the .mu file itself (the stuff with the '#' symbol), I forget if this upsets the SixPack program. Please see below for what type of file output that I have been able to use. Then in the end you should have two columns, instead of the three that you had in your mail that you sent to the list. If you want me to send you an example file, just e-mail me. Example output of a file that I exported from Athena to imported into SixPack: 7068.0174 -0.18245200 7068.9274 -0.18305700 7070.0074 -0.18422800 7070.9874 -0.18216700 7071.9974 -0.18503600 7072.8774 -0.18276100 7074.0574 -0.18661000 7075.1174 -0.18699300 7076.0174 -0.18723800 7076.9074 -0.18667400 7077.9074 -0.18584000 7079.0474 -0.19024300 I hope this helps! Andrew Campos" Hi all, Thanks a lot Andrews, the procedure you describes definitely works in all the cases of SIXPack except in case of SAMView. I had asked the same question to Sam webb sir and I am lucky that I got a response from him too. The response is: "Hi Abhijeet - The file attached got added as text to the message, so I copied it and pasted it into a notepad document. Make sure there is not a blank line at the end of the data. I've attached my file. When you load, it'll come up with the generic reader. Choose column 1 as E, column 2 as I0 and column 3 as I1. Make sure that you have "1" line selected as the offset (to ignore the header). It should read correctly and then make sure you plot MuT, not MuF. Worked simply for me. Also make sure you are doing this in the viewer and not in another module. The SamView module imports all data, and writes a 2 column ascii. The other use a plain, 2 column ascii format. Hope that helps. Sam" The file sent by Sam webb sir is attached. Thus, now I am able to understand how to plot the data in SAMView as well as other analysis sections. Thanks to mailing list members. with regards Abhijeet Gaur

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How to calculate F-value for XANES PCA results
by Andrew 27 Jan '10

27 Jan '10

Hi everyone, I was looking through the literature on how to handle PC analysis data and saw that there are several different methods you can use for determining how many components there are in the series of scans. Included in SixPack are the indicator function, scree test, and the ability to quickly do the reduced eigenvalue ratios. I've been digging through the literature as to how to calculate the F-values. The closest to an answer that I got was: "The above-mentioned reduction of the body of experimental data, that is, the decision of what components correspond to the noise and what are the principal components, is now made on the basis of an F test of the variance associated with eigenvalue k and the summed variance associated with noise eigenvalues (k+1, ..., c). The null hypothesis is that a given factor k is a member of the pool of noise factors. The probability that an F value would be higher than the current value is given by %SL (percentage of significance level). Thus, the kth factor is accepted as a principal component if %SL is lower than some test level." (Garcia 1995). We ran the PCA on the reduction of iron while scanning at increased temperatures. I checked the foil standard but did not see any shift in the max at 7112, we scanned at 0.5 eV intervals (2 eV resolution at the beam). I thought I understood what that statement was saying but I'm almost certain I'm doing something wrong. I have attached the .xlsx file that I was working on and hope someone can point me to the right direction. The file includes the components of the PCA and some of the variances that I was calculating. If there is a paper that someone shows an actual calculation of this in the supplemental materials that would have been exactly what I was looking for! Thanks for the help! Andrew Campos Fernandez-Garcia, M., C. Marquez Alvarez, and G.L. Haller, The Journal of Physical Chemistry, 1995, 99(33), 12565-12569.

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Re: [Ifeffit] SIXPack : How to plot data file
by Andrew 25 Jan '10

25 Jan '10

Vijay, I have used SixPack sometimes. The programming is a little less forgiving than Athena and Artemis for inputting of data. What I would try if I were you is first importing your data into Athena. I've only used this program for PCA and LCF so I don't know if this will work for the other types of analysis but this is what I do to get my data working. 1) Import the data into Athena (which requires that you specify your mu0, muE) 2) Click on the checkbox for the individual file that you want to make "ready" for SixPack 3) Go to file -> saved marked group to file as -> mu(E) .. (( if you want to export it as normalized that is fine but make sure you do your background subtraction, I still save it as a .mu in that case anyhow but I just choose norm(E) instead of mu(E) )) 4) Then Athena prompts you with "marked".. What you need to do is to save it as a .mu file ((or .chi if you're doing EXAFS analysis, but I have not done that so you're going to have to figure out how to do that if that's what you're needing it for)).. So an example file name is one.mu.. (don't put numbers in your file name, the compiler doesn't like it, i.e. cu2ostd.mu is a bad file name) 5) I prefer to remove the header files from the .mu file itself (the stuff with the '#' symbol), I forget if this upsets the SixPack program. Please see below for what type of file output that I have been able to use. Then in the end you should have two columns, instead of the three that you had in your mail that you sent to the list. If you want me to send you an example file, just e-mail me. Example output of a file that I exported from Athena to imported into SixPack: 7068.0174 -0.18245200 7068.9274 -0.18305700 7070.0074 -0.18422800 7070.9874 -0.18216700 7071.9974 -0.18503600 7072.8774 -0.18276100 7074.0574 -0.18661000 7075.1174 -0.18699300 7076.0174 -0.18723800 7076.9074 -0.18667400 7077.9074 -0.18584000 7079.0474 -0.19024300 I hope this helps! Andrew Campos

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Re: [Ifeffit] SIXPack : How to plot data file
by Abhijeet Gaur 24 Jan '10

24 Jan '10

Hi all, As I already said I am not able to find any column of mu(E) in the column assingment, so I am not able to plot it. But, when I opened the E, I0, It format file the SIXPack is giving the following error Error: 1 IndexError Exception in Tk callback Function: <method generic.pressedabutton of generic instance at 01054EE4> (type: <type 'instance method'>) Args: (<Tkinter.Event instance at 010B23FC>,) Event type: ButtonPress (type num: 4) Traceback (innermost last): File "Pmw.pyc", line 1772, in __call__ None File "xasinput.pyc", line 1413, in pressedabutton None File "xasinput.pyc", line 1432, in readgenericdata None IndexError: string index out of range ================================================ Event contents: char: ?? delta: 1 height: 0 keycode: 1 keysym: ?? keysym_num: 1 num: 1 send_event: 0 serial: 9011 state: 0 time: 3310421 type: 4 widget: .20405404.16206244.16205940.12263724.16545596.17214596.17274484.17277060.17279988 width: 0 x: 23 x_root: 176 y: 13 y_root: 404 Error: 2 TypeError Exception in Tk callback Function: <method Main.loaddatafile of Main instance at 00D5ACCC> (type: <type 'instance method'>) Args: () Traceback (innermost last): File "Pmw.pyc", line 1772, in __call__ None File "spsamview.pyc", line 366, in loaddatafile None File "spsamview.pyc", line 423, in selectfile None File "spsamview.pyc", line 511, in rescaleplot None File "spsamview.pyc", line 567, in makeplot None TypeError: unsupported operand type(s) for / I am not able to understand these errors. I am attaching the data file ( Cu foil data) that I am trying to open in SIXPack. With thanks Vijay Hinge

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Request for ZrB2 structure file
by ashfaq ahmad 24 Jan '10

24 Jan '10

Dear Can any one send me structure/Atom file of ZrB2 compound. Mine is not working properly. Ashfaq _________________________________________________________________ Windows Live Hotmail: Your friends can get your Facebook updates, right from Hotmail®. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

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Re: [Ifeffit] SIXPack : How to load data file
by Carlo Segre 24 Jan '10

24 Jan '10

Please take a look at Matt newville's response on the mailing list. You ned to provide more specifics for us to be able to help. For example, attach the data file you are having problems with and provide all error messages that appear. C.S. On Sun, 24 Jan 2010, Rashmi Shrivastava wrote: > Hello Sir, > Sorry for replying late. > I am running SIXPack on Windows-XP version. I had already opened these data > file in Athena and had done analysis on them. But when I try to open these > data files in SIXPack, column assingment is required. First I tried to open > the E, mu(E) format text file, SIXPack asks for column assingment, but there > is no column for mu(E). Then I tried E, I0, It data format and I checked the > respected column, but still not able to plot the data. Each time it is > giving some error in data plotting like background error, plotting error. > The data is loading but I am not able to plot it. > > With thanks > Vijay Hinge > Research Scholar > Ujjain (India) > On Fri, Jan 22, 2010 at 7:50 PM, Carlo Segre <segre(a)iit.edu> wrote: > >> >> Hi Rashmi: >> >> What platform are you running on? >> >> Carlo >> >> >> On Fri, 22 Jan 2010, Rashmi Shrivastava wrote: >> >> Hi all, >>> I am doing some data analysis of XANES as well as EXAFS data using >>> data analysis software SIXPack. I am not able to load any data file. I >>> used >>> E and mu(E) data format file. Also I try to open E, I0, It data format >>> file >>> but still not able to open or plot any data. I also tried to open the >>> example data given with the programm, but got the same result. I had gone >>> through the SIXPack Documentation, but not able to get how to load a data >>> file. If someone can please guide me, I will be very thankful. >>> >>> with regards >>> Vijay Hinge >>> School of Studies in Physics >>> Vikram University, Ujjain (INDIA) >>> >>> >> -- >> Carlo U. Segre -- Professor of Physics >> Associate Dean for Graduate Admissions, Graduate College >> Illinois Institute of Technology >> Voice: 312.567.3498 Fax: 312.567.3494 >> segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org >> > -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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Re: [Ifeffit] Ifeffit Digest, Vol 83, Issue 22
by Abhijeet Gaur 23 Jan '10

23 Jan '10

Dear Rashmi, Vijay, Abhijeet, ...., Can you please ask this question more precisely? Asking for "guidance" is a bit too vague to expect a helpful answer. > I am doing some data analysis of XANES as well as EXAFS data using > data analysis software SIXPack. I am not able to load any data file. This is confusing. How would you be able to use SIXPack if you are not able to load any data file? Is the program not responding at all? Does it crash when trying to load particular files?? I have no idea. Again, please ask a specific question (for example: why can I not open the attached data file with SIXPack?), and give as much relevant information as you can: what operating system are you using, what you did (File->Open: did a dialog box open??), what SIXPack "does" (any error messages, for example), Can Athena open the file, and so on. We're not there to see what you are (and are not) doing. Please remember that you are sending this request for help to hundreds of people hoping that one of them will be kind enough to volunteer to answer. Being polite is wise, but being clear and to the point is also important. Cheers, --Matt Hello Sir, Thanks for your suggestions. Actually sometimes we are not able to frame the question correctly, which is also one of the reason of not getting a response. To be specific, I had already opened these data file in Athena and had done analysis on them. But when I try to open these data files in SIXPack, column assingment is required. First I tried to open the E, mu(E) format text file, SIXPack asks for column assingment, but there is no column for mu(E). Then I tried E, I0, It data format and I checked the respected column, but still not able to plot the data. Each time it is giving some error in data plotting like background error, plotting error. The data is loading but I am not able to plot it. I think now I had made myself clear for getting some response. With thanks Vijay Hinge

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Re: [Ifeffit] Fiiting Result
by Abhijeet Gaur 22 Jan '10

22 Jan '10

Hi Abhijeet, Sorry, I guess Cu2O is coordinated by 2 oxygen atoms and 12 cu atoms. If the cluster of atoms that you give to FEFF doesn't match the structure of the sample then the fit will not work. But I think that your structure isn't obviously wrong. Cheers, Shelly Hi Madam Thanks for youe response. Actually, I had tried the fitting by taking the data of Cu2O from the database, but still there are same problem like low SO2, negative SS2, high energy shift delE. If you can please suggest me a paper in which the fitting results of Cu2O and CuO are published, I can compare my results with the published results. I just want to make it clear that where I am going wrong. Also, I am sorry to all members of mailing list for asking the same problem again and again. With thanks Abhijeet Gaur

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