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

Unable to export flattened normalized XANES spectra from Athena 0.9.24
by Jeff Catalano 09 Dec '15

09 Dec '15

I am looking for some help with a possible error on my part or bug associated with exporting normalized mu(E) spectra from Athena 0.9.24 64-bit on Windows 10 Pro 64-bit. I have some Si XANES data with a challenging background shape that is well removed through careful normalization in Athena, as long as the "Flatten normalized data" option is checked. When I save the current group as norm(E), what is saved is the non-flattened normalized data. The checkbox for flattening the data has no effect on what is exported despite changing what is plotted. I have verified this by comparing the files exported the the flatten box checked or unchecked. I have tried this with multiple data files loaded in multiple formats (raw beamline data, simple two-column E and mu data, PRJ files) and the effect is always the same. It is also unaffected by the normalization ranges I select. No matter what options I select Athena 0.9.24 will only save non-flattened norm(E) data. This behavior is different from what I remember, and I have verified that in version 0.8 of Athena the exported norm(E) was the flattened data, provided that the flatten box was checked (of course). I have been unable to determine if I have any errors in the settings in version 0.9.24 but all parameters that I can find are identical in both 0.9.24 and 0.8. I have also uninstalled and reinstalled Athena 0.9.24 and the effect is still the same. Has anyone else noticed this problem? Is this a bug? Thank you, Jeff -- Jeffrey G. Catalano, Associate Professor Department of Earth and Planetary Sciences Washington University 1 Brookings Drive, Campus Box 1169 Saint Louis, MO 63130 USA http://aqgeochem.wustl.edu/

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Most probably a bug or something.
by pushkar shejwalkar 02 Dec '15

02 Dec '15

Dear All, I have recently found this particular problem with plotting my graphs in k fitting. This is a problem with athena as well as artemis. When I plot the graphs in R or E or q there is no problem, but when I do so in k suddenly these four black circles show up on the left side of the graph. Interestingly this has appeared suddenly just now and after this (probably i can recollect exactly) I could not maximize my plotting window at all. although if I drag the corners it can be resized and these four circles then appears relatively smaller (basically it does not exapnds with the window. Anybody else have this problem? is there a quick fix? I am not sure if this is a bug or not so I am sending this here. my operating system is Windows 10, Athena and artemis 0.9.22 8GB RAM. (Please let me konw if anything else is needed) Pictures of these problem is attached below. I am attaching R-space just to show that it doesnt happen for the R-space. First picture is Athena, second is from Artemis fitting. [image: Inline image 4] [image: Inline image 2][image: Inline image 3] -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 5
by Enyuan Hu 02 Dec '15

02 Dec '15

Dear all, Thank you all for the kind help. I didn't know CuO is so useful in the sense that asking for its spectrum would reveal the abundant kindness in this community :) Enyuan On Wed, Dec 2, 2015 at 10:26 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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. Re: Ifeffit Digest, Vol 154, Issue 1 (Soma Chattopadhyay) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Dec 2015 20:14:04 -0600 > From: Soma Chattopadhyay <soma.tifr(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 1 > Message-ID: > <CAMYsB8ucwLRpSNGFK1aA8LbuWb03t5fOajSjdPU= > SGerD30jQQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Enyuan > Attached is my athena project file with Cu foil, CuO and Cu2O data in > athena. > They have references foils with them. > best > Soma > > On Wed, Dec 2, 2015 at 7:38 PM, Enyuan Hu <enhu(a)bnl.gov> wrote: > > > Dear Matt, > > > > I'm sorry to be persistent but I noticed that the reference spectrum (Cu > > foil I assume) for these two CuO data doesn't seem to correct. I conclude > > this after I made comparison using the Cu foil data from the database and > > my own previous measurement. If it's not bothering you, can you help me > > look into that? Thanks. > > > > Enyuan > > > > On Wed, Dec 2, 2015 at 8:08 PM, Enyuan Hu <enhu(a)bnl.gov> wrote: > > > >> Dear Riti and Matt, > >> > >> Thank you two very much for the timely help. I didn't even know the > >> existence of these two libraries. Thanks again for letting me know such > a > >> valuable resource. > >> > >> regards, > >> Enyuan > >> > >> On Wed, Dec 2, 2015 at 7:40 PM, < > >> ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > >> > >>> 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. CuO XAS spectrum (Enyuan Hu) > >>> 2. Re: CuO XAS spectrum (Ritimukta Sarangi) > >>> 3. Re: CuO XAS spectrum (Matthew Marcus) > >>> 4. Fwd: Most probably a bug or something. (pushkar shejwalkar) > >>> > >>> > >>> ---------------------------------------------------------------------- > >>> > >>> Message: 1 > >>> Date: Wed, 2 Dec 2015 18:32:11 -0500 > >>> From: Enyuan Hu <enhu(a)bnl.gov> > >>> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > >>> Subject: [Ifeffit] CuO XAS spectrum > >>> Message-ID: > >>> < > >>> CAJud35MbtedoHtgoN3yFJgJ3squ+L5LCVpp1uNm0Tf4vwpWENA(a)mail.gmail.com> > >>> Content-Type: text/plain; charset="utf-8" > >>> > >>> Dear all, > >>> > >>> I'm analyzing some Cu compounds spectra and was wondering if anyone has > >>> the > >>> CuO XAS spectrum and is willing to share. Thanks. > >>> > >>> best regards, > >>> Enyuan > >>>

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Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 1
by Enyuan Hu 02 Dec '15

02 Dec '15

Dear Riti and Matt, Thank you two very much for the timely help. I didn't even know the existence of these two libraries. Thanks again for letting me know such a valuable resource. regards, Enyuan On Wed, Dec 2, 2015 at 7:40 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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. CuO XAS spectrum (Enyuan Hu) > 2. Re: CuO XAS spectrum (Ritimukta Sarangi) > 3. Re: CuO XAS spectrum (Matthew Marcus) > 4. Fwd: Most probably a bug or something. (pushkar shejwalkar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Dec 2015 18:32:11 -0500 > From: Enyuan Hu <enhu(a)bnl.gov> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] CuO XAS spectrum > Message-ID: > < > CAJud35MbtedoHtgoN3yFJgJ3squ+L5LCVpp1uNm0Tf4vwpWENA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I'm analyzing some Cu compounds spectra and was wondering if anyone has the > CuO XAS spectrum and is willing to share. Thanks. > > best regards, > Enyuan >

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CuO XAS spectrum
by Enyuan Hu 02 Dec '15

02 Dec '15

Dear all, I'm analyzing some Cu compounds spectra and was wondering if anyone has the CuO XAS spectrum and is willing to share. Thanks. best regards, Enyuan

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Issue with Compatibility between versions of Athena
by Nirala Singh 26 Nov '15

26 Nov '15

Hello, I have recently downloaded Athena and was sending a project file to a colleague who uses an older version. When I sent it, I checked 'Backwards compatible project file', then saved the project and closed Athena, then sent the file. I had selected some normalization parameters as follows: [image: Inline image 2] When he opened the file, most of the parameters were the same, except the window type (changed from 'Hanning' to 'kaiser-bessel'). Is there any reason for this? Any way to maintain the window function between versions? [image: Inline image 1] Thank you,

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Fitting parameters corrleations between variables
by pushkar shejwalkar 24 Nov '15

24 Nov '15

Dear All, I am trying to fit in Pd compound and the fit that I obtained looks kinda good. I used Pd metal and Pd(OAc)2 shells for fitting. These standards were collected and fitted simultaneously and I got the SO2 value there as 0.67 with Pd foil coordination number as 12 which is correct when considered Pd foil CN. Next while fitting the actual sample (unknown) I used the formula in SO2 column as amp*N1 and put amp as 0.67 and N as 1. I kept N1 as variable (Guess). same I did for the second shell of Pd-O with N2. amp is kept on SET value of 0.67. After fitting I received the N1 and N2 value as 5.6 (0.5) and 1.6 (0.7) (roughly). however, when I checked the correlations between the variables I got the values as given in the log file attached. I saw there is some correlation between bkg01_01 and N2 and many such correlations between bkg values. I have so far never seen such correlations. What are the implications of these correlations? does this means that my fitting assumptions are incorrect. does correlations values in negative indicates something? Thank you very much for the input. By the way my RBKG is 1.2 in athena and I used this same file for fitting purpose and on artemis I used rmin 1.2 and rmax 3.4. All these information are in log file attached Any help in understanding this is appreciated. -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Zinc Sulfite Reference Spectrum
by Elisabeth E Feld 16 Nov '15

16 Nov '15

Dear All, I am studying the oxidation state of Sulfur using XANES and need a reference spectrum of Zinc Sulfite (ZnSO3) for comparison. I do not have access to taking the spectrum myself and currently do not have any spectrum grabber tool to pull the reference from a paper. If you could help me out by sending me a Zinc Sulfite spectrum, I would greatly appreciate it! Thank you, Elisabeth Elisabeth Feld Ph.D. Candidate Dellinger Research Group Chemistry Department Superfund Research Center Louisiana State University 338 Choppin Hall Baton Rouge, LA 70803 efeld1(a)lsu.edu

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 30
by Christopher Thomas Chantler 16 Nov '15

16 Nov '15

With Ifeffit-like, you can test these assumptions with an explicit chi^2_r, and indeed the answer does and must depend upon your actual individual error bars. The other factor here is how correlated your choice of parameters are which of course reaches that limit much faster. :) ------------------------------------------------------------ Christopher Chantler, Professor, FAIP Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS President, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au chantler(a)me.com http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html http://optics.ph.unimelb.edu.au/~chantler/home.html ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Tuesday, 17 November 2015 5:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 153, Issue 30 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. Re: Problem with Perl interpreter (Bruce Ravel) 2. Re: Hello (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Mon, 16 Nov 2015 07:48:54 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem with Perl interpreter Message-ID: <5649D0B6.3050108(a)bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed On 11/16/2015 02:53 AM, Wojciech Olszewski wrote: > The timeline of this problem was as follows: > 1) Demeter was working fine; > 2) One day I couldn't run any of the Demeter software - error message "Per interpreter has stopped working; > 3) Reinstallation of Demether - the problem is still there; > 4) Installation of perl (in other folder, not the same as Demeter) - the problem is still there; > 5) Mail to mailing list; > 6) Deinstallation of Demether and Perl; > 7) Installation of Demeter. > Unfortunately the problem is still there. I receive the same error message. Wojciech, Step 2 really suggests that this is a problem local to your computer. In recent weeks, there have been a few reports of anti-virus software blocking some component of perl or Demeter. In the time period between steps 1 and 2, was AV updated on this computer? Could you disable AV (as a test of course)? Or configure AV to explicitly allow Demeter to run? B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ------------------------------ Message: 2 Date: Mon, 16 Nov 2015 11:18:56 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Hello Message-ID: <CA+7ESbrzTzUkpPHj0CFZ6HErN5Hp_jMHJynJa0rUZ+XSM3dqPA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Riti, On Fri, Nov 13, 2015 at 6:25 PM, Ritimukta Sarangi <ritimukta(a)gmail.com> wrote: > Hi Bruce and Matt, > Are there any obvious examples of where Sterns criteria is shown to be > incorrect? Meaning that 2delkdelR/pi +2 has been shown to over predict the > number of available independent parameters? I have often been asked this by > students/users and failed to explain it well, except for taking of talking > sources or error such as systematic, spline, etc. > Thanks! > -Riti > > That's an excellent question. To be honest, I don't think this has been tested in great detail, with the main issue being "when can you truly tell that you've used too many parameters". We typically rely on "when adding a variable doesn't improve reduced chi-square" as that measure. But, the definition of reduced chi-square that we use includes a value for N_idp already, so we're more or less *imposing* the Stern rule. I think lots of us have observed cases where the Stern rule is definitely optimistic. And that might be understandable because the Stern rule doesn't include a separate measure of the noise in the data, or what the distribution of "the effect" of the parameters would be on the signal. That is, one can always increase the R range to 20 Angstroms, and so increase N_idp. But if you're trying to fit 25 variables for the part of the signal between 1.5 and 2.5 Ang, there is probably going to be very hard to get good measures of all 25 variables. The Stern rule sort of doesn't account for this, except in the sense of giving guidance. It would be interesting the revisit this with a better statistical treatments of information. There are, for example, statistical values like the Akaike Information criterion ( https://en.wikipedia.org/wiki/Akaike_information_criterion) and related values that might be useful for better understanding when one is using too many parameters. --Matt

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Problem with Perl interpreter
by Wojciech Olszewski 16 Nov '15

16 Nov '15

I have a problem with Demeter package. Up to yesterday everything was fine. Now when I try to start any program (Athena, Artemis...) I receive error message: Perl interpreter has stopped working (The application was unable to start correctly (0xc0000005)). Installation of perl (strawberry-perl-5.22.0.1-64bit.msi) didn't solve the problem. Unfortunately all the log files ("C:\Users\<username>\AppData\Roaming\Demeter\<name>.log") are empty. I am using the Demeter 0.9.24 on 64-bit Windows 7. I would be really grateful for help in solving this problem. Thank you in advance, Wojciech -- ALBA Synchrotron <http://www.albasynchrotron.es> Wojciech Olszewski BL22 - CLAESS: Core Level Absorption & Emission Spectroscopies - Experiments Division ALBA SYNCHROTRON LIGHT SOURCE Ctra. BP 1413 km. 3,3 | 08290 | Cerdanyola del Vallès| Barcelona | Spain <http://www.albasynchrotron.es/AboutUs/Access> (+34) 93 592 4059 www.albasynchrotron.es <http://www.albasynchrotron.es>| wolszewski(a)cells.es <mailto:wolszewski@cells.es> **Please, do not print this e-mail unless it is absolutely necessary. **Si heu rebut aquest correu per error, us informo que pot contenir informació confidencial i privada i que està prohibit el seu ús. Us agrairíem que ho comuniqueu al remitent i l'elimineu. Gràcies. Si ha recibido este correo por error, le informo de que puede contener información confidencial y privada y que está prohibido su uso. Le agradeceré que lo comunique a su remitente y lo elimine. Gracias. If you have received this e-mail in error, please note that it may contain confidential and private information, therefore, the use of this information is strictly forbidden. Please inform the sender of the error and delete the information received. Thank you.

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