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

Multiple Atom.inp in Feff
by Christopher Patridge 17 Jan '13

17 Jan '13

Hi all, Is there a way to remove data sets, feff.inp, or atoms.inp from the main window list? I know this question was raised at one of Bruce's XAFS seminars at Diamond. I looked at the current Demeter List of Things to Do and did not see specifically removing them, just reorganizing lists. I guess it is not really a bug, just annoying, but for some reason, probably user error and impatience, my artemis file saved several "atoms.inp" windows in the Feff list and now I cannot get rid of them. Thanks, Chris Patridge -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

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S02 question
by Eugenio Otal 15 Jan '13

15 Jan '13

Hi all, I have a question about S02 measurement in samples for CN calculation. By example, If I have an oxynitide, LaTiO2N, Can I use TiO2 as standard for S02 even the Ti in LaTiO2N is coordinated to O and N? In a more extreme case, is possible to use metals? Which are the recommendations and limits? Regards, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Prof. Dr. Eugenio H. Otal UNIDEF - CONICET - CITEDEF San Juan Bautista de La Salle 4397. Villa Martelli (B1603 ALO) Buenos Aires Argentina TEL: +54 11 4709-8158. FAX: +54 11 4709-8241. and UTN - Santa Cruz Regional Faculty Av. Inmigrantes 555 Río Gallegos (9400) Santa Cruz Argentina TEL: +54 2966 429173 FAX: +54 2966 42-9173 E-mail: eugenio.otal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

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k-range question & R-factor
by Christopher Patridge 15 Jan '13

15 Jan '13

Hello Users, I was looking for an opinion about the chi(k) signal in a set of data I am analyzing. Brief background, this is a set of in-situ XAS data collected at the Fe K edge from a working electrochemical cell at a range of potentials during charge; I did not collect the data. I suspect the feature at ~ 8 angstroms-1, although present in all the spectra is noise or glitch and wondered if I am being overly cautious? My conservative range ( k = 2-7 and R = 1-2) really constrains the model Nidp = 3.31. Luckily, multiple datasets ( 8 ) to the rescue to give me some flexibility. In a multiple dataset fitting, is the R-factor of the whole set just the average or total mismatch across all the datasets or it calculated another way? Working towards happiness, Chris Patridge -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

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Re: [Ifeffit] Ifeffit Digest, Vol 119, Issue 19
by Denis Testemale 15 Jan '13

15 Jan '13

Hello Chris. - I don't have an answer regarding the R-factor. - Noise or glitch: how does I0 look like? Is the glitch you suspect visible in I0 at this energy? If you're refering to the feature that points downwards at 8A-1, it actually shifts with the spectra (I can see two groups of spectra in this k-range) so a glitch seems doubtful to me. Can you tell more about the collection of data (transmission, fluorescence, thickness of the sample, temperature, etc.)? By looking at the data, and if you confirm that I0 is glitch-free, I would be more suspicious about the data in the range 10-14A-1 than this 8A-1 feature. Cheers denis > Today's Topics: > > 1. k-range question & R-factor (Christopher Patridge) > > > > Hello Users, > > I was looking for an opinion about the chi(k) signal in a set of data I > am analyzing. Brief background, this is a set of in-situ XAS data > collected at the Fe K edge from a working electrochemical cell at a > range of potentials during charge; I did not collect the data. I suspect > the feature at ~ 8 angstroms-1, although present in all the spectra is > noise or glitch and wondered if I am being overly cautious? > > My conservative range ( k = 2-7 and R = 1-2) really constrains the model > Nidp = 3.31. Luckily, multiple datasets ( 8 ) to the rescue to give me > some flexibility. In a multiple dataset fitting, is the R-factor of the > whole set just the average or total mismatch across all the datasets or > it calculated another way? > > Working towards happiness, > > Chris Patridge > -- Denis Testemale Institut Néel FAME beamline at ESRF +33 476 881 045

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improving fitting
by Zhaomo Tian 11 Jan '13

11 Jan '13

1 0

Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 119, Issue 15
by Monson, Todd 09 Jan '13

09 Jan '13

When making my own feff input file, how should the data be delimited. When looking at existing feff input files I see a mixture of different spaces and tabs and am unsure how I should separate coordinates, ipots, tags, etc. Thanks, Todd -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, January 09, 2013 11:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 119, Issue 15 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: Larch 0.9.17 available for download and testing (Matt Newville) 2. Re: Larch 0.9.17 available for download and testing (Yu-Sheng Chen) 3. self absorption correction (sumitk(a)barc.gov.in) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Jan 2013 16:07:28 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch 0.9.17 available for download and testing Message-ID: <CA+7ESbq8w5MOAFu-rRJUi71WpVDjoNXG6VOpmiD_xryztVFQdQ(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Bruce, Again, sorry (ever so slightly -- the skiing was great!!) for the delay. I think (not 100% sure) I understand have solved the trouble with wxmplot on ubuntu. On an ubuntu 12.04 system (that had been upgraded a few times, and is begging to be updated to 12.10), I saw that importing wxmplot raised an error because maplotlib requires wx version 2.8 or greater but a regular old "import wx" was using the antique wx 2.6 series. I would be tempted to say that ubuntu is acting strangely by assuming "import wx" means "oldest possible version of a library", but I'm sure fixing at my end is easier than fixing all installed Ubuntu systems. I've updated wxmplot to version 0.9.11, which now correctly requires wx 2.8 or higher. You should be able to now do easy_install or install with 'python setup.py install' from the wxmplot-0.9.11 source kit linked at http://newville.github.com/wxmplot/installation.html I also had to make sure that larch was insisting that wx 2.8 or higher was being used. These changes are now pushed into the github distribution. With these changes, I could successfully install wxmplot and larch on an Ubuntu. I think that must be the same problem you were seeing, but I'd be happy to hear your experience. --Matt On Wed, Jan 2, 2013 at 1:51 PM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > Matt, > > I am having some troubles getting Larch installed on one of my Ubuntu > machines. "sudo python setup.py install" complains about wxmplot > being missing. OK, I did > > bruce@lachesis [xraylarch] > sudo -E easy_install wxmplot > sudo: unable to resolve host lachesis.bnl.gov > Searching for wxmplot > Best match: wxmplot 0.9.10 > Processing wxmplot-0.9.10-py2.7.egg > wxmplot 0.9.10 is already the active version in easy-install.pth > > Using /usr/local/lib/python2.7/dist-packages/wxmplot-0.9.10-py2.7.egg > Processing dependencies for wxmplot > Finished processing dependencies for wxmplot > > and tried again. > > bruce@lachesis [xraylarch] > sudo python setup.py install > sudo: unable to resolve host lachesis.bnl.gov > Checking dependencies.... > == Cannot Install Larch: Required Modules are Missing == > wxmplot is REQUIRED > > Please read INSTALL for further information. > > OK. I cloned a copy of wxmplot from your github repo and installed it > by hand with no problem. However, same result when trying to setup > xraylarch. > > Any advice? > > Thx, > B > > -- > > 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 > > Homepage: http://xafs.org/BruceRavel > Software: https://github.com/bruceravel > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 2 Date: Tue, 8 Jan 2013 23:21:54 +0000 From: Yu-Sheng Chen <yschen(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch 0.9.17 available for download and testing Message-ID: <63D4F9008F0BD04FAC515D20F0CC6A46437D035A(a)CARSMAIL2.CARS.APS.ANL.GOV> Content-Type: text/plain; charset="us-ascii" Hello Mark. I think you got 3 shifts this coming run. Yu-Sheng **************************************** Yu-Sheng Chen, Ph.D. Center for Advanced Radiation Sources The University of Chicago c/o APS/ANL 9700 S. Cass Ave. Bldg. 434 D Argonne, IL 60439 USA Tel: +1 630-252-0471 Fax: +1 630-252-0460 EMail: yschen(a)cars.uchicago.edu -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville Sent: Tuesday, January 08, 2013 4:07 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Larch 0.9.17 available for download and testing Hi Bruce, Again, sorry (ever so slightly -- the skiing was great!!) for the delay. I think (not 100% sure) I understand have solved the trouble with wxmplot on ubuntu. On an ubuntu 12.04 system (that had been upgraded a few times, and is begging to be updated to 12.10), I saw that importing wxmplot raised an error because maplotlib requires wx version 2.8 or greater but a regular old "import wx" was using the antique wx 2.6 series. I would be tempted to say that ubuntu is acting strangely by assuming "import wx" means "oldest possible version of a library", but I'm sure fixing at my end is easier than fixing all installed Ubuntu systems. I've updated wxmplot to version 0.9.11, which now correctly requires wx 2.8 or higher. You should be able to now do easy_install or install with 'python setup.py install' from the wxmplot-0.9.11 source kit linked at http://newville.github.com/wxmplot/installation.html I also had to make sure that larch was insisting that wx 2.8 or higher was being used. These changes are now pushed into the github distribution. With these changes, I could successfully install wxmplot and larch on an Ubuntu. I think that must be the same problem you were seeing, but I'd be happy to hear your experience. --Matt On Wed, Jan 2, 2013 at 1:51 PM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > Matt, > > I am having some troubles getting Larch installed on one of my Ubuntu > machines. "sudo python setup.py install" complains about wxmplot > being missing. OK, I did > > bruce@lachesis [xraylarch] > sudo -E easy_install wxmplot > sudo: unable to resolve host lachesis.bnl.gov > Searching for wxmplot > Best match: wxmplot 0.9.10 > Processing wxmplot-0.9.10-py2.7.egg > wxmplot 0.9.10 is already the active version in easy-install.pth > > Using /usr/local/lib/python2.7/dist-packages/wxmplot-0.9.10-py2.7.egg > Processing dependencies for wxmplot > Finished processing dependencies for wxmplot > > and tried again. > > bruce@lachesis [xraylarch] > sudo python setup.py install > sudo: unable to resolve host lachesis.bnl.gov > Checking dependencies.... > == Cannot Install Larch: Required Modules are Missing == > wxmplot is REQUIRED > > Please read INSTALL for further information. > > OK. I cloned a copy of wxmplot from your github repo and installed it > by hand with no problem. However, same result when trying to setup > xraylarch. > > Any advice? > > Thx, > B > > -- > > 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 > > Homepage: http://xafs.org/BruceRavel > Software: https://github.com/bruceravel > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ Message: 3 Date: Wed, 9 Jan 2013 10:28:17 +0530 From: sumitk(a)barc.gov.in To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] self absorption correction Message-ID: <335f18a7175b0c8a9d74662ec1c2dfe7.squirrel(a)bts.barc.gov.in> Content-Type: text/plain;charset=UTF-8 Thanks Bruce. Till the time i look into the suggested works, here is the missing informations. Question: how to check the appropriateness of the self absorption correction? I don't have corresponding transmission data. The question came to my mind when i compared the uncorrected (of courese corrected for dead time) data and the corrected (with SiO2Eu0.002 formula; the formula corresponds to the mole (roughly atom)percentage. The edge jump enhanced after correction to ~1 from ~0.04. Material: Eu(III) sorbed on silica. Sumit -- Sumit Kumar Scientific Officer(E) Radioanalytical Chemistry Division Bhabha Atomic Research Centre Mumbai, India-400 085. Phone: +91-22-2559 4093/0644 (O). ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 119, Issue 15 ****************************************

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Larch 0.9.17 available for download and testing
by Matt Newville 08 Jan '13

08 Jan '13

Hi Folks, I'm happy to announce the first full release of Larch, the next generation of Ifeffit. This includes a kit for source installation and a binary installer for Windows. A primitive Larch GUI is included that provides a command-line interface and a browser / help system for data in the Larch session. Essentially all the EXAFS and XANES functionality of Ifeffit 1,2 is reproduced in Larch, with several significant improvements. The current version (0.9.17) should still be considered "beta" software in that bugs should be expected, but Larch is now ready for detailed "field-testing" and use. It you're using Ifeffit for scripting (that is, not using the GUIs Athena, Artemis, SixPack, or Prestopronto that call Ifeffit), you should start using Larch now. Several months ago, I described the goals and status of Larch (see http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012-June/010586.html) which is still accurate. Since then, the biggest effort has been in documentation, finishing some of the details of Feffit() fitting, and testing. Larch is available at http://xraypy.github.com/xraylarch/ and http://cars.uchicago.edu/xraylarch/ Any feedback on any part of Larch is welcome. I am especially interested in hearing reports from people trying the Windows installer -- I've tested it only on 3 Windows7 machines. I also reiterate my plea for people to get involved in the development and extension of these tools. A main motivation for Larch's implementation and design was to make it very easy to add new features and experiment with new algorithms and methods for analysis. If you're interested in helping Bruce or I develop these codes, please let us know. Some of you may have noticed that support for the Ifeffit 1.2 series has been very poor recently, including the fact that building for Mac OS X has fallen far behind. With this release of Larch, I'm very happy to formally end support for Ifeffit 1.2. I'm willing to use, and help others use, the older versions of Ifeffit, Athena, etc, but there will be no more releases or bug fixes for the Ifeffit 1.2 series. The code is available if someone else wants to maintain it. Thanks, --Matt Newville

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Correction for self absorption in fluorescence mode XAFS data
by sumitk＠barc.gov.in 08 Jan '13

08 Jan '13

Hi, I am analyzing a Eu-L3 edge XAFS data measured in fluorescence mode. My question is regarding the appropriateness of the self absorption correction of the data. I am aware that by supplying chemical formula along with other requisite informations (angle, etc.) I can execute the self absorption correction in Athena. Also, by comparing data measured in transmission and fluorescence modes the correction can be achieved. I have only six scans of fluorescence mode measurement and by applying the correction to these scans in Athena, I have observed enhanced amplitude in mu(E) data. I am not able to see how to check the appropriate of correction. An Athena file is attached to look into. Expecting the community to help, Sumit Sumit Kumar Scientific Officer Radioanalytical Chemistry Division Bhabha Atomic Research centre, Mumbai India. Ph: +91-22-2559 4093. -- Sumit Kumar Scientific Officer(E) Radioanalytical Chemistry Division Bhabha Atomic Research Centre Mumbai, India-400 085. Phone: +91-22-2559 4093/0644 (O).

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Deglitching in Athena 0.9.14
by Lyle Gordon 07 Jan '13

07 Jan '13

Dear Bruce and Ifeffit users, I just installed the latest version of Demeter, 0.9.14, on my Windows 7 computer. I tried to deglitch a dataset in x(E). Upon clicking "choose a point" the window pops up telling me to double click in the gnuplot window. I can select a point but there doesn't appear to be any feedback in the UI about which point was selected until after clicking ok. Then after ok I get a large "E". It is difficult to tell sometimes exactly which point was selected as the E is quite large. I guess this is turning into more a "bug" report/feature request, but I felt the previous interface in Athena 0.8.054 gave much more feedback during the deglitching process of removing points. I was wondering if there was a setting that could change back to the old style or if this was a decision based on the limitation of gnuplot/perl. I hope this submission is alright for the mailing list. In the future I could post these "issues" on github. Thanks very much, Lyle

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Using this mailing list effectively
by Zhaomo Tian 07 Jan '13

07 Jan '13

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