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

Re: [Ifeffit] Help with importing binary files from NSLS BM X15B in athena (Bruce Ravel)
by Raoul-Marie Couture 30 Jan '13

30 Jan '13

Dear Bruce, The patch worked, I was able to configure the plugin and import the binary data. I changed the default columns, otherwise some files were imported scrambled: Energy :1 (that one was ok) I0 : 6 (that one was ok) Narrow (I imported I_Trans instead): column 7 Trans (I imported Total_fluo instead): column 8 Wide (I imported S K-alpha fluo instead): column 9. Thanks for the quick and helpful reply. Raoul ________________________________________ 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: January 30, 2013 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 119, Issue 31 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. Look for paper about WL (Gudrun Lisa Bovenkamp) 2. Re: Help with importing binary files from NSLS BM X15B in athena (Bruce Ravel) 3. Re: Look for paper about WL (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 30 Jan 2013 04:27:35 +0100 From: "Gudrun Lisa Bovenkamp" <bovenkamp(a)physik.uni-bonn.de> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Look for paper about WL Message-ID: <web-12374983(a)be2.uni-bonn.de> Content-Type: text/plain;charset=iso-8859-1; format="flowed" Dear all, I need reference (paper) to say that WL refers to anti-bonding orbitals and in the same context that pre-edge refers to bonding orbitals. Is there any paper that can help me? Thanks, Lisa ------------------------------ Message: 2 Date: Wed, 30 Jan 2013 10:03:49 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Help with importing binary files from NSLS BM X15B in athena Message-ID: <1855179.1CSfgNSBKa(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" On Wednesday, January 30, 2013 02:17:35 AM Raoul-Marie Couture wrote: > I'm trying to import binary files generated at BM X15B of NSLS, at the S > K-edge. I selected the corresponding plugin, and Athena (Demeter 0.9.14) > does not import the columns 7-10 containing the Io, It, IF and S > Kalpha-fluo. It only imports the first few columns and they don't contain > the information I need. If I ask Athena to import more columns it crashes > and exit. When I use the utility at BM X15B to convert the binary files in > simple text files, Athena does not recognize the text files as data file. > I'm I doing something wrong ? Any idea how to solve this problem ? I have > attached a binary file, its text translation (using the utility available > at BM X15B), and a screenshot of what happens when I import a binary file. The problem seems to be one of column selection. I am suspicious that a detail of how the data are saved to the binary files may have changed since I wrote the X15B plugin many years ago. Attached are two file that you should be able to drop in place on top of your current installation. Put both files in C:\strawberry\perl\site\lib\Demeter\Plugins The file "X15B.pm" wil replace the version of the file that is already there. The file "x15b.demeter_conf" is new. Make sure that you save them with filenames *exactly* as written above. For instance, if you let Outlook save "X15B.pm" as "X15B.pm.txt", it won't be recognized by Athena and everything I say below won't work. The new file will allow you configure the X15B plugin. In the Plugin Registry page, rightt click on the X15B entry. See: http://bruceravel.github.com/demeter/aug/other/plugin.html#athena%27splugin… The variables set using that configuration file, tell Athena which columns from the original data file (also which columns from the text conversion using the beamlilne tool) should be preserved when Athena converts the binary blob to an ascii column file. Most of the columns are filled with zeros, which is why the plugin wants to discard those columns. Side note: Athena deals very pooly with ascii data file that don't have the energy in the first column, which is why it has trouble reading the text file from the beamline tool. I would like to hear back from you about how this works out. If it works well for you, then it will be included in the next release of the software. If there are still problems -- then I need to know. B PS: It is possible that the "x15b.demeter_conf" file has the columns for narrow and wide backwards. Let me know if you think that's the case. I am writing this email without wandering down to X15B to ask Paul the details. -- 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

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Look for paper about WL
by Gudrun Lisa Bovenkamp 30 Jan '13

30 Jan '13

Dear all, I need reference (paper) to say that WL refers to anti-bonding orbitals and in the same context that pre-edge refers to bonding orbitals. Is there any paper that can help me? Thanks, Lisa

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Help with importing binary files from NSLS BM X15B in athena
by Raoul-Marie Couture 30 Jan '13

30 Jan '13

Dear all, I'm trying to import binary files generated at BM X15B of NSLS, at the S K-edge. I selected the corresponding plugin, and Athena (Demeter 0.9.14) does not import the columns 7-10 containing the Io, It, IF and S Kalpha-fluo. It only imports the first few columns and they don't contain the information I need. If I ask Athena to import more columns it crashes and exit. When I use the utility at BM X15B to convert the binary files in simple text files, Athena does not recognize the text files as data file. I'm I doing something wrong ? Any idea how to solve this problem ? I have attached a binary file, its text translation (using the utility available at BM X15B), and a screenshot of what happens when I import a binary file. Thanks for the help Regards, Raoul Couture <https://sites.google.com/site/couturerm/>

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Different R-factor values
by Christopher Patridge 25 Jan '13

25 Jan '13

Hello List, I know that Horae is no longer supported but I had quick question about the R-factor. I search the mailing list and found this post from 2006 concerning different R-factors in the fit log I have a question about Artemis log file. I noticed that two r-factors are > reported in the log file. One is in the fifth line and it is called > 'R-factor' and the other one is under the data set fitting conditions and > it is called 'r-factor for this data set'. They have in general different > values. What does it mean? Which is the difference between the two? It probably means that I am calculating something wrongly. Here's the concept. If you do a multiple data set fit and you have some value of R-factor, you would like to know how that misfit is partitioned among the data sets. That is, you'd like to know if one set is contributing to the misfit for significantly than the others. When Ifeffit computes the R-factor, it is for the entire fit. My idea in Artemis was to use the formula for R factor from page 18 of http://cars9.uchicago.edu/~newville/feffit/feffit.ps <http://cars9.uchicago.edu/%7Enewville/feffit/feffit.ps> on each data set in a multiple data set fit and report that in the log file. At some point, I must have convinced myself that I was doing the calulcation in Artemis identically to how it is done in Ifeffit. If you are seeing different values, it would seem I was mistaken. I'll make an entry in my to do list to look into that. I am reviewing some older analysis projects from artemis and just wanted to know which R-factor more accurately describes the misfit? I suspect the average over the k weights values since this was adopted in Demeter? 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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(D)Artemis and (D)Athena crash - perl not responding
by Matthias Filez 24 Jan '13

24 Jan '13

Dear all, Several days ago, I was using (D)Artemis of the Demeter with Strawberry Perl package version 0.9.13.1 on a Windows 7 64-bit Operating System. Suddenly, the software crashed when opening (D)Artemis. Ever since, (D)Artemis and (D)Athena do not respond anymore when I open them. The windows pop up, but the buttons inside the window do not appear anymore and the software gets stuck. When trying to check for a solution, "perl.exe does not respond" is given as a comment. (D)Hephaestos works fine. (D)Atoms functions until I load an .inp file, then it gets stuck too. I already tried to reinstall and to update to the newest version (9.14), but nothing helps. I tried to install Strawberry Perl's newest version, but since the necessary modules are included in the Demeter software this is probably useless. Does someone know what to do? Thanks a lot, Matthias Filez _____________________ Ir. Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: <http://helpdesk.ugent.be/e-maildisclaimer.php> http://helpdesk.UGent.be/e-maildisclaimer.php

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Artemis crash and data set limit
by Christopher Patridge 23 Jan '13

23 Jan '13

Hi List, My project file crash about five minutes and I found the dartemis log file attached before opening the program again which I hope will explain the problem. is there a limit to the number of datasets in Artemis? Thanks, Chris -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

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self absorption correction
by sumitk＠barc.gov.in 22 Jan '13

22 Jan '13

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).

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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

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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

4 3

Using this mailing list effectively
by Zhaomo Tian 06 Jan '13

06 Jan '13

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Using this mailing list effectively
by Ravel, Bruce 06 Jan '13

06 Jan '13

> I think you are really right, I am in too great a hurry that I lost my patience to set a time to learn basics quietly. Thanks for reminding. > And for my second question, could you give me some suggestion too? Mr. Tian, Asking questions is an art. Anyone can barf out sentences that end with a question mark, but asking questions that will prompt a useful and constructive discussion is a subtle and skillful business. Both Chris and I tried to tell you that in our earlier responses, but apparently there is a need to be more explicit. You are doing some things wrongly. I say this not to be mean and not to diminish you, but because I spend a lot of my professional time teaching people how to do XAS. It is important to me that people practice our craft well. This mailing list is a powerful tool to that end. When it is used well, the people who solicit help from this list profit significantly. When it used poorly, the people who volunteer their time answering questions become frustrated and the person asking the questions goes away with nothing. So ... here are three comments: (1) I am frustrated that you are not using the most recent version of my software. You are using a version of Artemis that is about 4 years old. I have no intention of continuing support for the older versions of my software. (2) Your second question refers to 4 sets of data, which you posted to the mailing list not in an Athena project file, but in an Artemis project file. That's odd. It would be much easier to examine the data in the form of an Athena project file. Many of the issues in your recent line of questioning referred to S02. As Scott pointed out, the evaluation of S02 is related to the determination of the normalization and background. If you want people to help you with your actual question, it would be prudent to provide the data in a form that allows examination of all steps of the data processing. My point here is that you simply must think about how you pose your question -- that includes thinking hard about how to present your data to the person whose help you are soliciting. (3) Your first email on the topic of these Cu films was somewhat misleading in that your initial complaint seemed to be about a strange measure of coordination number on a Cu foil. In that email, you gave a hint as to the actual form of the data, but scant information about how the data were measured and none about how the data were processed and analyzed. After prompts from Scott and other, you have provided a bit more information about your actual measurement, but not enough to actually know what's going on. As long as your line of questioning remains vague as to the details of the problem, the best you can expect are vague answers of the sort that you have already received. Since I am suggesting that you be more thoughtful and explicit in how you communicate here on the list, it is important that I do the same. Here is an example of what I consider to be a well-asked question. My example comes from a posting that I myself made to the WxPerl mailing list last year. WxPerl is the programming tool I use to make the GUIs Athena, Artemis, and Hephaestus. At the time, I was having a problem getting menus to post properly when making right-mouse clicks in various places in Athena. While the question is rather technical and I don't expect a non-programmer to follow all the details, it is still instructive: http://www.nntp.perl.org/group/perl.wxperl.users/2011/03/msg7929.html Note first that in five brief lines of text I summarized my problem. I then gave a complete example of how someone else could reproduce my problem on their own computer. I then explained both what I expected to happen and what actually happened. The point here is that I took the time to condense my question into a form that the people at the other end could understand and address with a minimum of effort. Sure enough, I got useful responses from 2 knowledgeable (and, no doubt, very busy) people. Mr. Tian, to the extent that it seems like I am singling you out for special criticism, I sincerely apologize. But you have been posting to this mailing list rather often of late and you are doing so in a way that is probably not getting you the sort of results you would like to see. I understand that this is an English language mailing list and that it is difficult to be as expressive in another tongue as you can be in your own. (I really do understand that -- I have suffered through learning two other languages in my life. It really is hard.) But you have to try if you want to get useful results. B

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Re: [Ifeffit] Problem downloading windows installer for Demeter
by Ravel, Bruce 06 Jan '13

06 Jan '13

Javier, Thanks for reporting this problem. This is related to a recent change in how GitHub handles large binary files. I thought I had fashioned a solution. Turns out that I was mistaken. I have come up with a different solution for distributing the Installer and Updater files and I've updated the links at http://bruceravel.github.com/demeter/ Please go back and try again. Sorry for the inconvenience. Also, please use the Ifeffit mailing list (http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) for this sort of thing rather than emailing me directly. Cheers, B ________________________________________ From: Javier Alonso [jalonsomasa(a)gmail.com] Sent: Sunday, January 06, 2013 7:59 AM To: Ravel, Bruce Subject: Problem downloading windows installer for Demeter Dear Dr. Ravel, Firts, I'd like to personally thank you for Demeter: it really helps me a lot with my XAS data analysis. And now the problem: I'm trying to download the windows installer for Demeter from the webpage: http://bruceravel.github.com/demeter/ but I keep receiving the same error message again and again: Error: blob is too big I think this is something related to Github and the limit of file sizes, but I haven't been able to find an alternative downloading site or similar. Thanks in advance, Javier Alonso -- Javier Alonso Masa Departamento de Electricidad y Electrónica Facultad de Ciencia y Tecnología. Universidad del País Vasco 48940 Leioa(Spain) http://www.gmmmt.net/ Phone: +34 94 601 5400 / +34 695325749

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(no subject)
by Zhaomo Tian 05 Jan '13

05 Jan '13

1 0

(no subject)
by Zhaomo Tian 04 Jan '13

04 Jan '13

3 2

Cu fitting with and without CO adsorption
by Zhaomo Tian 04 Jan '13

04 Jan '13

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Understanding effect of dopant using ARTEMIS
by Devender 03 Jan '13

03 Jan '13

Hi, Happy new year! I am a graduate student in material science at RPI. I am interested in understanding doping of elements in bismuth telluride (Bi2Te3). By understanding I mean, where it is going (interstitial sites or replacing any element in crystal) and what it is doing (changing band structure, electronic states etc.). For that, we carried experiments at beamline X19A at BNL couple of months ago. On primary analysis using ATHENA, we see some indications of interestitial site occupancy (attached is ChiR vs radial distance plots). To confirm this hypothesis, I am thinking of simulating spectra using ARTEMIS. Plan is- 1) First, match spectra of bismuth telluride with standard 2) Add dopant at interstitial sites and other possible sites, and simulate spectra to see if it matches with experimental spectra. I am seeking help/guidance on following, 1) Getting started with ARTEMIS- I have started learning ARTEMIS but still don't understand a lot of parameters. I will appreciate if someone can send me tutorials on recent version of ARTEMIS, feff tutorials on some websites are for command line version. I don't understand many of the parameters in ARTEMIS and any detailed tutorial will really help. I don't want to tweak parameters without understanding them completely. 2) Input atom file for ARTEMIS- I have cif file for Bi2Te3, how can I import that in "ATOMS" for making input file for ARTEMIS? Once I can create Bi2Te3 crystal using ATOMS, I think I can add Cl (dopant) to simulate other spectra easily. I would love to hear any feedback on approach too. Thanks and regards, Devender www.rpi.edu/~devend/

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background subtraction process in Athena
by Zhaomo Tian 03 Jan '13

03 Jan '13

3 2