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

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

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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

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