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

Artemis (FEFF) question
by Louis Forto 12 Jul '16

12 Jul '16

Dear All, I am trying to run a FEFF calculations on a quaternary glass , when I import crystalline data obtained from ICSD website and try to run FEFF to calculate the scattering paths of nearest neighbour atoms relative to absorbing atom, I get an error message that says " generate one or more common positions and their occupancies sum to more than 1". I don't know how to go about this, any help , I will appreciate. Thanks.

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Athena crash on mac on import
by George Sterbinsky 08 Jul '16

08 Jul '16

Hello, Athena crashes upon import of the attached project file. I am using the latest release of Athena for mac (0.9.22) on OSX 10.10.5. I am able to open the file on windows. The message that is printed to the terminal when Athena crashes is pasted below. Please let me know if any further information would be helpful. Thank you, George [!!!] bkg_funnorm is not an attribute to set for Demeter::Data=HASH(0x7fe2e57967c8) at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/MooseX/SetGet.pm line 9. MooseX::SetGet::set(Demeter::Data=HASH(0x7fe2e57967c8), "bkg_spl2e", 110.195726042215, "y_offset", 0, "bft_rwindow", "hanning", "fft_kwindow", "hanning", ...) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm line 411 Demeter::Data::Prj::_record(Demeter::Data::Prj=HASH(0x7fe2e5785c70), 5, "psmtj") called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm line 197 Demeter::Data::Prj::record(Demeter::Data::Prj=HASH(0x7fe2e5785c70), 1) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena/IO.pm line 802 Demeter::UI::Athena::IO::_prj(Demeter::UI::Athena=HASH(0x7fe2dc0226a8), "/Users...sta"..., "/Users...sta"..., 1, "") called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena/IO.pm line 164 Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x7fe2dc0226a8)) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 859 Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x7fe2e28ff570), Wx::CommandEvent=SCALAR(0x7fe2e5781840), Demeter::UI::Athena=HASH(0x7fe2dc0226a8)) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 782 Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x7fe2e28ff570), Wx::CommandEvent=SCALAR(0x7fe2e5781840)) called at /opt/local/bin/athena line 44 eval {...} called at /opt/local/bin/athena line 44

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Re: [Ifeffit] How to change the data file in Dartemis?
by Isabelle Kieffer 08 Jul '16

08 Jul '16

Dear Bruce, dear all, Just to add some input and precise my question. The problem I encounter with "replace this chi(k)" did not appear to me until I tried to fit a spectrum twice with two different normalisations. In this case, after a fit on the first spectrum, I "replace this chi" with another that is normalised differently, and when I try to fit, it stops with the following error message: This data came from the the same source as another data group. You seem to be trying to increase your number of independent points by fitting the same data more than once in a multiple data set fit. Seeing that, I wondered whether "replace this chi" was doing what I thought. The upgrade did not change anything. I just tried with a colleague working under windows and the result is also the same. Shall I do differently to fit those two really similar spectra? Thank you for your help, Isabelle On 01/07/2016 21:08, Bruce Ravel wrote: > On 07/01/2016 01:57 PM, Isabelle Kieffer wrote: >> You mean that when you "Replace this chi(k)", it asks what to do, or it >> supposes that you want to fit new data with the same model? > > What I mean is: upgrade. Many of the problems you are reporting have > been fixed already. If you upgrade and still see these problems, make > a bug report and I will look into it. > > B > > -- Isabelle KIEFFER, Ingénieur de Recherche CNRS, Ligne CRG FAME (BM30B) ESRF - The European Synchrotron CS 40220 - 38043 Grenoble Cedex 9 - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50

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Athena and Artemis on the Mac
by Bruce Ravel 08 Jul '16

08 Jul '16

A few minutes ago, I made a post suggesting a work-around to a problem reported by a Mac user. My suggestion was an inherently horrible solution. That sort of line-by-line hackery is completely unsustainable. The real solution is that that fellow and his colleague should both be using the most recent version of Athena. If Athena and Artemis are to be supported on the Mac, then someone is going to have to find the time and willingness to maintain the Mac packaging. Joe Fowler did an amazingly generous thing when he made the MacPorts package, but Joe does not (to my knowledge) use Athena and Artemis for his own work. Someone who is invested in the use of the software simply has to step up. I myself have neither the resources nor the interest in doing so. If no one steps up, then there simply won't be support for my software on the Mac. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Breaking off spec files within Athena
by Katharine Elizabeth Silberstein 07 Jul '16

07 Jul '16

Hi, The Cornell High Energy Synchrotron Source (CHESS) primarily uses SPEC software for XAS data collection. The data output is one continuous file containing individual scans. We are able to break off scans to import into Athena. For the convenience of CHESS users, is there any way for Athena to recognize a continuous file besides manually setting data ranges during import? Thanks, Katie Silberstein CHESS Postdoctoral Associate

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How to change the data file in Dartemis?
by Isabelle Kieffer 01 Jul '16

01 Jul '16

Dear all, I am using artemis from Demeter and I am unable to "change the current data file (that is, to apply this fitting model to a different data set)" as it was possible with the "open file" function of the old artemis. This function openned a popup window asking to choose between "read a new data file" or "change the current data file". If I use the "open project or data" function of Dartemis (or the "Add" button of the "Data sets" frame), it opens the data set in a new window. Then, I am unable to use the paths and parameters used for the previous fit. Any attemp to export, transfer or drag/drop paths or parameters has either no effect or crashes the program. If I use the "Replace this chi(k)" function, it automatically chooses to "read a new data file (that is, to do multiple data set fitting)" without opening any popup window asking my choice. I suppose I did not find the good way to apply my fitting model to a new data set. Thank you for advice. Isabelle -- Isabelle KIEFFER, Ingénieur de Recherche CNRS, Ligne CRG FAME (BM30B) ESRF - The European Synchrotron CS 40220 - 38043 Grenoble Cedex 9 - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50

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How to input atoms in solid solution for Artemis
by Fuxiang Zhang 24 Jun '16

24 Jun '16

Hi, All, I am new in using EXAFS techniques. Just wondering how to input atomic structure of NiFe solid solution to Artemis. It has a simple Ni-structure, but both Ni and Fe occupy the same site. If I use partial occupancy, Artemis program does not allow. Anyone can give me an ideal? Also the coordination number N cannot be refined in this simple system (12), is that right? In fact I just want to get the N through the fitting of EXAFS because of the partial occupancy. Thank you very much Fuxiang Zhang

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Re: [Ifeffit] Ifeffit Digest, Vol 160, Issue 17
by Ditty Dixon 24 Jun '16

24 Jun '16

Hello Fuxiang, A small suggestion Please also don't forget to try multiple edge data fitting if you already measured your data in both Fe and Ni edge, this may actually reduce the number of parameters to use. You need just on parameter Fe-Ni/Ni-Fe should be same when looking from both atom Hope it helps, Ditty On Jun 23, 2016 23:48, <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: How to input atoms in solid solution for Artemis > (Scott Calvin) > 2. Re: How to input atoms in solid solution for Artemis > (Fuxiang Zhang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 23 Jun 2016 16:23:36 -0400 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] How to input atoms in solid solution for > Artemis > Message-ID: <F8C55BBE-4E8E-436E-97C4-35387D9B5B02(a)gmail.edu> > Content-Type: text/plain; charset="utf-8" > > One additional thought: > > Distinguishing Ni-Ni and Ni-Fe by creating two different feff paths and > fitting the spectrum as a mixture of the two is very difficult, to put it > mildly, as both Anatoly and Matt indicated. > > But the bond length determined by your fit may be able to give you a clue, > particularly when compared to appropriate standards. Depending on the > details of your structure, the average bond length may depend on the > fraction of sites occupied by iron to a degree which is measurable by > EXAFS. Even if you simply use a nickel-nickel scattering path in feff to > model your structure, differences in bond length could be indicative of > changes in site occupancy. > > Ideally, this could be done by creating a series of standards with known > iron-nickel ratios, fitting the bond length for each, and then comparing a > fit of a sample with a similar structure but unknown iron-nickel ratio to > the results for the standards. > > ?Scott Calvin > Sarah Lawrence College > > > On Jun 23, 2016, at 3:41 PM, Fuxiang Zhang <zhangfx(a)umich.edu> wrote: > > > > Hi, Matt and Anayoly, > > Thank you very much for the help. > > > > Fuxiang > > > > On Thu, Jun 23, 2016 at 1:51 PM, Anatoly I Frenkel <afrenke2(a)yu.edu > <mailto:afrenke2@yu.edu>> wrote: > > Whatever you decide to do, remember that Ni Ni and Ni Fe pairs look very > similar by EXAFS, so it does not matter how you end up doing it. > > You can as well use pure Ni but you may want to consider both fcc and > bcc structure for making the model because the alloy may end up to be > either that or that, especially if it is a nanoalloy. > > > > Anayoly > > > > > > > > Sent from my Verizon Wireless 4G LTE Tablet > > > > > > -------- Original message -------- > > From: Fuxiang Zhang <zhangfx(a)umich.edu <mailto:zhangfx@umich.edu>> > > Date: 6/23/2016 12:51 PM (GMT-05:00) > > To: ifeffit(a)millenia.cars.aps.anl.gov <mailto: > ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] How to input atoms in solid solution for Artemis > > > > Hi, All, > > I am new in using EXAFS techniques. Just wondering how to input atomic > structure of NiFe solid solution to Artemis. It has a simple Ni-structure, > but both Ni and Fe occupy the same site. If I use partial occupancy, > Artemis program does not allow. Anyone can give me an ideal? > > Also the coordination number N cannot be refined in this simple system > (12), is that right? In fact I just want to get the N through the fitting > of EXAFS because of the partial occupancy. > > Thank you very much > > > > Fuxiang Zhang > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov <mailto: > Ifeffit(a)millenia.cars.aps.anl.gov> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > >

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report bugs
by 储胜启 23 Jun '16

23 Jun '16

Hi, deal bruce, I have found a bug. When I click the button ‘Run Atoms’ in Artemis program, it will crash suddenly. I have tried this in different OS, Windows XP and Win7, and got the same error. The log file said as follows: Demeter version 0.9.24 Can't call method "workspace" on an undefined value at C:/MyProgramm/DemeterPerl/perl/site/lib/Demeter/UI/Atoms/Xtal.pm line 1004. Best wishes, -Shengqi Chu Beijing Synchrotron Radiation Facility, Beijing 100049，China

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Use of restraint
by Maureen Le Bars 22 Jun '16

22 Jun '16

Hello, I have a couple of questions about data analysis on artemis I used a restraint for my fits. I've read some documentation about it and found Matt Newville's talk (https://pubweb.bnl.gov/~frenkel/BNLworkshop2001/newville.pdf) It is reported that a restraint adds a "V" term to the chi-square (slides number 16 and 17). According to this formula, what is the number that artemis gives for the "restrain" parameter at the end of the fit? How should we consider this number in the evaluation of the fit ? I also don't really know very much about the scaling factor to apply in the formula : scale*penalty(X,a,b). I've read that the square root of chi-squareseems to be a good size from some of Bruce Ravel's answers in ifeffit mailing list. How does the scaling factor control the restraint ? What is its relationship with the chi-square ? Thank you in advance for your help, Maureen /PhD student at CIRAD - ADEME// //CEREGE - Europôle de l'Arbois// //BP 80// //13545 Aix en Provence Cedex 4 France +33 4 42 97 15 48/

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