June 2016 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Regarding time resolved XAS
by Chris Milne 26 Jul '16

26 Jul '16

Hi Mazhar, Usually time-resolved (pump-probe) XAS is measured in data set pairs at each X-ray energy: one with laser on, one with laser off. This means that you can always directly reference your laser-excited measurement to your laser un-excited measurement. To calibrate to an absolute scale you would then use a reference foil as normal and shift both data sets according to the reference values. If you had significant delays between your laser on/off measurements then drifts and other noise sources will affect your data, making it very difficult to determine a reliable difference signal. You could try to use a reference foil measurement to correct for these kinds of drifts but you need to be very careful with the corrections to ensure you aren’t just seeing an artifact. Ideally you would be measuring laser on/off differences on a millisecond to microsecond timescale between acquisitions, this gets rid of most of the possible noise sources. Best, Chris > On 30 May 2016, at 19:00 , 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. Regarding time resolved XAS (mazhar iqbal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 May 2016 06:20:36 +0000 (UTC) > From: mazhar iqbal <mazharphy_05(a)yahoo.com> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Regarding time resolved XAS > Message-ID: > <349705754.1395970.1464589236411.JavaMail.yahoo(a)mail.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > hello.. I am sorry if am not posting on right place. > I want to ask about the aligning the XAS spectra that is given in Athena. Can we do the alignment of time resolved spectra? As you know that the resolved spectra (IR pump X-ray probe) may have edge shift due to laser pumping. Do you think that the same method of the alignment can be applied here as well. An additional piece of information is that ?we have a reference fluorescence line always on the screen that well behind the K absorption edge. > Hoping to see your response.? > Best Regards >

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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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NiO-test-athena-project
by mazhar iqbal 17 Jun '16

17 Jun '16

Hello I would appreciate valuable comments on the NiO spectrum processed in athena. I am a new in this area so please comment on any mistake I have made while processing. Best Regards

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Athena crash on Mac when exporting empirical standard
by Chloe Yi-Yi Wu 17 Jun '16

17 Jun '16

Hi all, I'd like to export an empirical standard from Athena to fit EXAFS with Artemis. However, once I clicked on the element for scattering in the pop-up window, Athena was frozen and no .es file was generated. Does anyone know how to fix the problem? Thanks, Chloe -- Yi-Yi (Chloe) Wu Kung Research Group Dept. of Chemical and Biological Engineering Northwestern University Evanston, IL USA

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Sorbed complex in Atoms
by Gnu script 09 Jun '16

09 Jun '16

Dear All, I am relatively new to Ifeffit and Artemis. I am trying to find a way to create four-shell model of an outer-sphere complex in Atoms or some other way readable by Atoms. I have no idea about the geometry, space group but some rough guess of bond-distances. The model to test against the EXAFS data is: Ni is the central atom Ni-O first shell Ni-Ni second shell Ni-Ti third shell Ni-Si fourth shell The model aims to test the adsorption of Ni on the surface of Ti-containing silicate mineral. Could you please help. Thanks.

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Question about fuzzy degeneracy
by Mirko 09 Jun '16

09 Jun '16

Hey, I am quite new to EXAFS and therefore very glad about this mailing list, it helps a lot. My question is about the fuzzy degeneracy mentioned in the paper "Path degeneracy and EXAFS analysis of disordered materials" (Ravel, B. J Synchrotron Radiat. <http://www.ncbi.nlm.nih.gov/pubmed/25343794>2014 Nov;21(Pt 6):1269-74.) I investigate disordered systems like aqueous salt solutions and would like to use the method on my FEFF calculation. However, I obtained my structure for the FEFF calculation from a MD-Simulation and would like to average over several hundreds of FEFF calculations. To handle this amount of data I use LARCH, which doesn’t have the feature to degenerate similarpaths to one. I would like to use the method by myself to degenerate the first coordination shell of my oxygen atoms around the salt. How do you merge the FEFF parameters from each scattering paths after they are grouped together in a bin with the extended pathfinder algorithm (I think, you can’t just make an average of for example the phase shift or the mean free path … right?) Best regards and thanks a lot! Mirko ------------------------------------------------------------------------

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Substantial problems running ATOMS in Demeter 0.9.24
by Jeff Catalano 08 Jun '16

08 Jun '16

The message sequence from this morning prompted me to inquire if anyone can provide help with ATOMS crashing on my own computer. I am running Demeter 0.9.24 on Windows 10 Pro 64. I did a fresh install of Demeter after having removed all older versions of Demeter 0.9, including the Demeter folders in C:\Users\<username>\AppData\Roaming\. My problem is unfortunately simple and something I do not know how to fix: Whenever I hit the "Run Atoms" button, stand-alone atoms crashes. The program simply dies, and no files are written. I am able to enter text, save an atoms.inp file, and reload an atoms.inp file, but "Run Atoms" crashes the program. I have tested this with a simple compound, NaCl, using the attached atoms.inp file. Note that I don't want to work on NaCl, I just used this to test a simple structure. The log file associated with the crash is attached. The log file says Windows 8, but I think this is just hows Windows 10 shows up as that is what I am running, from a clean Windows 10 install. Anyway, when I load this atoms.inp file or enter the same information by hand the program crashes. I was able to load and run this atoms.inp file in the old version of atoms (3.0.1) and produced the attached feff_oldATOMS.inp file. I thus don't think it is a data entry problem. I hope that I have provided enough information. I have no problems running ATHENA, ARTEMIS, or HEPHAESTUS. Given the log file I suspect this is something unique to my computer, but I am stumped as to what it could be as I am running a standard OS with a standard install on Demeter. Thank you, Jeff -- Jeffrey G. Catalano, Associate Professor Department of Earth and Planetary Sciences Washington University 1 Brookings Drive, Campus Box 1169 Saint Louis, MO 63130 USA http://aqgeochem.wustl.edu/

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