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

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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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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Re: [Ifeffit] Artemis file opening
by Dien.Li＠srs.gov 06 Jun '16

06 Jun '16

Hi, Bob and Bruce With upgrading the Demeter 9;24, I am able to open files from 9.21. Thanks you all. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Date: 06/06/2016 03:01 PM Subject: Ifeffit Digest, Vol 160, Issue 8 Sent by: "Ifeffit" <ifeffit-bounces(a)millenia.cars.aps.anl.gov> 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: Ifeffit Digest, Vol 160, Issue 7 (Dien.Li(a)srs.gov) 2. Re: Ifeffit Digest, Vol 160, Issue 7 (Farquhar, Erik) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2016 13:50:42 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 160, Issue 7 Message-ID: <OF0754ACB2.B29F1774-ON85257FCA.00619402-85257FCA.006206D8(a)srs.gov> Content-Type: text/plain; charset="us-ascii" Hi, Bob and Bruce Thank for your quick response. No, I have not upgrade to 9.24 yet, because if one version Artemis is not able to open another version files, I am worried about that I can not open my all other current files, maybe the newer version is able to open the older version files. By the way, when I clicked the Artemis fitting file from my collaborator, after I saw Artemis picture logo, and several Artemis window flashed, and then gone, so that I failed to open. Thanks for any instruction. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Date: 06/06/2016 01:06 PM Subject: Ifeffit Digest, Vol 160, Issue 7 Sent by: "Ifeffit" <ifeffit-bounces(a)millenia.cars.aps.anl.gov> 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. Questions (Dien.Li(a)srs.gov) 2. Re: Questions (Robert Gordon) 3. Re: Questions (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2016 11:50:05 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Questions Message-ID: <OF4DB5BE28.5E4C9E2D-ON85257FCA.0056CE0F-85257FCA.0056FBB2(a)srs.gov> Content-Type: text/plain; charset="us-ascii" Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from my collaborator, anyone can instruct or help? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Re: [Ifeffit] Ifeffit Digest, Vol 160, Issue 7
by Dien.Li＠srs.gov 06 Jun '16

06 Jun '16

Hi, Bob and Bruce Thank for your quick response. No, I have not upgrade to 9.24 yet, because if one version Artemis is not able to open another version files, I am worried about that I can not open my all other current files, maybe the newer version is able to open the older version files. By the way, when I clicked the Artemis fitting file from my collaborator, after I saw Artemis picture logo, and several Artemis window flashed, and then gone, so that I failed to open. Thanks for any instruction. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Date: 06/06/2016 01:06 PM Subject: Ifeffit Digest, Vol 160, Issue 7 Sent by: "Ifeffit" <ifeffit-bounces(a)millenia.cars.aps.anl.gov> 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. Questions (Dien.Li(a)srs.gov) 2. Re: Questions (Robert Gordon) 3. Re: Questions (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2016 11:50:05 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Questions Message-ID: <OF4DB5BE28.5E4C9E2D-ON85257FCA.0056CE0F-85257FCA.0056FBB2(a)srs.gov> Content-Type: text/plain; charset="us-ascii" Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from my collaborator, anyone can instruct or help? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Questions
by Dien.Li＠srs.gov 06 Jun '16

06 Jun '16

Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from my collaborator, anyone can instruct or help? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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atoms crashes
by Jesús Eduardo Vega Castillo 03 Jun '16

03 Jun '16

Hello everyone, I have manually introduced the crystal structure of La4Fe3O10 into Atoms and generated and .inp file. The structure contains 2 sites of La, 2 sites of Fe and 4 sites of O. When I try to run Atoms from this file it crashes. This is the inp file: ## This Atoms file was generated by Demeter 0.9.24 ## Demeter written by and copyright (c) Bruce Ravel, 2006-2015 title = La4Fe3O10 (LSFC) space = I 4/m m m a = 3.83900 b = 3.83900 c = 27.87050 alpha = 90.00000 beta = 90.00000 gamma = 90.00000 rmax = 5.00000 core = Fe1 # polarization = 0.0 0.0 0.0 shift = 0.00000 0.00000 0.00000 atoms # el. x y z tag La 0.00000 0.00000 0.56860 La1 La 0.00000 0.00000 0.70130 La2 Fe 0.00000 0.00000 0.00000 Fe1 Fe 0.00000 0.00000 0.13840 Fe2 O 0.00000 0.50000 0.13810 O1 O 0.00000 0.00000 0.06980 O2 O 0.00000 0.00000 0.21050 O3 O 0.00000 0.50000 0.00000 O4 Any help would be appreciated. Yours, Jesús

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Re: [Ifeffit] Heavy Scatterer Resonance
by Matt Newville 02 Jun '16

02 Jun '16

Pieter, Please use the ifeffit mailing list for questions about XAFS Analysis. I am CCing this reply to that list. On Thu, Jun 2, 2016 at 2:35 AM, Pieter Tack <Pieter.Tack(a)ugent.be> wrote: > Dear Dr. Newville, > > > During the analyses of some metallic Au EXAFS I noticed the Au-Au single > scatter first shell is characterised by a split peak in the chi(R) > spectrum. I was wondering what caused this, as I would expect a single > scatter path resulting in only one scatter distance and thus one peak in > the chi(R). However, I could not find much on the matter except for a quote > of you stating it is "due to the resonance in the scattering for heavy > scatterers" ( > http://permalink.gmane.org/gmane.science.physics.ifeffit/2352 ) > In short: XAFS chi(R) is *NOT* a pair distribution function, due mostly to the complex electron scattering that alter the amplitude and shift the phase of potoelectron in addition to the simplistic "backscatter from a point source atom". The most obvious effect of this is a ~0.5 Ang shift to lower R from the value you might expect if chi(R) was a pair distribution function. Other effects include broader and asymmetric peaks, and the resonance effect such as you notice for heavy elements (easily noticeable for Z>40 or so, but unmistakable for Z > 60 -- that Z is for the *scattering atom*). At certain energies (or for a narrow range of energies), the photo-electron has very low scattering probability from a heavy element, and the phase jumps dramatically, as if the electron was able to tunnel through or hop over the potential well of the scattering atom. This is usually (and I think properly) called a Ramsauer-Townsend resonance. There are many papers, review articles, and slides from talks available that describe this in more detail. Google "ramsauer townsend effect exafs" for detailed articles. > I don't really understand what this means, which physical process causes > this. Could you perhaps provide me with additional info on this matter or > direct me to some papers that explain this? > > > Thanks in advance! > > Best regards > > Pieter Tack > > > --- > X-Ray Micro-Spectroscopy and Imaging Group > Department of Analytical Chemistry > Ghent University > Krijgslaan 281 S12 > B-9000 Ghent > Belgium > Phone: +32 (0)9 264 4723 > Fax: +32 (0)9 264 49 60 > --Matt

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Regarding time resolved XAS
by mazhar iqbal 31 May '16

31 May '16

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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Re: [Ifeffit] difference spectra- Ifeffit Digest, Vol 159, Issue 23
by sb2c08＠gmail.com 31 May '16

31 May '16

This is very helpful thank you. To give a little bit of context, the reaction is a solution of W(CO)6 irradiated at 266nm, to give W(CO)5*, it would be good to find the overall change of CO distance, especially as the multi scattering dominates the EXAFS. Just as a final point, the difference spectrum is taken from the normalised after and before laser spectra, so supposing the difference is fitted directly in Artemis (and coordination number is known/assumed), the amplitude factor will give an indication of the % change, supposing the Debye-Waller factor is similar to the ground state W(CO)6? But normalisation I find is the first difficult issue. Thanks Bruce and Anatoly and I will look over the references for some direction. Stu > On 31 May 2016, at 19:20, 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: Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > (sb2c08(a)gmail.com) > 2. Re: Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > (Bruce Ravel) > 3. Re: Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 31 May 2016 18:23:42 +0100 > From: sb2c08(a)gmail.com > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, > Issue 21 > Message-ID: <A5D4B2A5-A353-4813-BFC0-A31105BE4B21(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > I am familiar with the software and apologies I did mean Artemis in terms of fitting and understand that there is no pump probe button. > > To be clearer, can I make the excited state and ground state models in Artemis, take the data and difference (which can be done in Athena) and use that as a direct comparison, perhaps as you would with XANES data? I understand my data but I do not understand the best method to try get at least a first shell fit from the EXAFS region, collected by taking the difference of the ground state from the excited state, and can this be done in anyway via Artemis through some data analysis. > > >> On 31 May 2016, at 14:07, 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. Difference spectra (sb2c08(a)gmail.com) >> 2. Re: Difference spectra (Bruce Ravel) >> 3. Re: Regarding time resolved XAS (Bruce Ravel) >> 4. Atoms on the WEB (alessandro longo) >> 5. Re: Atoms on the WEB (Bruce Ravel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Mon, 30 May 2016 18:25:21 +0100 >> From: sb2c08(a)gmail.com >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: [Ifeffit] Difference spectra >> Message-ID: <A460A00C-45B0-4ED5-969C-6FB3BF0C67A2(a)gmail.com> >> Content-Type: text/plain; charset=us-ascii >> >> Hi, >> We recently collected laser pump-probe XAS data out to k=9. The process to get the excited state is to take the laser off minus the laser on data. I'm a little unsure in terms of trying to fit the difference EXAFS and is it possible via Athena? So far I model the EXAFS of the excited state and take away from the ground state model and compare visually. The only way I can think is to work out the % conversion and add that % of laser off back to the difference data in order to get the real EXAFS of the excited state, which can be fitted through Athena. But this is really difficult and probably inaccurate? >> Thanks for any help or suggestions, >> Stu >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 31 May 2016 08:19:14 -0400 >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Difference spectra >> Message-ID: <574D8142.8060001(a)bnl.gov> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >>> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >>> We recently collected laser pump-probe XAS data out to k=9. The >>> process to get the excited state is to take the laser off minus the >>> laser on data. I'm a little unsure in terms of trying to fit the >>> difference EXAFS and is it possible via Athena? So far I model the >>> EXAFS of the excited state and take away from the ground state model >>> and compare visually. The only way I can think is to work out the % >>> conversion and add that % of laser off back to the difference data in >>> order to get the real EXAFS of the excited state, which can be fitted >>> through Athena. But this is really difficult and probably >>> inaccurate? >> >> >> Of course it's not possible to fit and EXAFS spectrum in Athena. >> Artemis is the program for fitting the EXAFS. >> >> I am unclear on what you have tried so far, so I am a little unsure what >> kind of answer you are looking for. Artemis was not really written with >> your sort of experiment in mind. That said, if your problem is fit some >> theory from Feff to a measured spectrum with some fitting model -- that >> is what Artemis is for. As with any difficult problem, you need to >> understand your data and your model and you need to understand Artemis >> well enough to implement the fit. But there is no magical, hidden >> button that says "fit my pump-probe data." >> >> B >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 31 May 2016 08:22:59 -0400 >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: mazhar iqbal <mazharphy_05(a)yahoo.com>, XAFS Analysis using Ifeffit >> <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Regarding time resolved XAS >> Message-ID: <574D8223.3080109(a)bnl.gov> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >>> On 05/30/2016 02:20 AM, mazhar iqbal wrote: >>> 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. >> >> Well, you have told us what you have tried nor what problem you are >> actually facing. If the question is "does Athena help you align data?" >> I think you already know that the answer is yes. >> >> I don't understand the business about a "fluorescence line always on the >> screen". How do you propose to use that to align your XAS data? >> >> In the case of a situation where you are purposefully changing the >> chemical state of the sample, then you need to have some absolute >> reference by which to perform the alignment -- a reference spectrum >> measured simultaneously, an encoder reading on the monochromator, >> something that allows you to do the chore. >> >> You question is a bit vague and open-ended. Without more information or >> a more focused question, I don't know how to help you further. >> >> B >> >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 31 May 2016 14:49:50 +0200 >> From: "alessandro longo" <alessandro.longo(a)cnr.it> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: [Ifeffit] Atoms on the WEB >> Message-ID: <20160531124332.M60406(a)cnr.it> >> Content-Type: text/plain; charset=utf-8 >> >> Hi to everyone, >> >> I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. >> I don't want to disturb to much, but I was wondering why now this beatifull tool does't >> work anymore. It works only to create the atoms.inp, but it was nice to have the >> feff.inp ready from the web application. The main motivation is somtimes the ifeffit >> tool is not installed. >> Sorry If i took your time and thank you for your answer. >> best >> Alessandro >> >> -- >> Ph.D Alessandro Longo >> researcher of National Council Research >> ISMN-CNR >> e-mail: alessandro.longo(a)cnr.it >> phone: 00390916809359 >> fax : 00390916809399 >> >> Open WebMail Project (http://openwebmail.org) >> >> >> ---------- Original Message ----------- >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Sent: Tue, 31 May 2016 08:19:14 -0400 >> Subject: Re: [Ifeffit] Difference spectra >> >>>> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >>>> We recently collected laser pump-probe XAS data out to k=9. The >>>> process to get the excited state is to take the laser off minus the >>>> laser on data. I'm a little unsure in terms of trying to fit the >>>> difference EXAFS and is it possible via Athena? So far I model the >>>> EXAFS of the excited state and take away from the ground state model >>>> and compare visually. The only way I can think is to work out the % >>>> conversion and add that % of laser off back to the difference data in >>>> order to get the real EXAFS of the excited state, which can be fitted >>>> through Athena. But this is really difficult and probably >>>> inaccurate? >>> >>> Of course it's not possible to fit and EXAFS spectrum in Athena. >>> Artemis is the program for fitting the EXAFS. >>> >>> I am unclear on what you have tried so far, so I am a little unsure what >>> kind of answer you are looking for. Artemis was not really written with >>> your sort of experiment in mind. That said, if your problem is fit some >>> theory from Feff to a measured spectrum with some fitting model -- that >>> is what Artemis is for. As with any difficult problem, you need to >>> understand your data and your model and you need to understand Artemis >>> well enough to implement the fit. But there is no magical, hidden >>> button that says "fit my pump-probe data." >>> >>> B >>> >>> -- >>> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >>> >>> National Institute of Standards and Technology >>> Synchrotron Science Group at NSLS-II >>> Building 535A >>> Upton NY, 11973 >>> >>> Homepage: http://bruceravel.github.io/home/ >>> Software: https://github.com/bruceravel >>> Demeter: http://bruceravel.github.io/demeter/ >>> _______________________________________________ >>> 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 >> ------- End of Original Message ------- >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Tue, 31 May 2016 09:05:43 -0400 >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Atoms on the WEB >> Message-ID: <574D8C27.4090907(a)bnl.gov> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >>> On 05/31/2016 08:49 AM, alessandro longo wrote: >>> Hi to everyone, >>> >>> I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. >>> I don't want to disturb to much, but I was wondering why now this beatifull tool does't >>> work anymore. It works only to create the atoms.inp, but it was nice to have the >>> feff.inp ready from the web application. The main motivation is somtimes the ifeffit >>> tool is not installed. >>> Sorry If i took your time and thank you for your answer. >>> best >>> Alessandro >> >> It would be nice if you started a new thread for a new question rather >> than hijacking an existing thread.... >> >> Last December, the computer that hosted the web atoms tool died >> dramatically. When Matt rebuilt that server, atoms did not get >> restored. The web version of atoms was based on very out date code. >> >> Bottom line is that I need to rewrite the web atoms tool using the >> current code base. >> >> It's on my list of things to do. >> >> B >> >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> 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 >> >> >> ------------------------------ >> >> End of Ifeffit Digest, Vol 159, Issue 21 >> **************************************** > > > > ------------------------------ > > Message: 2 > Date: Tue, 31 May 2016 13:44:12 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, > Issue 21 > Message-ID: <574DCD6C.6080800(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/31/2016 01:23 PM, sb2c08(a)gmail.com wrote: >> To be clearer, can I make the excited state and ground state models >> in Artemis, take the data and difference (which can be done in >> Athena) and use that as a direct comparison, perhaps as you would >> with XANES data? I understand my data but I do not understand the >> best method to try get at least a first shell fit from the EXAFS >> region, collected by taking the difference of the ground state from >> the excited state, and can this be done in anyway via Artemis through >> some data analysis. > > > While it seems like Artemis specifically wants traditional EXAFS data as > its input, that's not really the case. It just wants something wiggly > that can be Fourier transformed. > > While it seems like Artemis wants a full Feff calculation and all the > path files that come from it with all the degeneracies that Feff thinks > it has, that also is not really the case. > > I don't know what your data are or what they look like (you haven't told > us), so I will make up a scenario off the top of my head. Hopefully > that will still be instructive. > > Suppose that our ground state is a pure metal -- say iron metal. Iron > metal has a near neighbor at about 2.5A. Suppose that our secondary > state includes some iron oxide -- that has a neighbor at about 1.9A and > a correspond peak at a much shorter distance. > > Suppose we can guess the amount of pure metal in the secondary state. > Then we could do some simple arithmetic to isolate (approximately!) the > oxide contribution. This will resemble an iron oxide standard, but with > much smaller amplitude. > > Seems to me that this difference spectrum could be fit in Artemis by > running Feff on the oxide, parameterizing the fit much like a > conventional spectrum, but giving the model enough freedom to have a > much smaller amplitude. That is, you cannot force the fit to have an > S02 of around 0.9 -- like a normal fit -- and the full coordination > number of the normal oxide. Something in the fitting model must be > introduced to allow the amplitude to be small enough to fit the > difference data properly. > > You, then, need to have a way of interpreting this much smaller > amplitude in a way that makes sense for the problem at hand. > > To say all that another way ... your difference data has Fourier > components ... Feff provides Fourier components ... you supply a model > (and an interpretation!) that fits Feff's Fourier components to the > Fourier components in your data. If your data can be described by Feff, > Artemis can do the describing. > > HTH, > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 3 > Date: Tue, 31 May 2016 18:20:20 +0000 > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, > Issue 21 > Message-ID: > <545F89325F51764C902D37B42C9F4D530210471863(a)YUWEXCPM11.yuad.uds.yu.edu> > > Content-Type: text/plain; charset="us-ascii" > > Hi Stu, > > In full agreement with Bruce, what you want to do can be done, and it was done a few times before. > I think the first group that applied conventional EXAFS analysis to differential signals was Pettifer et al in Nature (2005), to analyze EXAFS in magnetrostrictors measured at different values of magnetic field. Then, C. Konig et al did a similar trick for a catalyst under different atmospheres. They also used conventional EXAFS equation to fit the difference because the model allowed them to do so (the changes in the amplitude factors was also an amplitude factor and could be obtained from the fit because the fitting program does not know what the meaning of amplitude factors is, you do. > > I want to warn you that normalization of the amplitude of your EXAFS data will be the trickiest part because it depends on how many absorbing species changed structure during the excitation. > > In my work we also used this method in a couple of papers, Spanjers et al (for Pd nanoparticles under Ar and inert environment), and Korobko et al, (2015) using electrostrictors with and without applied electric field. The latter example is here: > > https://pubweb.bnl.gov/~frenkel/CGO/CGO-modulations.pdf > > The references to Pettifer and Konig works are Refs 19 and 20. > > Regards, > Anatoly > > P.S. If anyone is interested, a postdoctoral position has just opened up in my group, for research of electromechanical materials. Please contact me for further information: frenkel(a)bnl.gov > > ________________________________________ > From: Ifeffit [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Bruce Ravel [bravel(a)bnl.gov] > Sent: Tuesday, May 31, 2016 1:44 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > >> On 05/31/2016 01:23 PM, sb2c08(a)gmail.com wrote: >> To be clearer, can I make the excited state and ground state models >> in Artemis, take the data and difference (which can be done in >> Athena) and use that as a direct comparison, perhaps as you would >> with XANES data? I understand my data but I do not understand the >> best method to try get at least a first shell fit from the EXAFS >> region, collected by taking the difference of the ground state from >> the excited state, and can this be done in anyway via Artemis through >> some data analysis. > > > While it seems like Artemis specifically wants traditional EXAFS data as > its input, that's not really the case. It just wants something wiggly > that can be Fourier transformed. > > While it seems like Artemis wants a full Feff calculation and all the > path files that come from it with all the degeneracies that Feff thinks > it has, that also is not really the case. > > I don't know what your data are or what they look like (you haven't told > us), so I will make up a scenario off the top of my head. Hopefully > that will still be instructive. > > Suppose that our ground state is a pure metal -- say iron metal. Iron > metal has a near neighbor at about 2.5A. Suppose that our secondary > state includes some iron oxide -- that has a neighbor at about 1.9A and > a correspond peak at a much shorter distance. > > Suppose we can guess the amount of pure metal in the secondary state. > Then we could do some simple arithmetic to isolate (approximately!) the > oxide contribution. This will resemble an iron oxide standard, but with > much smaller amplitude. > > Seems to me that this difference spectrum could be fit in Artemis by > running Feff on the oxide, parameterizing the fit much like a > conventional spectrum, but giving the model enough freedom to have a > much smaller amplitude. That is, you cannot force the fit to have an > S02 of around 0.9 -- like a normal fit -- and the full coordination > number of the normal oxide. Something in the fitting model must be > introduced to allow the amplitude to be small enough to fit the > difference data properly. > > You, then, need to have a way of interpreting this much smaller > amplitude in a way that makes sense for the problem at hand. > > To say all that another way ... your difference data has Fourier > components ... Feff provides Fourier components ... you supply a model > (and an interpretation!) that fits Feff's Fourier components to the > Fourier components in your data. If your data can be described by Feff, > Artemis can do the describing. > > HTH, > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > _______________________________________________ > 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 > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > 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 > > > ------------------------------ > > End of Ifeffit Digest, Vol 159, Issue 23 > ****************************************

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Problems Running Athena, Artemis and Hephaestus on P.C. with Windows 7 Enterprise Operating System
by Johnson, Mark 31 May '16

31 May '16

Dear XAS Colleagues, I recently had to give up my Windows XP operating system and begin using Windows 7, the Enterprise version (I work for the U.S. Government). So I downloaded and installed the software, but when I try to launch them I see the software Icon briefly, but it does not launch. Digging around I found the following error logs below. Does anyone have any advice on how to proceed? My PC does have 16 Mb of RAM. Could that be the problem? Any suggestions would be appreciated. Thanks! MGJ ========================================================================== From: Dathena.log BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter.pm line 54. Compilation failed in require at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 24. BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 24. Compilation failed in require at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dathena.bat line 43. BEGIN failed--compilation aborted at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dathena.bat line 43. Started at 2016-05-26T12:28:22 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin perl version: v5.18.2 backend: ifeffit @INC: C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/vendor/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib . Can't load 'C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib/DynaLoader.pm line 190. at (eval 18) line 1. Compilation failed in require at (eval 18) line 1. BEGIN failed--compilation aborted at (eval 18) line 1. ============================================================================================= >From dartemis.log BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter.pm line 54. Compilation failed in require at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm line 26. BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm line 26. Compilation failed in require at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 42. BEGIN failed--compilation aborted at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 42. Started at 2016-05-26T12:30:29 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin perl version: v5.18.2 backend: ifeffit @INC: C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/vendor/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib . Can't load 'C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib/DynaLoader.pm line 190. at (eval 18) line 1. Compilation failed in require at (eval 18) line 1. BEGIN failed--compilation aborted at (eval 18) line 1.

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Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, Issue 21
by sb2c08＠gmail.com 31 May '16

31 May '16

I am familiar with the software and apologies I did mean Artemis in terms of fitting and understand that there is no pump probe button. To be clearer, can I make the excited state and ground state models in Artemis, take the data and difference (which can be done in Athena) and use that as a direct comparison, perhaps as you would with XANES data? I understand my data but I do not understand the best method to try get at least a first shell fit from the EXAFS region, collected by taking the difference of the ground state from the excited state, and can this be done in anyway via Artemis through some data analysis. > On 31 May 2016, at 14:07, 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. Difference spectra (sb2c08(a)gmail.com) > 2. Re: Difference spectra (Bruce Ravel) > 3. Re: Regarding time resolved XAS (Bruce Ravel) > 4. Atoms on the WEB (alessandro longo) > 5. Re: Atoms on the WEB (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 May 2016 18:25:21 +0100 > From: sb2c08(a)gmail.com > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Difference spectra > Message-ID: <A460A00C-45B0-4ED5-969C-6FB3BF0C67A2(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hi, > We recently collected laser pump-probe XAS data out to k=9. The process to get the excited state is to take the laser off minus the laser on data. I'm a little unsure in terms of trying to fit the difference EXAFS and is it possible via Athena? So far I model the EXAFS of the excited state and take away from the ground state model and compare visually. The only way I can think is to work out the % conversion and add that % of laser off back to the difference data in order to get the real EXAFS of the excited state, which can be fitted through Athena. But this is really difficult and probably inaccurate? > Thanks for any help or suggestions, > Stu > > > > ------------------------------ > > Message: 2 > Date: Tue, 31 May 2016 08:19:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Difference spectra > Message-ID: <574D8142.8060001(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >> We recently collected laser pump-probe XAS data out to k=9. The >> process to get the excited state is to take the laser off minus the >> laser on data. I'm a little unsure in terms of trying to fit the >> difference EXAFS and is it possible via Athena? So far I model the >> EXAFS of the excited state and take away from the ground state model >> and compare visually. The only way I can think is to work out the % >> conversion and add that % of laser off back to the difference data in >> order to get the real EXAFS of the excited state, which can be fitted >> through Athena. But this is really difficult and probably >> inaccurate? > > > Of course it's not possible to fit and EXAFS spectrum in Athena. > Artemis is the program for fitting the EXAFS. > > I am unclear on what you have tried so far, so I am a little unsure what > kind of answer you are looking for. Artemis was not really written with > your sort of experiment in mind. That said, if your problem is fit some > theory from Feff to a measured spectrum with some fitting model -- that > is what Artemis is for. As with any difficult problem, you need to > understand your data and your model and you need to understand Artemis > well enough to implement the fit. But there is no magical, hidden > button that says "fit my pump-probe data." > > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 3 > Date: Tue, 31 May 2016 08:22:59 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: mazhar iqbal <mazharphy_05(a)yahoo.com>, XAFS Analysis using Ifeffit > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Regarding time resolved XAS > Message-ID: <574D8223.3080109(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/30/2016 02:20 AM, mazhar iqbal wrote: >> 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. > > Well, you have told us what you have tried nor what problem you are > actually facing. If the question is "does Athena help you align data?" > I think you already know that the answer is yes. > > I don't understand the business about a "fluorescence line always on the > screen". How do you propose to use that to align your XAS data? > > In the case of a situation where you are purposefully changing the > chemical state of the sample, then you need to have some absolute > reference by which to perform the alignment -- a reference spectrum > measured simultaneously, an encoder reading on the monochromator, > something that allows you to do the chore. > > You question is a bit vague and open-ended. Without more information or > a more focused question, I don't know how to help you further. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 4 > Date: Tue, 31 May 2016 14:49:50 +0200 > From: "alessandro longo" <alessandro.longo(a)cnr.it> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Atoms on the WEB > Message-ID: <20160531124332.M60406(a)cnr.it> > Content-Type: text/plain; charset=utf-8 > > Hi to everyone, > > I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. > I don't want to disturb to much, but I was wondering why now this beatifull tool does't > work anymore. It works only to create the atoms.inp, but it was nice to have the > feff.inp ready from the web application. The main motivation is somtimes the ifeffit > tool is not installed. > Sorry If i took your time and thank you for your answer. > best > Alessandro > > -- > Ph.D Alessandro Longo > researcher of National Council Research > ISMN-CNR > e-mail: alessandro.longo(a)cnr.it > phone: 00390916809359 > fax : 00390916809399 > > Open WebMail Project (http://openwebmail.org) > > > ---------- Original Message ----------- > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Tue, 31 May 2016 08:19:14 -0400 > Subject: Re: [Ifeffit] Difference spectra > >>> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >>> We recently collected laser pump-probe XAS data out to k=9. The >>> process to get the excited state is to take the laser off minus the >>> laser on data. I'm a little unsure in terms of trying to fit the >>> difference EXAFS and is it possible via Athena? So far I model the >>> EXAFS of the excited state and take away from the ground state model >>> and compare visually. The only way I can think is to work out the % >>> conversion and add that % of laser off back to the difference data in >>> order to get the real EXAFS of the excited state, which can be fitted >>> through Athena. But this is really difficult and probably >>> inaccurate? >> >> Of course it's not possible to fit and EXAFS spectrum in Athena. >> Artemis is the program for fitting the EXAFS. >> >> I am unclear on what you have tried so far, so I am a little unsure what >> kind of answer you are looking for. Artemis was not really written with >> your sort of experiment in mind. That said, if your problem is fit some >> theory from Feff to a measured spectrum with some fitting model -- that >> is what Artemis is for. As with any difficult problem, you need to >> understand your data and your model and you need to understand Artemis >> well enough to implement the fit. But there is no magical, hidden >> button that says "fit my pump-probe data." >> >> B >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> _______________________________________________ >> 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 > ------- End of Original Message ------- > > > > ------------------------------ > > Message: 5 > Date: Tue, 31 May 2016 09:05:43 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Atoms on the WEB > Message-ID: <574D8C27.4090907(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/31/2016 08:49 AM, alessandro longo wrote: >> Hi to everyone, >> >> I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. >> I don't want to disturb to much, but I was wondering why now this beatifull tool does't >> work anymore. It works only to create the atoms.inp, but it was nice to have the >> feff.inp ready from the web application. The main motivation is somtimes the ifeffit >> tool is not installed. >> Sorry If i took your time and thank you for your answer. >> best >> Alessandro > > It would be nice if you started a new thread for a new question rather > than hijacking an existing thread.... > > Last December, the computer that hosted the web atoms tool died > dramatically. When Matt rebuilt that server, atoms did not get > restored. The web version of atoms was based on very out date code. > > Bottom line is that I need to rewrite the web atoms tool using the > current code base. > > It's on my list of things to do. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > 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 > > > ------------------------------ > > End of Ifeffit Digest, Vol 159, Issue 21 > ****************************************

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Difference spectra
by sb2c08＠gmail.com 31 May '16

31 May '16

Hi, We recently collected laser pump-probe XAS data out to k=9. The process to get the excited state is to take the laser off minus the laser on data. I'm a little unsure in terms of trying to fit the difference EXAFS and is it possible via Athena? So far I model the EXAFS of the excited state and take away from the ground state model and compare visually. The only way I can think is to work out the % conversion and add that % of laser off back to the difference data in order to get the real EXAFS of the excited state, which can be fitted through Athena. But this is really difficult and probably inaccurate? Thanks for any help or suggestions, Stu

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ISO Calcite + dolomite EXAFS
by Matthew Marcus 27 May '16

27 May '16

Does anyone have Ca K-edge EXAFS data they can share for calcite and dolomite? I took some, but it seems to disagree with FEFF as to the position of the Ca-(Ca,Mg) peak. mam

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