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

Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects
by Mengling Yi Stuckman 20 Mar '14

20 Mar '14

Sorry I think my attachment didn't go through. Maybe the zip file will work. Mengling On Thu, Mar 20, 2014 at 9:22 AM, Mengling Stuckman <menglingyi1023(a)gmail.com > wrote: > Thanks, Bruce, > > I'm sending a couple. One is new that I didn't do any fit. The other is > old that contained my fitting. Both of them can't open in my Artemis. > > Mengling > > > On Wed, Mar 19, 2014 at 5:47 PM, Bruce Ravel <bravel(a)bnl.gov> wrote: > >> >> Can you humor me and send me one of your .fpj files? I would like to >> examine its contents. >> >> B >> >> >> On 03/19/2014 05:36 PM, Mengling Stuckman wrote: >> >>> Thank you, Bruce, >>> >>> This is the complete log file: >>> >>> "Started at 2014-03-19T14:26:09 >>> Win7Enterprise (64-bit) Service Pack 1Service Pack 16176012102561 >>> >>> >>> PATH: >>> C:\windows\system32;C:\windows;C:\windows\System32\ >>> Wbem;C:\windows\System32\WindowsPowerShell\v1.0\;C:\ >>> strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\ >>> strawberry1\perl\bin;C:\strawberry1\perl\site\bin;C:\ >>> strawberry1\c\bin;\\admin.netl.doe.gov >>> <http://admin.netl.doe.gov>\it\Oracle11g\product\11.2.0\client_1\bin; >>> >>> >>> perl version: v5.12.3 >>> >>> @INC: >>> C:/strawberry/perl/site/lib >>> C:/strawberry/perl/vendor/lib >>> C:/strawberry/perl/lib >>> . >>> >>> Can't call method "workspace" without a package or object reference at >>> C:/strawberry/perl/site/lib/Demeter/Fit.pm line 1550." >>> >>> or this very last sentence will change to >>> >>> "Can't call method "group" on an undefined value at >>> C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 466." >>> if I open a different .fpj file. >>> >>> Because the first few lines were similar to what I saw in Athena log >>> file when Athena is working, I didn't cite these. >>> >>> Thank you very much for double-checking it! >>> >>> I did try to check the permission of that folder by adding a file into >>> that folder and extracting a zip file into that folder. Neither had any >>> problem. I do have permission of that folder. >>> >>> I also tried to open my files in Artemis installed on several other >>> computers in my workplace. Other computers didn't work as well. I guess >>> it might be a problem with the operating system/software conflict in my >>> workplace? I didn't install any other software by myself. All the other >>> updates for antivirus or Windows 7 are automatic through workplace >>> system management that I don't have control. I might be able to call IT >>> support tomorrow to see if they know anything about the system that >>> might have conflict with Demeter. >>> >>> "Without being able to watch this on one of my computers, I can only >>> guess what the problem might be by examining the two lines of code you >>> cite." >>> >>> I am wondering how to examine the two lines of code I cited. Maybe I >>> could talk to IT support about the code and see if there is anything >>> they or we can do to fix that. >>> >>> Really appreciated for your replies! I know this is a very personalized >>> computer problem, not related to your software, which might be beyond >>> your duty to fix. So really thankful for your help! >>> >>> Mengling >>> >>> >>> On Wed, Mar 19, 2014 at 4:44 PM, Bruce Ravel <bravel(a)bnl.gov >>> <mailto:bravel@bnl.gov>> wrote: >>> >>> On 03/19/2014 04:19 PM, Mengling Stuckman wrote: >>> >>> >>> Again, the message showing in the log file is: >>> "Can't call method "workspace" without a package or object >>> reference at >>> C:/strawberry/perl/site/lib/__Demeter/Fit.pm line 1550." >>> >>> >>> or sometimes: >>> >>> "Can't call method "group" on an undefined value at >>> C:/strawberry/perl/site/lib/__Demeter/UI/Artemis/Project.pm line >>> >>> 466." >>> >>> >>> Are you quite sure that is the only text in the log file? >>> >>> Demeter first writes several lines about the environment in which >>> Demeter is operating. The error message is almost always followed by >>> several lines of backtrace. All of that provides context for me to >>> understand the proximal cause of the problem. If you extract a part >>> of the log file, then that context is lost to me. >>> >>> >>> Demeter also seemed to work fine last week and only stopped >>> working >>> yesterday. I didn't update anything on my work computer, so I >>> don't >>> know what is causing the problem. >>> >>> >>> Artemis worked on that computer last week and does not work this >>> week? >>> And you did nothing to change the computer? Something doesn't add >>> up. >>> >>> Did your anti virus software update? Did your institution's system >>> administrators perform an update? Did you install any new software? >>> Anything? It's hard for me to understand how the behavior of the >>> program can change simply by walking away for a few days. >>> >>> Without being able to watch this on one of my computers, I can only >>> guess what the problem might be by examining the two lines of code >>> you >>> cite. >>> >>> My best guess is that something is preventing you from unpacking the >>> project file. An .fpj file is nothing more than a zip file with a >>> different file extension. It gets unpacked in %APPDATA%\stash (where >>> %APPDATA% is the location of the log file). That means that you have >>> to have permission to write files to that location. So, my best >>> guess >>> is that something is preventing you from writing to that space. I >>> have no guess for what the cause of that is. >>> >>> So, check the permission of that folder. Try making a file in that >>> folder by hand. Try extracting a zip file buy hand into that folder. >>> >>> If not that, then I'm afraid I'm out of ideas. >>> >>> >>> B >>> >>> >>> -- >>> Bruce Ravel ------------------------------__------ bravel(a)bnl.gov >>> <mailto:bravel@bnl.gov> >>> >>> >>> National Institute of Standards and Technology >>> Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 >>> Building 535A >>> Upton NY, 11973 >>> >>> Homepage: http://xafs.org/BruceRavel >>> Software: https://github.com/bruceravel >>> _________________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.__gov >>> <mailto:Ifeffit@millenia.cars.aps.anl.gov> >>> http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit >>> >>> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >>> >>> >>> >>> >>> >>> -- >>> Mengling Stuckman >>> ORISE Research Fellow >>> National Energy Technology Laboratory >>> U.S. Department of Energy >>> Pittsburgh, PA >>> STUCKMAN.MENGLING(a)CONTR.NETL.DOE.GOV >>> <mailto:STUCKMAN.MENGLING@CONTR.NETL.DOE.GOV> >>> Office: 412-386-7387 >>> >>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >>> >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://xafs.org/BruceRavel >> Software: https://github.com/bruceravel >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> > > > -- > Mengling Stuckman > ORISE Research Fellow > National Energy Technology Laboratory > U.S. Department of Energy > Pittsburgh, PA > STUCKMAN.MENGLING(a)CONTR.NETL.DOE.GOV > Office: 412-386-7387 > -- Mengling Yi Stuckman Graduate Research Assistant Civil and Environmental Engineering and Geodetic Science Ohio State University 2070 Neil Ave., Columbus, OH, 43210

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Inequivalent atomic positions (V2O5 xerogel)
by Douglas Langie da Silva 18 Mar '14

18 Mar '14

Dear all, I am working with EXAFS data of V2O5 xerogel. In this form, the V2O5 present a monoclinic structure formed by bi-layers of VO5 pyramids intercalated with water molecules. Fig 1 attached presents a view of the V2O5 xerogel structure. There are two Vanadium atoms per unit cell, each one surrounded by oxygen atoms at distinct distances, characterizing two inequivalent sites. My question is how to fit the data in dartemis considering the two inequivalent positions? My first approach was run Feff two times. Then I get two theoretical models, one for V1 atoms and the other for the V2 atoms. Each of Feff runs are present attached as model V1 and model V2. After that I transfer the paths of the first shell of each model to dartesmis data windows (fig 2) and proceed with the fit. We pay attention in the site fraction of each vanadium atom in order to setup the S02 parameter for each model. Without attempting at this point with the numbers, the final results are present in Fig. 3 e 4. Fig 4 presents the log file and the results for the each patch. My question is: this procedure is valid? Since now thak you. -- Douglas Langie da Silva Instituto de Física e Matemática Departamento de Física Universidade Federal de Pelotas Campus Universiário s/n CP 354 Pelotas/RS CEP 96010-900 55 53 32757477 55 53 32757345 Douglas Langie da Silva Physics Department Federal University of Pelotas POBox 354 Pelotas/RS ZCode 96010-900 55 53 32757477 55 53 32757345

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EXAFS Fitting for Ni sorb to bacterial biomass and Mn oxides
by Sathish Mayanna 18 Mar '14

18 Mar '14

Dear all So far, this forum has been very helpful for me to learn and understand how to fit EXAFS spectra of Mn oxides, thanks everyone for your suggestions. Recently, I am working with Ni k-edge EXAFS and I have kind of similar question as Abhijeet Gaur (Ifeffit Digest, Vol 133, Issue 1), in my case, I am trying to fit EXAFS spectra of Ni(II) sorbed to bacterial biomass and Mn oxides (attached). I followed the Matt suggestions by replacing Ni in place of Mn after running Atoms (birnessite model) to generate feff.inp. I have two questions regarding this: 1) Ni(II) can be surface sorbed and or incorporated into Mn oxide structures. But, I cannot generate paths for this particular r-space. What and how can I edit the feff calculations? (attached). 2) Ni(II) sorp to bacterial biomass via some organic ligands (humic or carboxylic acids): The first shell mainly associates with Ni-O distances, there might be also Ni-C distances in later shells. I am wondering, how can I input the C in atoms or feff calculations? I would be happy to receive your comments. Regards Sathish

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Re: [Ifeffit] Ifeffit Digest, Vol 133, Issue 1
by Abhijeet Gaur 13 Mar '14

13 Mar '14

Hi Matt, Thanks for your suggestion. I will use this for the analysis of my sample. I have a query that what if I change the Mn by Zn at the Atoms page calculation so that the feff.inp file has already Zn instead of Mn. Is there any difference between the two methods. With thanks Abhijeet On Wed, Mar 12, 2014 at 10:30 PM, <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. Analysis of EXAFS data of a Zn sample with the theoretical > model of a similar Mn sample (Abhijeet Gaur) > 2. Re: Analysis of EXAFS data of a Zn sample with the > theoretical model of a similar Mn sample (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Mar 2014 19:22:42 +0530 > From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Analysis of EXAFS data of a Zn sample with the > theoretical model of a similar Mn sample > Message-ID: > <CAEq27Q1tZfmsb+-3HK2= > gWhK3ZGdXbSue79wpRT7wedG_nAjLQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I am trying to analyse the EXAFS data of Zn sample whose > structure is not available. > The crystallographic data is available for a Mn sample which is > likely to have same coordination environment as Zn sample . > Is it possible to use the theoretical model generated for Mn > sample for the EXAFS analysis of the Zn sample? > How much error is expected in the structural parameters > obtained from such fittings? > > With thanks in advance > > -- > Dr. Abhijeet Gaur >

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Analysis of EXAFS data of a Zn sample with the theoretical model of a similar Mn sample
by Abhijeet Gaur 12 Mar '14

12 Mar '14

Hi all, I am trying to analyse the EXAFS data of Zn sample whose structure is not available. The crystallographic data is available for a Mn sample which is likely to have same coordination environment as Zn sample . Is it possible to use the theoretical model generated for Mn sample for the EXAFS analysis of the Zn sample? How much error is expected in the structural parameters obtained from such fittings? With thanks in advance -- Dr. Abhijeet Gaur

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Saving and reopening project files in Artemis 0.9.18.2 on Windows 8.0 Pro x64
by Godfrey, Ian 28 Feb '14

28 Feb '14

Dear All, I'm encountering a problem whenever I save a fitting project in Artemis (I have tried both the "Save Project" and "Save Current Fit" options from the file menu) and then try to reopen it . I have only encountered the issue with quick first shell fits, but I haven't tried anything else recently. Specifically the parameters in the paths list are reset to their default value (while those in the GDS window are not) when I reopen the file and when I try and fit the data again Artemis gives a message that: "This data file does not exist" The data file has not been moved, deleted or otherwise modified on my computer. It may be relevant that I'm not importing an Athena project into Artemis, but I'm importing a chi(k) file (*.cho) exported from Viper (https://www.cells.es/Beamlines/CLAESS/software/viper.html) (export chi(k) on original grid). I also frequently get a "perl.exe has stopped working A problem caused the programme to stop working correctly. Windows will close the program and notify you if a solution is available" error from Windows when exiting Artemis, which could be related. I have attached Artemis log files from running the software to both save and open a project and I have attached an example problematic project file. To reproduce: * Start Artemis * File > Import > chi(k) data * Import a chi(k) data file * Set up a quick first shell fit * Customise some of the parameter names * Run a fit * File > Save Current Fit or File > Save Project (as) * Close Artemis * Reopen the saved project file * The parameter names in the paths list have been reset to their default (but those in GDS have not) * Run a fit * Artemis will complain that the data file is missing If anyone has any suggestions for a workaround or knows whether this is a bug in Artemis or a problem at my end I'd be grateful to hear. Thanks, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme, Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London. i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> 02076 794864

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Fwd: problems with setting parameters in new Artemis (Demeter 0.9.16)
by Cristina Alonso Escobar 28 Feb '14

28 Feb '14

Dear All, I am trying to fit the first FT shell in Artemis with a mixture of two different compounds (octahedral and tetrahedral models). I would like to quantify the ratio between this two compounds in my sample so I decided to multiply So2 by a parameter called "a" in one model and by "(1-a)" in the other. I would like to know: 1.- How can I restrain "a" ? I tried to manually add a restraint, but I do not know how to make an interval restraint...( 0<a<1) 2.- If you select "restrain" and after in the math expression "build restrain from ..." What is the meaning of scale by? Why the program duplicate the restrain (i.e restrain- a and restrain- res_a - 1* penalty (a, 0, 1)? I think I am not doing well because the value of my parameter "a" is suspiciously always 0. Thank you in advance, *** *** *** *** *** *** *** *** *** Cristina Alonso-Escobar. PhD student Instituto de Tecnología Química (UPV-CSIC) Avda. de los Naranjos s/n 46022 Valencia (Spain) http://itq.upv-csic.es Tfno: +34 96 387 7800 Fax: +34 96 387 9444 ----- Terminar mensaje reenviado ----- *** *** *** *** *** *** *** *** *** Cristina Alonso-Escobar. PhD student Instituto de Tecnología Química (UPV-CSIC) Avda. de los Naranjos s/n 46022 Valencia (Spain) http://itq.upv-csic.es Tfno: +34 96 387 7800 Fax: +34 96 387 9444

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3rd and 4th parameter in Artemis path fitting
by RAFAYAHER＠alum.us.es 26 Feb '14

26 Feb '14

Hello, I have been analyzing some EXAFS data with Artemis, and I was wondering what are the 3rd and 4th parameters in the path parameters window. Best regards, Rafael.

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XAS position at India Technology Center
by Shelly Kelly 25 Feb '14

25 Feb '14

Dear XAS community: *Job Description: XAS Specialist* UOP Honeywell has strong capabilities in the area of X-ray absorption spectroscopy, tomography, XRD, XPS, and molecular modeling. The group is now seeking for an XAS modeling specialist to strengthen its team further. The position is based at Honeywell India Technology Center. *Responsibilities:* - EXAFS modeling and interpretation of spectra from catalysts and adsorbents - Contribute to the planning and implementation of in situ X-ray absorption spectroscopy experiments. - Ability to assess the quality of XAS data as collected and to identify problems. - Generation of XAS data reports using Athena/Artemis include: comparisons of XANES and EXAFS spectra, linear combination fitting of XANES spectra, and EXAFS interpretation of the spectra in terms of metal speciation. - Participate in all departmental safety activities and conduct all work with a high degree of attention to safety. - Utilize six-sigma tools as necessary to implement project work. *Basic Candidate Qualifications:* - PhD in physics, chemistry, and chemical engineering or similar is required. - Minimum of 2 year experience with synchrotron beam line operations and data analysis. (This experience can include graduate level work within an academic environment.) *Additional Candidate Qualifications:* - Experience in Industrial Catalysis Research or Materials Research setting is considered ideal. - Excellent oral and written communication skills. - Knowledge of FEFF, x-ray optics, and instrument automation is considered a strong plus. - Strong demonstration of ability to work in a team environment across various time zones - Ability to travel up to 10% on an annual basis Thank-you, Shelly Kelly Applicants please provide CV and references to Dr. Shelly Kelly at Shelly.Kelly(a)Honeywell.com

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EXAFS with multiple absorbers
by Francisco Garcia 22 Feb '14

22 Feb '14

Dear users, I would like to know if FEFF8 or FEFF9 can compute the EXAFS when multiple absorbers are present in the sample. Thank you.

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