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

Re: [Ifeffit] athena error message.....
by Bruce Ravel 10 Dec '13

10 Dec '13

On 11/30/2013 05:17 PM, William Nash wrote: > Heya Bruce, > > I'm trying to use Athena to process some XANES data from the Diamond > Synchrotron (UK). I went to the demeter webpage and downloaded/ran the > installer and the updater. However, when I try to run athena, I get an > error message: > > (Window Title: "perl.exe - Entry Point Not Found") > > The procedure entry point __gxx_personality_v0 could not be located in > the dynamic link library libstdc++-6.dll. > > Is this an error you are familiar with? I don't seem to be able to get > around it. It time permits, would you mind giving me some guidance. > > Grateful thanks, > William > First off, please use the Ifeffit mailing list http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ which is the proper place to ask questions about and report problems with the software. As you can see, I have CCed my response to you and to the mailing list. Please continue correspondence on this topic via the mailing list. The most likely source of this problem is the one discussed here http://cars9.uchicago.edu/ifeffit/Demeter/MingwFix that is, that you have another version of MinGW installed on your computer, either that you yourself installed or that was installed by another application. This fellow, for example, had installed GnuPG and this triggered a similar conflict to what you see. http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04031.html Another possible problem is that you have another version of perl itself installed on you computer, again possibly as part of the installation of another package. HTH B -- 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

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Re: [Ifeffit] Ifeffit Digest, Vol 130, Issue 13
by Sathish Mayanna 10 Dec '13

10 Dec '13

Dear Matt and Bruce Thanks, I thought its a common problem, i will be more specific in this message. I am using windows 7, 64 bits and/or 32 bits Operating System, installed with updating 0.9.18.2 Demeter, its in the folder C:\strawberry. To deglitch the single point of EXAFS data using Athena, after CHOOSE A POINT option, when I double click on the plot of k space, it does choose a point randomly and I can remove that particular point, but unfortunately, I cannot move or select the point which I want to remove. It always choose a random point by its own. Do I miss something here ? Regards Sathish On Mon, Dec 9, 2013 at 8:49 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. Athena 0.9.18.2 deglitch option (Sathish Mayanna) > 2. Re: Athena 0.9.18.2 deglitch option (Bruce Ravel) > 3. Re: Athena 0.9.18.2 deglitch option (Matt Newville) > 4. Re: Itinerant vs localized XAFS (Latta, Drew E.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Dec 2013 19:24:33 +0100 > From: Sathish Mayanna <satty334(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Athena 0.9.18.2 deglitch option > Message-ID: > <CABVfawmnabGT= > S+iEwy-1bv0f6jSLRQc9gga+hSg0KjmaE5Cdg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all > > I wondering, if anyone has problem with the option deglitch in Athena > especially for 32 or 64 bits Windows system? > > Would be really great, if anyone could help me to solve the problem, I have > a EXAFS data with huge glitch and the software do not choose/remove the > points and sometimes it crashes. > > Regards > Sathish >

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Artemis path like function crashing
by stephen.price＠diamond.ac.uk 10 Dec '13

10 Dec '13

Hi, I'm writing to report a crash of the path like function of Artemis, version 0.9.18 on Windows 7, 64 bit (the same thing also happened on my old windows XP machine). I have followed the procedure below several times on both machines and get the same result: · Load processed data from Athena of Pt nanoparticle, load and run Pt.inp in ATOMS (from atomsdb), run FEFF - click on path like tab · Make histograms from molecular dynamics time sequence - in this case from DL_POLY · Load HISTORY file from molecular dynamics - specify Rmin (e.g. 2.4 Å) Rmax (3.0) and bin size (0.005) · Plot RDF - in this case it loads in 503 time steps in increments of 10 and plots RDF after about 1 minute · I click on "Drag SS path from here" and drag to the path list - the message "making Fpaths n of 66" appears at the bottom of the window · As it is rebinning the last Fpath Artemis crashes with the log error "Can't locate object method "pathfinder_index" via package "Demeter::FPath" at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Path.pm line 254, <F> line 9" (dartemis.log attachment) · The final line mentioned in the dartemis.log sometimes varies e.g. <F> line 133 or <F> line 177 · This crash is independent of the Athena project, simulation HISTORY file (whether a 10 MB or a 100 MB file), choice of Rmin/max and bin size I can run a simple first/multi shell fit on the Pt nanoparticle, save and reopen the project (Pt test.fpj) but cannot save and reopen a project during any stage of the path like process as this crashes Artemis ("create RDF dartemis.log" and "Pt create RDF.fpj" attachments). I haven't attached a sample MD simulation file here as I don't want to fill everyone's inbox! Any help would be appreciated. Thank you, Steve Dr Stephen Price PDRA Beamline I18 Diamond Light Source -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Itinerant vs localized XAFS
by Maurits Boeije 09 Dec '13

09 Dec '13

Dear XAFS specialists, We've performed an experiment at the ESRF in Grenoble to find experimental evidence of an electronic change in our system. We suspect, from ab initio calculations, that there is a change in how electrons are allocated in our Mn/Fe system. Calculations show that some electrons change from being itinerant at high temperatures, to being localized at low temperatures. We performed an XAFS experiment and hope to see a difference between the low and high temperatures measurements. There is always difference because the cell parameters change as function of temperature, and I used your Artemis program to investigate the influence of the cell parameters on the EXAFS signal. I can get a decent fit using the crystallographic data we have, but I'm not sure if I'm not throwing away any evidence of our electronic change. I can interpret a fitted interatomic distance of 2.1 A (compared to 2.0 A we got from diffraction) as being the mean interatomic distance in our sample, but I could also interpret it as a 0.1 A difference because of our suspected electronic change. The challenge now lies in seeing an electronic difference despite the crystallographic change. What we would ideally do, is to keep the (known) atomic positions and cell parameters fixed, fit the EXAFS parameters and see if we can predict either the high or low temperature spectrum. Do you think this is possible? Are there any parameters which are calculated by IFEFFIT who are not precise enough for such a conclusion? It could be that the effect we are looking for is so small that they are nullified by the assumptions in the EXAFS equation. I would appreciate any insight you could have in this particular problem. With kind regards, Drs. MFJ Boeije Fundamental Aspects of Materials and Energy TU Delft T +31 (0)15 27 83793 No trees were killed to send this message, but a large number of electrons were terribly inconvenienced

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Athena 0.9.18.2 deglitch option
by Sathish Mayanna 09 Dec '13

09 Dec '13

Dear all I wondering, if anyone has problem with the option deglitch in Athena especially for 32 or 64 bits Windows system? Would be really great, if anyone could help me to solve the problem, I have a EXAFS data with huge glitch and the software do not choose/remove the points and sometimes it crashes. Regards Sathish

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problem running (D)Artemis on non-unicode machine
by Andrei Shiryaev 09 Dec '13

09 Dec '13

Dear colleagues, Again I have problems running (D)Artemis on two Win7 and on Win XP machines with non-unicode names. I've raised the issue in September and Matt Newville suggested some recipe (see IFEFFIT mailing list on Sept 6). The suggested solution was the following: ======= Edit the file C:/strawberry/perl/site/lib/Demeter/UI/Artemis.pm so that, near the top it reads: use Archive::Zip qw( :ERROR_CODES :CONSTANTS ); $Archive::Zip::UNICODE = 1; ======= The solution was great in the sense that DEMETER at least starts (it was not the case before). However, when I try to fit anything imported from old or new Athena (importing old style Artemis project does not work, this was apparently already reported to the list) I am getting the following error message (also see attached screenshot): ======= error writing zip-style project at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 104 Demeter::UI::Artemis::Project::save_project('HASH(0xaf38efc)', C:/Documents and setting/ NON-UNICODE NAME.......... ========== I would be grateful if an idea how to solve this obstacle. All the best, Andrei Shiryaev PS In the example above DArtemis is installed on D:, but standard installation on C: gives exactly the same result.

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Fe2(MoO4)3 and FeMoO4
by Anatoly I Frenkel 06 Dec '13

06 Dec '13

Dear IFEFFIT users, If anyone has Fe K-edge spectra of Fe2(MoO4)3 and/or FeMoO4, and could email me the raw data, it will be gratefully acknowledged! Thank you very much, Anatoly Frenkel

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Re: [Ifeffit] fitting a specific k range
by fred.mosselmans＠diamond.ac.uk 06 Dec '13

06 Dec '13

What I find reassuring about Bruce's warnings is they allow you to think properly about what you are doing. Fortunately, unlike Chris, I am not of a size where I have to worry about falling down rabbit holes, unless American rabbits are much bigger than English ones. I would commend Matt's original question as it opened a debate with 3 of the mainstays of the list. That may not have been the intention but it makes interesting reading for us mailing list voyeurs. Cheers Fred Sent from Samsung tablet

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fitting a specific k range
by Matt Frith 05 Dec '13

05 Dec '13

Dear All, I need some help in fitting an amorphous iron oxyhydoxide sample. I am having difficulty producing a good fit, particularly in the k=4-6 range. Fitting this region well is very important for me, because if I add another metal(+3 oxidation state) into my system, this is where I observe the most quantifiable changes (The shoulder @ 5 A^-1 and the min @ 5.6 A^-1). Thus far I have been unable to fit the shoulder well enough to make meaningful comparisons. I have been fitting in kq with kmin=2.566 And kmax=10.877, and Rmin=1 and Rmax=3.5, and using the goethite O1.1, Fe.1, and Fe.3 paths. Attached is an Artemis file (P41_006_merge_norm_TRANS.fpj) for an amorphous Fe oxyhydroxide sample (Fe only, no other metals). The data was collected at the Fe K-edge. *Is there a way to fit just this region (k~4-6 range) in k? If so what is the best method for doing this? If not, does anyone have suggestions as to how I can improve my fitting? Should I fit the data in k since the shoulder is less evident in kq?* Thank you for your time. Sincerely, Matt Frith

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Er2O3 standard spectra
by Carlo Segre 04 Dec '13

04 Dec '13

Hello All: Does anyone have a reference spectrum of Er2O3? I have one but I am a bit concerned about the resolution and wish to compare. Thanks, Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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