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

Bug in Artemis 0.8.010?
by Joji Kuniya 31 Jul '07

31 Jul '07

Hi Bruce Thank you for new version of Artemis. It works so good. But there is a problem on my PC working. Artemis makes feff.inp files on the screen, but I can not save it. When I click save button on the Artemis palette, my PC only says only "ping". And, in the Echo palette, there is a message that "Artemis trapped one or more errors! Error message dumped to screen". Is there some good idea to solve thins problem? Thank you Joji Kuniya

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Debye Waller factors for Water Molecules
by Paul Fons 30 Jul '07

30 Jul '07

I am analyzing some Zn organo-metallic protein complexes and have take EXAFS data at low temperature at the Zn edge. I am now in the midst of trying to fit the data. For the mean squared relative displacement terms, I am using Grant's DFT parameterizations for the Zn-cysteine system. This is working fine. In one of my complexes, I also have a water molecule within the "first shell". Does anyone have a suggestion for a reasonable MSRD term for this (at 20 K)? Paul Dr. Paul Fons Nano-Optics Reseach Team Team Leader National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所近接場光応用工学研究センター近接場光基礎研究チーム　チーム長ポール・フォンス

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Basic question in XANES calculation
by Joji Kuniya 27 Jul '07

27 Jul '07

Dear Sirs I am a beginner in XANES analysis. I tried to XANES simulation of Pt by Artemis program. Artemis stopped the calculation by memory limitation. I tried to down cluster size and RMAX parameter, and added "NLEG 4" after FMS sentence on feff.inp. But Artemis stopped the calculation with the same warning again. Please teach me how to make a good feff.inp file for XANES analysis. My PC is a notebook type PC(ThinkPad T60 with 2G memory). Thnak you. Joji Kuniya

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PPC Macintosh version of Horae 65 on SourceForge
by Paul Fons 25 Jul '07

25 Jul '07

I have made a new Macintosh installer for the PPC version of Horae 065 available on sourceforge. It would be neat if it could be copied to the cars download list in the wiki as well. Let me know if there are any problems. It seems to work fine on my end. As there are now two versions, a PPC and an Intel version, I have included PPC in the installer name, e.g. Ifeffit-1.2.9-Mac10.4_PPC_horae65_pkg.dmg Paul p.s. perhaps we should put the Horae 065 installer for Intel on the SourceForge site as well?

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[Fwd: Re: Mac intel OSX - Feff6 whereabouts]
by Katie Evans 24 Jul '07

24 Jul '07

Thanks for the advice, but sadly it didn't work. I also tried deleting the whole .horae and Perl folders and then reinstalling iXAFS, but that didn't help either. I checked the artermisrc file and it does say feff6 in the correct place, it just doesn't seem to be able to find feff6. Any more tips? Cheers, Katy ---------------------------- Original Message ---------------------------- Subject: Re: [Ifeffit] Mac intel OSX - Feff6 whereabouts From: "Jeff Terry" <terryj(a)iit.edu> Date: Tue, July 17, 2007 6:53 am To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> -------------------------------------------------------------------------- Hi Katy, I ran into this problem about two weeks ago. I have no idea why, it had worked fine for a few months before that. Paul's suggestion worked for me. Jeff On Jul 16, 2007, at 3:09 PM, paul fons wrote: > I can't say I have had this problem with either of my Intel Macs, > but I do know a solution that seems to have worked for others... that is to delete the preferences file for artemis which is located in your home directory under ".horae" and is named "artemisrc". Note that the "." (dot) in the directory name. This causes the finder and the default unix file listing "ls" command to not output the name as such preference files are considered "noise". To > delete the preference file you should run the command "rm ~/.horae/ artemisrc". This hopefully will help things... > Paul > On Jul 16, 2007, at 2:46 AM, Katy Evans wrote: > >> Hi, >> >> Apologies if this question has a very simple answer but I can't work it out. I installed the iXAFS package onto my new Mac (OSX 10.4.8) and almost everything works very well and it is very >> pleasant to use so thankyou. >> >> BUT Feff6 won't run. >> >> I can fit to existing Feff calculations but I can't make new ones, from .inp files that used to work on my other computer, or from quick first shell calculations. >> >> The message from Artemis starts 'This error is probably due to having Artemis configured incorrectly and so it does not know how to run Feff on your computer...' and goes on to say that I should check the value of the Feff executable in Preferences, and set it to Feff6. So I checked it and it was indeed Feff6. >> >> I looked for Feff6 on my computer and could only find a Feff6.atp file in the Perl directory (/Library/Perl/5.8.6/darwin-thread- multi-2level/Xray/atp) - should there be anything else? I tried typing this address into the box for the Feff executable option but this didn't help. >> >> I tried to remove everything and reinstall from the disk image but I am not sure if that was successful since I still only got the option to 'upgrade' when I clicked on the installer package. Where are all the things I need to remove if I want to get rid of the old version? >> >> Thankyou, Katy >> >> >> Katy Evans Dept. App. Geol. >> k.evans(a)curtin.edu.au Curtin University >> Tel: 0061 8 9266 4682 Bentley >> Fax: 0061 8 9266 3153 GPO Box U 1987, WA6845 >> >> >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Paul Fons > Team Leader > Nano-Optics Research Team > paul-fons(a)aist.go.jp > > Center for Applied Near-Field Optics > National Institute of Advanced Industrial Technology > Tsukuba Central 4, Higashi 1-1-1 > Tsukuba, Ibaraki Japan 305-8562 > > tel. +81-298-61-5635 > fax. +81-298-61-2939 > > The following lines are in a Japanese font > ã305-8562 è¨åçã¤ãã°å¸ã¤ãã°ä¸å¤®æ± 1-1-1 > ç£æ¥æè¡ç·åç ç©¶æ > è¿æ¥å ´åå¿ç¨å·¥å¦ç ç©¶ã»ã³ã¿ã¼ > è¿æ¥å ´ååºç¤ç ç©¶ãã¼ã ããã¼ã é· > ãã¼ã«ã»ãã©ã³ã¹ > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Athena 0.8.053, Artemis 0.8.010, Hephaestus 0.16
by Bruce Ravel 22 Jul '07

22 Jul '07

Hi folks, Just in time for the APS XAFS summer school, I am pleased (and relieved!) to release the latest source code for my XAS analysis programs Athena, Artemis, and Hephaestus. Here is a discussion of the new features: http://cars9.uchicago.edu/iffwiki/HoraeVersion065 Tarballs with the new source code can be found at my web site and at SourceForge. Matt and I are very close to having a new installer package for Windows. We will make an announcement when it hits SourceForge and the Ifeffit website. Hopefully packages for Mac/Motorola, Mac/Intel, and debian will be available soon. This release features LOTS of fixed bugs and user interface improvements to all three programs. The biggest new feature in Athena is the project selection dialog, which is described here: http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/projsel.ht… Hephaestus sports an interesting new tool for helping you select the correct fluorescence filter: http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/hephaestus.html#p… As always, let me know about any comments, suggestions, observations, or bug reports you might have. Thanks to everyone who helped with this release. Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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feff6 and mac intel os x
by Katy Evans 18 Jul '07

18 Jul '07

Yay it works. I got the address for Feff6 by doing 'Show package contents' and then typed it into the Feff6 executable box, with Feff6 included at the end. And its all good. Thankyou for the suggestions and quick responses. Cheers, Katy Katy Evans Dept. App. Geol. k.evans(a)curtin.edu.au Curtin University Tel: 0061 8 9266 4682 Bentley Fax: 0061 8 9266 3153 GPO Box U 1987, WA6845

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Re: [Ifeffit] Problems with EXAFS Analysis software for MAC
by Ravel, Bruce D. 17 Jul '07

17 Jul '07

Ross, The Ifeffit mailing list is a superb resource for all your ifeffit+friends questions. http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ Among the many nice things about the mailing list is that there are a number of people who, unlike me, use the Mac and will know the answer to your question. I have taken the liberty of forwarding this along to the mailing list. You should join the list so that when someone answers, you will get the mail. Good luck, B -----Original Message----- From: Ross Williams [mailto:Ross.Williams@curtin.edu.au] Sent: Mon 7/16/2007 9:47 AM To: Ravel, Bruce D. Subject: Problems with EXAFS Analysis software for MAC Hi I am having problems running ATHENA, ARTEMIS, and HEPHAESTUS, well actually an of the programs in the package. I have a new Intel MacBook with OS X version 10.4.10. I installed the X11 SDK from the OS X dvd, after I install it I could install your package. However when I open on of the programs (by opening them in Applications/Ifeffit) I am prompted to pick a output device, "X11 graphics" or "aquaterm". Either choice the program icon appears briefly in the dock then dissappears, this happens for all the programs. Any advice would be appreciated. Thanks, Ross +++++++++++++++++++++++++ Ross Williams Centre for Materials Research Curtin University of Technology GPO Box U1987 Perth WA 6845 Western Australia ross.williams(a)curtin.edu.au

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Mac intel OSX - Feff6 whereabouts
by Katy Evans 16 Jul '07

16 Jul '07

Hi, Apologies if this question has a very simple answer but I can't work it out. I installed the iXAFS package onto my new Mac (OSX 10.4.8) and almost everything works very well and it is very pleasant to use so thankyou. BUT Feff6 won't run. I can fit to existing Feff calculations but I can't make new ones, from .inp files that used to work on my other computer, or from quick first shell calculations. The message from Artemis starts 'This error is probably due to having Artemis configured incorrectly and so it does not know how to run Feff on your computer...' and goes on to say that I should check the value of the Feff executable in Preferences, and set it to Feff6. So I checked it and it was indeed Feff6. I looked for Feff6 on my computer and could only find a Feff6.atp file in the Perl directory (/Library/Perl/5.8.6/darwin-thread- multi-2level/Xray/atp) - should there be anything else? I tried typing this address into the box for the Feff executable option but this didn't help. I tried to remove everything and reinstall from the disk image but I am not sure if that was successful since I still only got the option to 'upgrade' when I clicked on the installer package. Where are all the things I need to remove if I want to get rid of the old version? Thankyou, Katy Katy Evans Dept. App. Geol. k.evans(a)curtin.edu.au Curtin University Tel: 0061 8 9266 4682 Bentley Fax: 0061 8 9266 3153 GPO Box U 1987, WA6845

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Basic questions on XANES
by Ashley Harvey 14 Jul '07

14 Jul '07

Dear ifeffit users, This posting is with quite basic questions on XANES data processing. I am a somewhat new XANES experimentalist, in a group that does not typically use XANES, so I am lacking some basic knowledge. For normalization of XANES, my impression is that people generally normalize the spectra from ca. 50 eV up to 100 eV or more after the edge onset. Is there a standard acceptable normalization range for K edges? I have noticed that when I change the start of the normalization window by even a few eV, this can make substantial differences in the XANES when comparing two similar spectra (for example, change in peak and pre-edge peak intensities between XANES of one sample at two temperatures). I keep second-guessing my choice of normalization range. Second, I am also looking at the effect of the various ways to set E0. When I start with ifeffit's default (how is this determined?) and then proceed to set E0 to the zero-crossing of 2nd derivative, I'll get value X. When I change it to a set fraction of the edge step (is this legitimate?) I typically get a lower value, and then when I proceed again to set it to the 2nd derivative zero-crossing, I get a value different from the first time it was set to the zero- crossing. For example, the E0 at an Fe K edge: ifeffit default = 7128.9 eV 2nd derivative zero = 7128.8 set fraction = 7125.1 2nd derivative zero = 7125.5 The value given by the 2nd derivative zero-crossing is dependent on the previous E0 setting. I am having a hard time to move on to the actual interpretation of the data while I am still uncertain about such details. Thanks for your patience with some simple questions. Best, Ashley

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