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

Re: [Ifeffit] [FEFF8.4] Re(x) is .le. zero in besjn
by joshua jason kas 18 Oct '07

18 Oct '07

Hi Mauro, This is probably a bug in feff. There is probably a workaround. Can you send your feff.inp file and I will try to help find the right cards to make your file run. Also I will add this to a list of bugs to look at. Cheers, Josh > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 01 Oct 2007 18:17:50 +0200 > From: Mauro Rovezzi <rovezzi(a)esrf.fr> > Subject: [Ifeffit] [FEFF8.4] Re(x) is .le. zero in besjn ? > To: Ifeffit-ML <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <47011DAE.2010508(a)esrf.fr> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > A little question about a FEFF8 error message I have and I cannot > understand what it means : > > Re(x) is .le. zero in besjn > > This error is generated when I try to add the SCF to an EXAFS > calculation on MnO (manganosite) and the SCF iteration is at step 9 of 30. > > Seen that the cards in the feff.inp file are properly used (I normally > run SCF in EXAFS calculations) do you have any idea of what is going on? > > Thanks for your help, as usual! > > Mauro > > -- > Mauro Rovezzi <rovezzi(a)esrf.fr> > PhD student - GILDA BM08 c/o ESRF (Grenoble, FR) > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 56, Issue 1 > ************************************** >

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Re xanes feff8 sulfur
by Kelly, Shelly D. 16 Oct '07

16 Oct '07

Hi Eckard, I realize that you have posted a message every month for about 3 months in a row without any reply: Shame on us... I will try to answer some of your questions and maybe that will help to get some discussion going. The energy scale in feff8 is NOT defined as you would expect it to be for determining the absolute energy of an edge. The energy scale in FEFF8 is related to the difference between the energy level of the intersist (potential level inbetween the muffin tins that represent atoms) and the threshold energy level for the excitation of the electron. I realize that this doesn't solve your problem, but hopefully it will spark some discussion. Cheers, Shelly Mon Aug 13 06:00:19 CDT 2007 Does anybody know a person, who has experience respective the topics xanes+feff8 and sulfur K-Edges? I would be very thankful for an answer :-) sincerely yours, Eckhard Bosman Tue Jul 10 10:07:38 CDT 2007 Hello, i have problems with feff-xanes calculations related to pyrite. I try to get the k-edge of sulfur (as absorber) in FeS2. I get the edge at ~2472 eV and i think this is wrong because i get the same energy with gypsum and i think there should be an energyshift related to 2472 eV. My proceeding is as follows: calculate the atomic positions with the asymetric unit from the http://rruff.geo.arizona.edu/AMS/amcsd.php database (Pyrite spacegroup Pa3) respectively http://rruff.geo.arizona.edu/AMS/xtal_data/CIFfiles/00596.cif with "powdercell 2.4" feffrun with the feff.inp-file like in the attachment (thanks to Josh Kas for his feff-hints) I started the feff-run on the one hand with 12 atoms (unitcell) and on the other hand with 22 atoms (14x Fe and 8x S in the cube) After this i plotted from xmu.dat the absorbtion mu (column 4) as a function of the energy (column 1). The result is in the attachment too. I don't know why i get everytime the Sulfur-k-edge at the same position (for pyrite or gypsum) respectively without energyshift related to 2472 eV. many thanks for your help :-) Ciao, Eckhard Fri Jun 15 08:48:21 CDT 2007 Hallo @all, (first at all, sorry for my bad english) i'm a student working on my diploma thesis (nexafs/xanes) and my job is to simulate with FEFF 8.4 spectra, for example absorption as a function of energy (mu_(E)). I'm a newbie in this topic and i tried to get the k-edge of Sulfur for the substance gypsum (CaSO4 * 2(H2O)) and pyrite (FeS2). I'm interested in the XANES-range of the spectra not the EXAFS. I get everytime my peaks at ~2472 eV for Sulfur as absorber whatever substance i use (gypsum, pyrite,...). There are no differences with the peak position on the energy-scale or shifts. I'm really confused :-( I think, there should be differences in the spectra... I send you two feff.inp files from my feff-runs. My source is the mineralogy database (http://rruff.geo.arizona.edu/AMS/amcsd.php) where i get the data for the unitcell. Then i put the data in the XtalDraw program to get the positions of the Atoms in Angstrom, by the way i get i nice 3D-View of the unitcell :-). Then i put the values of the positions into feff... I simulated pyrite with 12 atoms and gypsum with 48. I'm appreciative for every help :-) ciao, Eckhard

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Linear Combination Fitting in Athena-
by Skya Fawcett 14 Oct '07

14 Oct '07

I'm doing linear combination fits using 10 standards total, and choosing to use at most 3 or 4 standards in the fit. The problem is that depending on which I choose, 3 or 4, the results vary significantly. Often one standard will show up in one fit using at most 3 standards and not in a fit using at most 4 standards. For example: Unknown A: Fit using at most 3 standards Standard 1= 0.213 Standard 2= 0.374 Standard 3= 0.413 Fit using at most 4 standards Standard 1= 0.282 Standard 2= 0.269 Standard 4= 0.102 Standard 5= 0.346 Unknown B: Fit using at most 3 standards Standard 1= 0.278 Standard 2= 0.745 Fit using at most 4 standards Standard 2= 0.694 Standard 3= 0.117 Standard 4= 0.227 Note that the same 10 standards are run in each case, its only the number I choose to use in the best fit that is varying. As you can see, hopefully, the results vary significantly. Any ideas as to why this might happen? Any advice you can give on attaining more consistent results would be greatly appreciated. Thank you! Skya Fawcett PhD Candidate Department of Geological Sciences and Geological Engineering Queen's University, Kingston, Canada

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Re: [Ifeffit] Intel Mac release of latest horae package 066
by Xue Rui 12 Oct '07

12 Oct '07

Hi, all. I come with some software problems. I am using a Mac with System Version: Mac OS X 10.4.10 (8R4031) Kernel Version: Darwin 8.10.3 I just installed the new version of horae package 066 released by Dr Paul Fons. Everything works ok except for the plot window: it just shows the lines, but not any words, numbers, not the scale of the coordinate, not the name of the file. Another problem is I can not print the plot. I tried the previous version written by Jeff, these problems went away but the feff6 did not work then. Anything I need to figure out for the system? Best wishes. Snow On Oct 4, 2007, at 1:00 PM, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > [Ifeffit] Intel Mac release of latest horae package 066

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Re: [Ifeffit] space group C-1
by Ravel, Bruce 09 Oct '07

09 Oct '07

Nan, You haven't quite given me enough information to actually help. In this case, I'd need to see the crystallographic reference, or at least the input data, for the problem at hand. This is point #5 at http://cars9.uchicago.edu/~ravel/software/bugs.html. B -- Bruce Ravel ----------------------------------- bravel(a)bnl.gov My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ -----Original Message----- From: Nan Jiang [mailto:Nan.Jiang@asu.edu] Sent: Tue 10/9/2007 5:59 PM To: bravel(a)anl.gov Subject: space group C-1 Dear Dr Ravel I use Atoms to generate clusters for FEFF calculations. My space group is C-1, which is not included in your table. I tried to use P-1 instead, but it does not work properly. There are four symmetries in C-4, but only 2 in P-1. Could you advise me on this? Thanks for your time. Nan Jiang

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Intel Mac release of latest horae package 066
by Paul Fons 04 Oct '07

04 Oct '07

I know Jeff Terry is busy and I wanted the latest release for the Intel Mac my own purposes so I built a release using the traditional (/Applications/Ifeffit) file structure (I said I needed quickly, right?) using gfortran. The new installer is on the sourceforge site under the ifeffit project (http://downloads.sourceforge.net/ifeffit/ Ifeffit-1.2.10-Mac10.4_Intel_horae66.dmg?use_mirror=osdn). I will update the Wiki as well to the new release. As I said, I made the release for myself and am sharing it -- meaning I have only tested it on the system I built it on (Mac Pro) and my Mac Book Pro laptop (for which I used the installer). It works on both of these systems just fine, but they are of course setup in a similar way. If anyone has any problems let me know (although I have an extended series of synchrotron runs coming up and my focus will be on my (day and night) job. Note that you *must* have installed the X11 environment (an optional install located on the restore disks that come with new Macs) for this to work (it runs under X11). 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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SCC Mailing List
by Anatoly Frenkel 03 Oct '07

03 Oct '07

Hello all: Our group, Synchrotron Catalysis Consortium, or SCC, at the NSLS has started a mailing list (SCC-Forum) to provide our users with an opportunity to discuss problems that are specific to nanocatalysis science. Most of our users come to SCC to perform in situ XAFS in catalysis reactors, collect time-resolved data, analyze low dimensional systems (e.g., nanoparticles, monolayers, nanorods, and their real time reactivity, as just a few examples) and thus may benefit from a specialized forum where these issues are addressed in depth. Postings by our list members would facilitate discussions of experimental setups needed to study a specific catalysis problem, experimental regimes, typical experimental pitfalls in these type of measurements and how to avoid them, data modeling tricks and know-how, etc. The purpose of the list is to help each other and the SCC group here at the NSLS by sharing your experience and stimulate further development of catalysis science done by XAFS and other synchrotron techniques. For those who are not familiar with SCC, a good starting point describing our activities is: http://www.yu.edu/scc. To subscribe to the SCC mailing list, and start receiving and sending postings, use as the entry point the main SCC web page: http://www.yu.edu/scc and click at the SCC Discussion Forum link in the bottom right. Note that you may choose to receive daily digests of the postings; regardless of your choice, you can access the message archives by logging in to the list using the main entry point above. The interface is the same as IFEFFIT; in fact, Matt kindly helped me to configure it to have the same settings as IFEFFIT, to make it easier for those who wants to subscribe to the both lists. Perhaps, such specialized lists could be set up in the future by other groups using XAFS, say, life sciences and environmental sciences, who will continue using IFEFFIT as a fantastic resource for general XAFS analysis advice but have their own list themes, as does SCC-Forum. Regardless of whether it may or may not be a good idea in general, I hope the SCC-Forum list will be a useful resource for you. Any comments, please let me know. Anatoly Anatoly Frenkel, Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Fax: (212) 340-7868 Email: anatoly.frenkel(a)yu.edu

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The common question!
by 沛昌蔡 02 Oct '07

02 Oct '07

To Dear Authors; We have accumulate some questions on attach ptt.file, that including theoretical and athena background removal file. In order to present our questions more clear and short, we make this way, Thanks for your time and help! Pei-chang Tsai 杜絕網路駭客，保障帳號安全 - 馬上設定 Yahoo!奇摩安全圖章！

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[FEFF8.4] Re(x) is .le. zero in besjn ?
by Mauro Rovezzi 02 Oct '07

02 Oct '07

Hi all, A little question about a FEFF8 error message I have and I cannot understand what it means : Re(x) is .le. zero in besjn This error is generated when I try to add the SCF to an EXAFS calculation on MnO (manganosite) and the SCF iteration is at step 9 of 30. Seen that the cards in the feff.inp file are properly used (I normally run SCF in EXAFS calculations) do you have any idea of what is going on? Thanks for your help, as usual! Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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Ifeffit 1.2.10
by Matt Newville 02 Oct '07

02 Oct '07

Hi Folks, I've just uploaded Ifeffit 1.2.10 to the cars.uchicago.edu and sourceforge.net sites. I'm posting both source code (ifeffit-1.2.10.tar.gz) and a Windows installer (ifeffit-1.2.10.exe) which includes the latest versions of Hephaestus, Athena, and Artemis. Installers for Mac users shouldn't be too far behind. For now, the downloads page at http://cars9.uchicago.edu/ifeffit/Downloads links to both 1.2.10 and 1.2.9 versions. It may take a day or so for the files to show up on all the sourceforge.net mirrors. The new Windows Installer reflects a new build process for the underlying library. This took some time to work out (you may recall some emails about this over the summer) , but we think it is working as well as any previous version. There are quite a few changes to Bruce's codes, all for the better. And this version does install and work on Windows Vista. For the source code kit, this now uses a new install location for PGPLOT, so if you're installing you must run PGPLOT_Install before installing ifeffit. Also in this version is support for (and default use of) gfortran instead of g77. If you need to use a different fortran compiler from the one found by default, you can use ./PGPLOT_Install --with-fortran=g77 ./configure --with-fortran=g77 make install As always, let us know if there are any problems. Cheers, --Matt

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