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

Hexagonal WO3
by Ying Zhou, Anorganisch-Chemisches Inst. 18 Nov '08

18 Nov '08

Dear All Recently, I got one compound, W/Mo oxide, which has the similar structure with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of this compound. So, we use the hexagonal WO3 model to refine the structure of our compounds. My question is that how can I get the FEFF file of this compound. Can I directly change some of W to Mo in FEFF file? or Do I need to add the Mo in the atom file? I do appreciate your help. Best wishes Ying

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Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source)
by Matt Newville 17 Nov '08

17 Nov '08

Hi Folks, I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu and sourceforge.net download sites. I have a Windows dll made for this bug fix version. If anyone is interested, this is currently at http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll This should be a drop-in replacement for the IFEFFIT_DIR\bin\ifeffit_12.dll on your system. Artemis.exe will not be updated from this dll, as it has this dlls "compiled in". Bruce will have to make a new Artemis.exe, and then we'll make a automatic update. Sorry for all the trouble, --Matt On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > Hi, > > This is my fault... and I apologize for the sloppiness and for being > late in fixing this. I've been mixing 'development/testing' and > 'production' versions, and haven't been very good at keeping them > cleanly separated. I think I have this mostly under control now, > but I will have to work on a decent "test suite". > > I think I found another reason to make a 1.2.11c version too, that the > mixing of "devel" and "production" > caused an experiment in how fitting was done to be the default, so > that the reported chi-square doesn't actually match the documentation > (instead of summing real and imaginary parts, it sums real and > magnitude components of the misfit, which is part of an experiment to > see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > another way to report chi-square and misfits is potentially a useful > approach, but it's not what is documented. Anyway, mixing devel and > production versions like this (for the past couple years, really) is > very sloppy on my part, and I apologize again. > > I actually have an ubuntu box now, though I built pgplot from source, > and have never made a .deb file. > There is a new source kit at > http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > post this to sourceforge this afternoon, and I'll also make a new DLL > for Windows and post all of these on the download page. I'll also make > a new updater for Windows. > > --Matt > > > On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> wrote: >> Carlo Segre wrote: >>> >>> Hi Mauro: >>> >>> I have now produced a package of ifeffit 1.2.11b. It is in Debian >>> unstable and available for Ubuntu intrepid and jaunty in my repository >>> >>> deb http://debian-xray.iit.edu intrepid main contrib non-free >> >> Carlo, >> >> Thank you very much for the package. >> >> Actually, I was able to build/install ifeffit 1.2.11b from source but >> not able to build than the Perl/Python wrappers and so no Horae&Friends >> from Bruce SVN. >> >> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and >> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" >> built from source (Bruce SVN). >> >> Everything seems fine but I still do not understand why ifeffit 1.2.11 >> has all these "IFF str = *" output as stated also by Gareth in his >> "Ifeffit 1.2.11b terminal output" post. Is it normal? >> >> Cheers, >> Mauro >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

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[PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source
by Mauro Rovezzi 17 Nov '08

17 Nov '08

Dear all, I decided to upgrade ifeffit-1.2.11 on my Ubuntu 8.10 (Intrepid Ibex) desktop machine. Well, up to now I have always worked with PGPLOT & Ifeffit binaries from Carlo that are just working fine but seen that they are still not ready for the new version I decided to build them by source. First of all let me say that Ifeffit builds fine if I use the "pgplot5" binary package, BUT, as stated by Matt in the README.PGPLOT, Ifeffit will compile without plotting support in this case. So the only way is to build also PGPLOT from source. Unfortunately the experience has failed both with the "PGPLOT_install" script and following steps in the "install-unix.txt". I have tried many possibilities but the make process interrupts on the drivers compilations. Seen that following "install-unix.txt" gives the same error (but on another driver!) of "PGPLOT_install", let's focus on this last procedure to try debugging the situation: $sudo ./PGPLOT_install ... [all fine until the PGPLOT make] [long list of errors + warnings like:] ... /home/mauro/local/ifeffit-1.2.11/pgplot/drivers/xwdriv_iff.c:4445: error: ‘XWdev’ has no member named ‘gc’ ... make: *** [xwdriv_iff.o] Error 1 ... [then the final error due to the bad compilation] collect2: ld returned 1 exit status make: *** [pgdemo1] Error 1 OK, I have described more or less the situation but I would not flood the list with technical mails, so if someone would help me with this issue we can continue in private and then send just the solution to the list. Anyway, the problem is not "urgent" seen that I can work with the 1.2.10 binary installation. Have a nice day! Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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about wolframite crystallographic file
by Yordy Licea Fonseca 17 Nov '08

17 Nov '08

Hi all, As soon as I load this attached CIF crystallographic file from ISCD in Artemis0.8.012 the software says: "Artemis trapped one or more errors! Error message dumped to screen." I can`t go on runnig Atoms as it seems to be a problem with the file. I have read the suggestion made in FAQ, but I can not manage to find the error. Could you help me, please? It would be nice once the problem been fixed to add this structure to Matt's atoms.inp database. Thanks you very much, Yordy -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: yliceafonseca(a)gmail.com

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Co doped ZnO
by Guvenc Akgul (gakgul) 15 Nov '08

15 Nov '08

dear all, I have 10%Co doped ZnO EXAFS data and I would like to figure out :Co-Co distance in the 10%Co doped ZnO.what will i do for this?if you can help to me about this i will be very glad. thanks all guvenc

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Sealed Sample Cell
by Bhoopesh Mishra 12 Nov '08

12 Nov '08

Dear All, I am planning to conduct an EXAFS experiment which involves dealing with methyl mercury. Obviously, I want to be as cautious as I can in sealing the sample. In that connection, I am wondering if anyone on this forum can advise me regarding the best way to have a completely sealed (air tight) sample holder. My requirements are given below. Third requirement is not as important as the first two. 1. Sample cell (or the front and rear exit) should be made of low scattering material that would not attenuate photons too much at ~ 10-12 keV. 2. The sample cell should be a perfectly sealed, as gaseous phase methyl mercury or even di-methyl mercury could be produced in the cell. 3. I would like to inject solution using syringe in the sealed sample holder (if possible, this requirement is not necessary). Among several possibilities, I am thinking of designing a cuvette shaped rectangular box with a thin bottom section, and probably using some sort of polypropylene such that scattering is as low as possible. It should be easy to put two silicon rubber septa on the top. Other possibility could be using a thick Beryllium window (and please forgive my naivete' here - isn't there some restriction in using Be) on both the front and back of a rectangular or cylindrical box with rubber stopper at the top. The easiest and probably the best would be to have a commercially available sample cell that can serve my purpose. I don't know any commercially available product like that. But I suspect, people who work with volatile material and/or radioactive material might know a lot about it. If you know anything, please write me back. Any comments, suggestions, or criticism would be highly appreciated. PS: Sealing with kapton tape (or any other thin film) might not be enough in this case as gaseous phase methyl mercury might diffuse through kapton, and also air might diffuse through kapton making the inside of the cell environment aerobic while I need to do this experiment anaerobically. Thanks for your help! Bhoopesh

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problem on opening data file
by Ruoshuang Huang 11 Nov '08

11 Nov '08

Hello All, Recently I found that I could not open my EXAFS data files using Athena any more. Previously I had no problem using Athena to do data analysis (the last time was in last year). Now when I try to open a data file, a small window appears saying this file 'could not be read by ifeffit as a data file'. This happened to both the old data files that could be opened previously and new ones that were obtained recently. All the raw data were taken on beamline X10C at NSLS in the format of .xfs. I appreciate it if someone could help and give me some suggestions. I've attached one of my data files as an example. Thank you so much, Ruoshuang

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Athena's application
by abhijeet gaur 06 Nov '08

06 Nov '08

> I am doing my research work on EXAFS . For > that I am using the software ATHENA for analyzing my data > which my guide had brought from SSRL ( USA ) . But there is > some problem in that , Athena is taking the data and > plotting it but is not giving the required parameters. I am > sending you the copy of that data . So if you can go through > it and suggest me what is the problem , I wil be very > thankfull . > > > > > > > Did you know? You can CHAT without downloading > messenger. Go to http://in.webmessenger.yahoo.com/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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Synchrotron Environmental Science meeting, Dec 11-13th, 2008 San Francisco CA
by Peter Nico 06 Nov '08

06 Nov '08

Hello All, I thought some readers of this list might be interested in the Synchrotron Environmental Science meeting described below and at the following link. http://esd.lbl.gov/sesIV08/index.html Even if I do say so myself, I think its going to be a very interesting conference form both a synchrotron science and environmental science point of view. Plus, its always nice to go to California in the winter. :) Thanks. --Peter *Synchrotron Environmental Science IV (SES-IV) Meeting, December 11 -- 13, 2008* <http://esd.lbl.gov/sesIV08/> * PREREGISTRATION DEADLINE IS NOV 14!* After Nov. 14, registration fees will increase. Please register at: http://www.regonline.com/Checkin.asp?EventId=649848 *PROGRAM HIGHLIGHTS INCLUDE:* * Key note perspective talks on CO2 sequestration, atmospheric chemistry, environmental remediation science, and marine sciences from world-leading scientists, with emphasis on the potential roles of synchrotron techniques. * Talks on new and emerging synchrotron techniques * Talks on developments in data acquisition hardware and software * Hands-on sessions at SSRL and ALS beam lines for prospective and new users * Introductory-level talks for prospective and new users * Facility reports from North American synchrotron sources * Poster session * * *CONFERENCE HOTEL INFORMATION -- Lodging Deadline is NOVEMBER 14* The lodging deadline for the Conference Hotel is also November 14th, however space is limited and is not guaranteed. The $152.00/per night rate at the Westin is actually less than the Government allowable in San Francisco of $164.00. Also, our rate is even lower than that offered through AGU of $164/night. You may extend your stay through the entire AGU session. You can make your lodging reservations for the Conference hotel by visiting: http://esd.lbl.gov/sesIV08/accomodations.html * ** KEY DATES:* *Early Discount Registration Closes November 14, 2008 Discount Lodging Registration Closes November 14, 2008* SES IV Conference Dates December 11 -- 13, 2008 Hands on Sessions December 11, 2008 Poster Session Evening, December 12, 2008 *COMPLETE MEETING PROGRAM* The complete Synchrotron Environmental Science IV (SES-IV) 2008 Meeting agenda is available at: http://esd.lbl.gov/sesIV08/program.html As you will see, the conference has a very exciting program! *HANDS ON SESSION:* On Thursday, December 11, there will be a tour and hands on training at beam lines at ALS or SSRL See web for more details and to enroll: http://esd.lbl.gov/sesIV08/session.html *QUESTIONS?* Please direct all questions or comments to CAValladao(a)lbl.gov. Best Regards, SES-IV 2008 Organizing Committee

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Re: [Ifeffit] Ifeffit Digest, Vol 69, Issue 3
by Gudrun Bovenkamp 04 Nov '08

04 Nov '08

Dear Bruce, thanks for your detailed answer. I tried Athena, Arthemis and the Six Pack programs. For all these programs it was not possible to open a certain file or save a project to a certain location. I also tried as you wanted me to get some error messages through the DOS command console, but the program just ended and did not send any comment to the cmd! It seems as if it ended in a correct way. And: the problem occurred just recently. I was wondering if anyone else had this problem. But it did not seem so. I talked to my administrator....and he suggested to delete my profile and renew it. Now the problem is solved. It was something on my computer. I am so sorry that I bothered you with this. Thanks, anyway. You are just great! Lisa

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