February 2010 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] kind of solve the problem (can't save files)
by Michael Gaultois 27 Feb '10

27 Feb '10

Good afternoon Jaziel! If it involves security, permissions, protection and all that jazz, try right clicking on the executable (the Athena program) and then selecting "Run as Administrator." See if it works. Sometimes if it involves permissions issue this can be the case. Can you provide any further details about these libraries you speak of? Specific error messages are very helpful in helping diagnose the problem. If it's on a shared computer, the system administrator might have frozen the operating system drive *(i.e.* they don't want people changing anything, so they prevent you from writing things to the C:), which might explain why you can save to external devices. Warm regards, Mike -- Michael Gaultois 165 - 110 Science Place Department of Chemistry University of Saskatchewan Saskatoon, SK S7N 5C9 Canada Tel: (306) 966-8422 Fax: (306) 966-4730 "La patience est amère, mais son fruit est doux." Phaedrus "We are like butterflies who flutter for a day and think it's forever." Carl Sagan > Message: 1 > Date: Fri, 26 Feb 2010 17:32:06 -0700 > From: Jaziel Soto <jaziel7somu(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] kind of solve the porblem... > Message-ID: > <d733687f1002261632n27063659o4daf76f61e9e682d(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi everyone (again), I kind of solve the problem. I can't save in C: but it > lets me save in external devices. I got some help and this person said the > problem might be something about security of vista and 7, something about > libraries (I don't know that much) the program uses that security doesn't > let me save on C: If someone has had a seemed problem have an idea of how > to > solve please comment... >

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kind of solve the porblem...
by Jaziel Soto 26 Feb '10

26 Feb '10

Hi everyone (again), I kind of solve the problem. I can't save in C: but it lets me save in external devices. I got some help and this person said the problem might be something about security of vista and 7, something about libraries (I don't know that much) the program uses that security doesn't let me save on C: If someone has had a seemed problem have an idea of how to solve please comment...

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Help, can't save anything on athena
by Jaziel Soto 24 Feb '10

24 Feb '10

Hi everyone, i'm using athena 0.8.061 and iffefit 1.2.11c installed on 32 bits widows 7. In a laptop toshiba (if it helps). My problem is that i can't save anything i work. I've tried everything that comes to my mind and i still cant save. I just hear a noise (advice) and nothing happens. I had vista, and i thought installing windows 7 might solve the problem but it didn't, so i'm asking for help now.

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Atomic concentration
by Bruce Ravel 24 Feb '10

24 Feb '10

> Dear Bruce, > I have a question about ATOMS application. I would like to get input file > of stoichiometric SrBi2Ta2O9 (SBT) and off-stoichiometric > Sr0.8Bi2.2Ta2O9(offstoich-SBT) with space group of A2 > 1am. How can I get the right crystal coordinations by changing the atomic > concentrations; i.e. decreasing Sr to Sr0.8 and increasing Bi2 to Bi2.2 in > off-stoichiometric Sr0.8Bi2.2Ta2O9 ? > Best Regards > > -- > O. Murat OZKENDIR I have forwarded this to the Ifeffit mailing list, which is the right place for questions like this. Here's some info about the mailing list as well as some hints on how to get more information about XAFS: http://cars9.uchicago.edu/ifeffit/BruceRavel/FormLetters/HelpRequest You question seems a little unclear and open-ended. Question 15 at http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling might help. Perhaps someone else on the list has some advice for you. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] ifeffit OS X 10.6
by Matt Newville 24 Feb '10

24 Feb '10

Hi Thorsten, Thorsten Bartels-Rausch <thorsten.bartels-rausch(a)psi.ch> wrote: > Hi Matt > > thanks for the ifeffit software package that we also use here at the Swiss Light Source (PSI SLS). May > I kindly ask, if you have a binary version of the package that runs under Os X 10.6 Snow Leopard (64 bit)? > Or should I follow the instruction to compile the package from source? Would you know if that works on > Snow Leopard. > > Thanks for any help. Seems as if I upgraded too fast. > best, thorsten Sorry, I don't know much about the status of binary packages for OS X other that what's listed on the download page. I wouldn't be surprised if Jeff Terry or Paul Fons had made a 64-bit version, but I don't know for sure. I'm sending this to the mailing list in case they or someone else knows more. Building from source on a Mac is not too painful if you have experience building software on Unix systems. --Matt

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standard values
by Neetu parsai 21 Feb '10

21 Feb '10

Hi all, I am searching for the values of mean free path and Debye waller factor of transition metals. Is there any citation available on these values? I want to understand how these are calculated. Mrs.Neetu Parsai Head Department of Engg.Physics Sanghvi Innovative Academy Indore. Residence: 130 Hemu colony, New G.D.C.Road, Indore-452015(M.P.) India.

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[OT] Ifeffit mailing-list available also on Gmane
by Mauro Rovezzi 20 Feb '10

20 Feb '10

Dear all, A short off-topic message to inform you that I have subscribed (in accord with Matt) the Ifeffit mailing-list to the http://gmane.org archive. This will permit to follow this (traffic-growing) discussion forum also via a newsreader or RSS feeds. Below a copy of the subscription. MR Begin forwarded message: Newsgroups: gmane.discuss.subscribe Subject: Re: subscribe ifeffit(a)millenia.cars.aps.anl.gov The following message is a courtesy copy of an article that has been posted to gmane.discuss.subscribe as well. * mauro.rovezzi (at) esrf.eu [2010-02-06 16:21]: > #gmane.science.physics.ifeffit ifeffit(a)millenia.cars.aps.anl.gov > Discussion of Ifeffit, Athena, Artemis, and SixPack, as well as > related X-ray Absorption Fine Structure (XAFS) analysis programs. > mailman dummy encode=encrypt > spam=ignore > lang=eng > url=http://cars9.uchicago.edu/ifeffit/ Subscription messages for the requested mailing lists have been sent. The resulting groups will be created when the first message arrives from the mailing lists. Wolfgang -- Gmane -- Mail To News And Back Again: http://gmane.org

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How to evaluate the fitted result by LCF?
by 康明亮 18 Feb '10

18 Feb '10

Dear, I want to consult how to evaluate the fitted result by LCF. R-factor within what range is reasonable and allowable? Attached are the fitted results, athena-SSRF.prj extention and .gif picture.Why there is still a large deviation for sample K (excluded FeSeO3 from this sample)? Thanks a lot! Best wishes Mingliang

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Athena Freezing Desktop
by David Ehle 16 Feb '10

16 Feb '10

Bruce, Sorry for the accusatory subject line - I can't prove Athena is the culprit but I figured that others with the same problem would be searching for similar terms. Running Athena from the current debian package for Lenny (2:1.2.11d-1) we have been seeing desktop freezes after some hard to characterize period of use. The time period seems to usually be a few hours, and there is a belief that it is connected to having more than a few raw data files open in Athena. Users have previously seen Athena crash/freeze when they have "too many" files open, or Athena open for "too long" but I haven't been able to get any firm numbers. The concern is that while previously when Athena crashed or froze, only Athena was effected. Now it seems that the whole desktop becomes non-responsive. The reason I'm suggesting there is a link between Athena and the Desktop (XFCE4) problem is that if you connect to the system via SSH and kill Athena, the Desktop becomes unfrozen and the user can continue with what they are doing. We have seen this occur on both beamlines, with different users and different data sets so I doubt it is data specific, but can send your some sample files if that will be useful. In one case I was able to collect an error message from the .xsession-errors file of a user who was experiencing the problem: ** (xfwm4:21854): WARNING **: Unmanaged net_wm_state (window 0x3800008) X Error: BadWindow (invalid Window parameter) 3 Major opcode: 7 Minor opcode: 0 Resource id: 0x329 kbuildsycoca running... Reusing existing ksycoca kbuildsycoca running... Reusing existing ksycoca kbuildsycoca running... Reusing existing ksycoca Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. I'm afraid I don't know if the lines before the lines that explicitly mention athena are related, or if these messages have anything to do with the desktop freezing problem - I think I have the seen the freeze without the errors. Please advise if we can provide you with other information to make figuring out easier. When this problem occurs at 3AM it really upsets our users (which tends to upset the staff when they get called about it...) so we have started running a second system just for Athena. Can you make any suggestions on the minimum vs optimal hardware for Athena? For tracking many (30+) raw data files to see how a run is progressing, can you suggest minimum RAM, CPU power, # of Cores? Thanks!! Please CC ehle(a)iit.edu with any responses as I'm not an active subscriber to this list. David Ehle MRCAT -IIT

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Is possible to shift the spectra in athena?
by 康明亮 16 Feb '10

16 Feb '10

Dear, I want to consult if is possible to shift a spectra in athena? As shown in the attached file athena.prj, I want to include red-(Se) to do LCF. But I forgot to measure the red-Se(0) spectra, only grey-Se(0) was measured. However, according to the literature, these two references have the same energy position only with different amplitude at the white line peak. Since the white line peak would shift if the same sample was measured at different facility, thus I need to do horizontal translate the spectra of red-Se(0) which measured at another facility. is it possible to do this in athena? Thanks! Best regards Mingliang

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