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

Re: [Ifeffit] iXAFS 2 beta 1 released
by Hind Al-Abadleh 07 Dec '07

07 Dec '07

Thanks Jeff and Matt for your timely reply. The software runs just fine now. Hind ---------------------------- Hind A. Al-Abadleh, Ph.D. Assistant Professor Chemistry Department, Wilfrid Laurier University Science Building 3020F 75 University Ave. W. Waterloo, Ontario N2L 3C5 Canada Ph.: (519) 884-0710 ext. 2873 Fax: (519) 746-0677 URL: http://www.wlu.ca/science/chemistry/halabadleh/ ---------------------------- >>>terryj(a)iit.edu 12/07/07 9:11 am >>> Hind, X11 would be in /Applications/Utilities/ You should install X11 off of your 10.4 DVD and then apply the update. Jeff On Dec 7, 2007, at 5:42 AM, Hind Al-Abadleh wrote: >Hi Jeff, > >This is great news. I downloaded the beta version, and got the error >message Apple's X11 for Mac OSX is not installed.... So, I >downloaded >the latest update for X11 from Apple's website from this page: >http://www.apple.com/downloads/macosx/apple/macosx_updates/x11update2006113… > >And when I tried to install it, an alert message came this system >doesn't need this update. So, now I'm baffled, and truly don't know >where to go from here. How would I check my system (OSX 10.4.11) for >the X11 already installed? > >Any advice will be very much appreciated. >Thanks, >Hind > > > > > >---------------------------- >Hind A. Al-Abadleh, Ph.D. >Assistant Professor >Chemistry Department, Wilfrid Laurier University >Science Building 3020F >75 University Ave. W. >Waterloo, Ontario N2L 3C5 Canada >Ph.: (519) 884-0710 ext. 2873 >Fax: (519) 746-0677 >URL: http://www.wlu.ca/science/chemistry/halabadleh/ >---------------------------- > >>>>terryj(a)iit.edu 12/07/07 12:15 AM >>> >Hi All, > >iXAFS version 2 for Mac OS X 10.4 and above has been released as a >beta version. We have tested this version on ppc and intel macs >running OS X 10.4 and 10.5. > >You must have Apple's version of X11 installed in order to use iXAFS. > >Ken McIvor put in yeoman's work to build the full ifeffit, horea suite >as a universal binary. He packaged it as a single drag and drop >installation within iXAFS. > >Ken wanted to post this message but had an illness in the family. >Hopefully, we can all thank Ken for his work to get this built in a >manner that should work on all modern Macs. > >A link to download this version of iXAFS can be found at the MRCAT >website: > >http://mrcat.iit.edu > >We forgot to put in the documentation that the iXAFS shell allows you >to run any of the programs from the command line ifeffit, feff6, etc. > >Jeff > > >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 Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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iXAFS 2 beta 1 released
by Jeff Terry 07 Dec '07

07 Dec '07

Hi All, iXAFS version 2 for Mac OS X 10.4 and above has been released as a beta version. We have tested this version on ppc and intel macs running OS X 10.4 and 10.5. You must have Apple's version of X11 installed in order to use iXAFS. Ken McIvor put in yeoman's work to build the full ifeffit, horea suite as a universal binary. He packaged it as a single drag and drop installation within iXAFS. Ken wanted to post this message but had an illness in the family. Hopefully, we can all thank Ken for his work to get this built in a manner that should work on all modern Macs. A link to download this version of iXAFS can be found at the MRCAT website: http://mrcat.iit.edu We forgot to put in the documentation that the iXAFS shell allows you to run any of the programs from the command line ifeffit, feff6, etc. Jeff

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Re: [Ifeffit] Graphics Problems in ATHENA
by Ravel, Bruce 05 Dec '07

05 Dec '07

Hi Sola, This is the sort of question that should go to the Ifeffit mailing list, so I am taking the liberty of CCing my answer there. > I recently encountered a problem with a .prj file in ATHENA. The first > issue was the notification that ATHENA may be out of memory and when I > checked the memory usage under the help menu, I found out that I was not > even using up to 1% of the memory. So, after closing the saved .prj > files, one with some groups removed and another one without removing > some groups, I tried to reopen the .prj but the graphics refused to > display. I have since rebooted the system and updated IFEFFIT, but still > no luck! This is not really enough information for me to figure out the nature of the problem you are seeing and I have never seen the behavior you describe, but I can give you a few hints. 1. Athena's way of guessing memory usage is extremely unreliable. In general it is a poor idea to import more than about 60 scans into Athena (that is, 60 scans of the typical step-scan variety with 10 volts steps in pre-edge, 1/2 volt steps through the edge, and 0.05 A^-1 steps in the EXAFS) or fewer if you are importing MED files with lots of columns or quick scans with lots of data points. This is not a shortcoming of Athena, rather it is a result of Ifeffit being written in Fortran. If you are running into memory issues, you should group your data in smaller chunks for import into Athena. 2. Perhaps there is something abnormal about the prj file, but I cannot know unless you attach an example that produces the poblem reliably. 3. Are there any messages in the console window that starts when you start Athena? That's the window that stays on the task bar after Athena starts. The messages i that window may be gobbledigoop to you, but they may provide me with information about the nature o fthe problem. If Athena is exiting before you can look at the console, try opening up a command window, changing directory to C:\Program Files\Ifeffit\bin (or wherever Ifeffit is installed) and running athena from the command line. That way, any error messages will be preserved. B -- Bruce Ravel ----------------------------------- bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National Laboratory Building 535A Upton NY, 11973 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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problems running athena on macOSX
by Hind Al-Abadleh 05 Dec '07

05 Dec '07

I have downloaded and successfully installed Ifeffit-1.2.10-Mac10.4_PPC_horae66. But every time I click on athena, the X11 and aquaterm message appears, and regardless of my choice, Athena won't launch and will automatically quit! I downloaded X11 from Mac website and while installing, a message came up telling me that I have a later version already installed on my mac. But still, can't get Athena to work. I also downloaded and installed iXAFS.app. After clicking on the iXAFS icon, a window appears to specify the path to data and three icons to Athena, Artimis, etc, but clicking on the icons won't take me any where! Any insight would be greatly appreciated. Thanks, Hind ---------------------------- Hind A. Al-Abadleh, Ph.D. Assistant Professor Chemistry Department, Wilfrid Laurier University Science Building 3020F 75 University Ave. W. Waterloo, Ontario N2L 3C5 Canada Ph.: (519) 884-0710 ext. 2873 Fax: (519) 746-0677 URL: http://www.wlu.ca/science/chemistry/halabadleh/ ----------------------------

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Re: [Ifeffit] Log-Ratio
by Frenkel, Anatoly 05 Dec '07

05 Dec '07

It adds (or subtracts) 2pi to the phase difference between the unkown and the standard as some times it does not eztrapolate to zero as 2k*delta r term should. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Wed Dec 05 06:22:28 2007 Subject: [Ifeffit] Log-Ratio Dear all, i have a question to the Log-Ratio/Phase-Differnce Analysis in Athena. What means the parameter 2pi jump? I did not find any help file for the ratio method. Best regards Jörg Haug _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Log-Ratio
by Jörg Haug 05 Dec '07

05 Dec '07

Dear all, i have a question to the Log-Ratio/Phase-Differnce Analysis in Athena. What means the parameter 2pi jump? I did not find any help file for the ratio method. Best regards Jörg Haug

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Check out my Facebook profile
by Tonya Vitova 02 Dec '07

02 Dec '07

Hi Ifeffit, I set up a Facebook profile with my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Tonya Here's the link: http://www.facebook.com/p.php?i=681514113&k=43GU3Z663WTO6FLGSAXY&r&v=2 ___________________ This e-mail may contain promotional materials. If you do not wish to receive future commercial mailings from Facebook, please click on the link below. Facebook's offices are located at 156 University Ave., Palo Alto, CA 94301. http://www.facebook.com/o.php?u=804872375&k=3da3f5

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negative amplitude
by Wojciech Starosta 30 Nov '07

30 Nov '07

Sorry if it is FAQ. But I spent some time on fitting without success and have not found answer to this. Does anybody could explain me if negative value of amplitude has any sense. I can get beautiful plot after fit, but unfortunately the message appear concerning negative value of amplitude (amplitudes). How to avoid it. Any written material will be very helpful. I know that I can define amplitude as squared value of new variable. But sometimes it does not work. Ifeffit stops with message that value of this variable cannot be determined With the best regards Wojtek Starosta Institute of Nuclear Chemistry and Technology 03-195 Warsaw, Dorodna 16 Institute of Nuclear Chemistry and Technology --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0649-1, 2006-11-18 Tested on: 2007-11-30 13:45:41 avast! - copyright (c) 1988-2007 ALWIL Software. http://www.avast.com

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(no subject)
by Bindu R. 27 Nov '07

27 Nov '07

could you tell me how does one tune the bond angles from the multiple scattreing paths? Bindu Dr.Bindu R. Visiting Scientist DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Mobile-919892536830 --------------------------------- Chat on a cool, new interface. No download required. Click here.

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Exafs distance resolution
by Eric Breynaert 27 Nov '07

27 Nov '07

Dear all, Is there a physical limitation determining exafs bond distance resolution? Very often the equation r = pi / 2 deltak is quoted as a measure for bond distance resolution. But as i understand this equation is related to the fourier transform traditionally used for exafs analysis. If exafs fitting is done in k-space, on the raw exafs data without applying fourier or any other filtering transformation is there a physical limitation determining exafs bond distance resolution? This question comes down to the following practical problem. If one has a theoretical model developed using computational chemistry that predicts two different bond lengths within one shell, e.g. an octahedral metal center surrounded by 6 oxygen atoms and this shell is predicted to be split in three subshells for wich the bond length differs only 0.05 angstroms; and this model can be fit very well in k-space with the splitted shell, off course keeping the number of fit parameters below the nyquist criterion. Is there in such a case any physical reason not to fit the experimental data with the splitted shell , but with an averaged 6-atom shell with a larger Debye Waller factor? Best regards, Eric Breynaert

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