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

copper 1st shell coordination number
by Zhaomo Tian 02 Jan '13

02 Jan '13

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(no subject)
by Zhaomo Tian 02 Jan '13

02 Jan '13

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Demeter installation (under Ubuntu)
by Denis Testemale 01 Jan '13

01 Jan '13

Dear Bruce and mailing list members, I'd like to report about the installation of the Demeter package under Ubuntu where everything went smoothly but a few glitches... ## Background: Ubuntu 12.10 Quantal, 3.5.0-19-generic with everything up to date as of today (December 18th). Demeter 0.9.14 (pulled from git today). I have Horae package installed and running (from Carlo's repos). I followed specific Ubuntu instructions at https://gist.github.com/3959252 (Dave Hughes' installation guide) ##First, one comment. You need to have the package gnuplot-x11 installed. For some reason, it was not installed in my case (although gnuplot was). This lead to many error messages during the './Build test' loop, and obviously the impossibility to plot anything when running (D)athena/artemis/hephaestus. At that time I did not think to try the change of the plotwith variable (gnuplot -> pgplot) as discussed in a previous ifeffit thread. I since reinstalled Ubuntu and this time installed gnuplot-x11 before Demeter. ##Then, a possible bug. It is reproducible everytime: - I launch Dathena from the command line without specifying the name of the project I want to open - I try to open a project (an old style Athena project) from the GUI (for example located at /home/denis/pathtothefolder/athena.prj) - I get an error message (a pop-up window, the terminal is quiet) saying '/home/denis/athena.prj is not readable', i.e. it looks for my file in my home folder and doesn't take into consideration the path to the file I input in the 'import data' dialog. - if I copy athena.prj from /home/denis/pathtothefolder/ to /home/denis/ then it works. - a workaround is: 'dathena /home/denis/pathtothefolder/athena.prj' In the case of Dartemis, it is a bit different: - if I try to open an old-style Artemis project through the dedicated old style import module (say, /home/denis/pathtothefolder/artemis.apj), there is a message at the bottom of the main Dartemis window saying: '/home/denis/artemis.apj is not an old style fitting project file'. Again it misses the complete path to the file. - if I try to open an old-style Artemis project through the 'open project of data' module, Dartemis crashes saying (in the terminal): Can't open($fh, '/home/denis/artemis.apj'): Aucun fichier ou dossier de ce type at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Files.pm line 89 Actually, the crash may not be a bug as I am trying to open an old Artemis project through the bad channel obviously, but notice that the path to the file it refers to is again wrong. ## I must add that my first installation of Demeter (before I reinstalled Ubuntu) was global (not following the non root specific commands of Dave Hughes' installation guide) and I already had this problem. Let me know if you want me to try different things to track the problem down. Many thanks. Cheers Denis -- Denis Testemale Institut Néel FAME beamline at ESRF +33 476 881 045

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The degeneracy and the coordination number
by Zhaomo Tian 26 Dec '12

26 Dec '12

5 4

Re: [Ifeffit] Novice FEFF user question
by Joshua Kas 21 Dec '12

21 Dec '12

Hi Melissa, You will need to set the FMS radius, which is blank at this point as seen in your screenshot. You should also set the SCF radius which is also blank. I would start with FMS 7.0 and SCF 5.0 and you can make them larger to check convergence. Another thing that is a bit strange in your calculation are the options after the XANES card. I would start by leaving these blank, so that the default energy grid is used. Josh Kas Message: 2 > Date: Fri, 21 Dec 2012 16:56:05 -0500 > From: Melissa Menard <mmenard81(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Novice FEFF user question > Message-ID: > <CA+Rj7Q9UmQ0O0FH210GSoAp+FfRSjtvWK9BjmFshrmkq= > 7foBw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I am new to FEFF and I have a small problem. I'm trying to produce a XANES > spectra of Cu (from the examples). I cannot seem to obtain the pre-edge > region in my result. I have attached a screen shot. Could you tell me how > to calculate the area before E0, i.e. from -50 to 50 eV. > > Thanks > Sincerely > > -- > M Menard, Ph.D. >

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Novice FEFF user question
by Melissa Menard 21 Dec '12

21 Dec '12

I am new to FEFF and I have a small problem. I'm trying to produce a XANES spectra of Cu (from the examples). I cannot seem to obtain the pre-edge region in my result. I have attached a screen shot. Could you tell me how to calculate the area before E0, i.e. from -50 to 50 eV. Thanks Sincerely -- M Menard, Ph.D.

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Per-data set R-factor
by Lyle Gordon 21 Dec '12

21 Dec '12

Dear iffefit users, I am using the latest version of Demeter/Artemis to fit some EXAFS data. I'm running Win 7 64. I found in Horae that when I fit multiple datasets it would output the R-factor for each dataset in the fit. I would really like these values in the newest version. I found on the todo list (https://github.com/bruceravel/demeter/blob/master/todo.org) [ ] per-data set R-factor reporting in log file is turned off. Is there a simple way to turn this "on"? If not I guess I can calculate it by hand from the Re/Im terms of the R space data and fit. To that end, if I have a few datasets it is tedious to export the data/fit files for each sample. Is there an automated way to export this data? Thanks very much, Lyle -- Lyle Gordon Department of Materials Science and Engineering Northwestern University 2220 Campus Drive Cook Hall 2036 Evanston, IL 60208 Tel: (847) 491-3584 Mobile: (847) 400-4071 http://lylegordon.ca

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How to refine the float
by Zhaomo Tian 21 Dec '12

21 Dec '12

2 1

How to refine the float
by Zhaomo Tian 20 Dec '12

20 Dec '12

2 1

Re: [Ifeffit] Demeter installation (under Ubuntu)
by Denis Testemale 19 Dec '12

19 Dec '12

Hello Bruce. There are no special characters only letters, numbers, and underscores. To be sure, I tried by placing the athena projects in ~/temp with the same result. Actually, I played a little bit more, and the behaviour is really strange: - consider the home folder /home/denis (I'll write ~ in the following) and a subfolder ~/A - I place an old style athena project in ~: named athena.prj - start dathena - open ~/athena.prj in dathena. It works. - cp athena.prj A/athena.prj - open ~/A/athena.prj in dathena. It works. - rm ~/athena.prj - reopen ~/A/athena.prj in dathena. It says: "/home/denis/athena.prj is not readable" - cp ~/A/athena.prj ~/. - reopen ~/A/athena.prj in dathena. It works. - and finally, I replace ~/A/athena.prj by another athena project (different), i.e., cp ~/some_random_athena_project ~/A/athena.prj - reopen ~/A/athena.prj in dathena. No error message BUT the project it opens is the old one, not the new random one I replaced the original one with... An additional info: the result of this sequence is the same if I let dathena run between each step ((but close the projects CTRL+W) or if I close (CTRL+Q) dathena at every step. What do you think of my Xmas gift Bruce? :-) Cheers denis Le 18/12/2012 19:54, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > ------------------------------ > > Message: 2 > Date: Tue, 18 Dec 2012 13:47:32 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter installation (under Ubuntu) > Message-ID: <3657129.uFgO795gez(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="us-ascii" > > > Hi Denis, > > As always, thanks a million for your feedback. This kind of thing has > a profoundly positive impact on the quality of the package. I am > really grateful. > > The gnuplot-x11 dependency is a good catch. Thanks. > > Unsurprisingly, I have no problems opening files on my computers. So > we need to figure out what is happening on yours that is not happening > on mine. My first suspicion involves character sets. > >> - if I copy athena.prj from /home/denis/pathtothefolder/ to /home/denis/ >> then it works. > What is "pathtofolder"? Specifically does it contains any accented > characters, ess-zets, eastern characters or anything else involving > unicode? > > B > -- Denis Testemale Institut Néel FAME beamline at ESRF +33 476 881 045

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