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

PCA component determination
by Santiago José Alejandro Figueroa 23 Jun '12

23 Jun '12

Dear all, Determine the number of components in Principal Component Analysis decomposition is usually a hard work, close to an art. Recently Malinowski discuss some methods in a paper that is proposed a new method (DRMAD): DOI: 10.1002/cem.1182 This last method has in the program developed by Carmelo Prestipino PCA_GUI.py (http://code.google.com/p/prestopronto/) developed with some advices of Marcos Fernandez-Garcia. There are many methods better than use the empirical IND funtion. The better is have a good knowledge of your system by other techniques or by the behavior, this additional information can be of the extreme importance if you have more than 2 components. Best regards, Santiago -------------------------------------------- Dr. Santiago J. A. Figueroa Pesquisador - Laboratório Nacional de Luz Síncrotron (LNLS) Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Rua Giuseppe Máximo Scolfaro, 10000 Caixa Postal 6192 - CEP 13083-970, Campinas(SP), BRASIL Tels.: (sala)19 3517-5063 / (xafs2)19 3512-1246 / (xafs1)1139 / (dxas)1141 Fax: 19 3512-1006 WEB: http://www.lnls.br BLOG: http://www.marevero.blogspot.com/

1 0

Re: [Ifeffit] on Tune and Detune
by Enyuan Hu 22 Jun '12

22 Jun '12

Dear Matthew, Thank you so much for the answer. It's crystal clear :) Enyuan

1 0

on Tune and Detune
by Enyuan Hu 21 Jun '12

21 Jun '12

Dear all, I'm new to the community and I was wondering if I can ask some basic questions here. I heard the beamline scientist mention "tune" and "detune" and I saw in some materials say "detune to get rid of high order harmonics", but what is "harmonics"? and why it's necessary to detune to get rid of high order harmonics? I'd really appreciate it if we can discuss this a little bit. Thanks. Enyuan

2 1

Sixpack, PCA controll, "IND" column
by Joerg Goettlicher 21 Jun '12

21 Jun '12

Hello, does anyone know the meaning of the IND column in the PCA controll field of sixpack (version 0.63)? I did not found a hint in the sixpack documentation. Best regards Joerg

3 3

Re: [Ifeffit] Horae examples with Mac distribution
by Scott Calvin 16 Jun '12

16 Jun '12

On Thursday, June 14, 2012 04:09:30 PM Bruce Ravel wrote: For the old software, look here: http://cars9.uchicago.edu/svn/horae/trunk/examples/ For the new software, look here: https://github.com/bruceravel/demeter/tree/master/examples or simply clone demeter from github. Then you'll get all the source along with the examples. I also keep a mountain of example data (much of which is in all three places) here: https://github.com/bruceravel/XAS-Education/tree/master/Examples Those are all the data used in my various XAS training lectures. Thanks, Bruce! The example data from your lectures is particularly helpful to know about. --Scott Calvin Sarah Lawrence College

1 0

Horae examples with Mac distribution
by Scott Calvin 14 Jun '12

14 Jun '12

Hi all, When I download the universal binary of Ifeffit (1.2.12) and Horae for Mac, it doesn't seem to include the folder of example files--or at least I can't find the files with a search. Are they actually there somewhere? If not, is there a way to download just those files? I've got a copy of them from past distributions, and I've now sent a copy of them to my student, so we're actually set. Still, I thought it worth asking on behalf of other Mac users. --Scott Calvin Sarah Lawrence College

2 1

Another brain teaser
by Anatoly I Frenkel 13 Jun '12

13 Jun '12

Here is another brain teaser in case anyone is bored. The solution was not at all obvious but very simple, as all brain teaser solutions should be. Anatoly

1 0

problem install horae ubuntu 12.04 Precise
by denis.testemale 12 Jun '12

12 Jun '12

Dear members of the list, dear Carlo, I'm currently trying to install horae on a colleague's computer. He recently switched to Linux (ubuntu) so I'm in charge of the installs until he's used to the new OS. We are facing a problem to install horae. The linux and (incomplete) horae install are: ###### ## lsb_release -a LSB Version: core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0-noarch:core-3.1-amd64:core-3.1-noarch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch Distributor ID: Ubuntu Description: Ubuntu 12.04 LTS Release: 12.04 Codename: precise ## dpkg -l | grep horae rc horae 071~svn536-1 interactive graphical processing and analysis of EXAFS data ## dpkg -l | grep pgplot5 ii pgplot5 5.2.2-18 large subroutine library for plotting scientific data ## dpkg -l | grep perl-tk ii perl-tk 1:804.029-1.1ubuntu2 Perl module providing the Tk graphics library ## dpkg -l | grep ifeffit ii ifeffit 2:1.2.11d-8~oneiric0 Interactive XAFS analysis program ###### As you see, we lack the libifeffit-perl library wich is confirmed by the error messages we get when trying to install horae (it's in french, but you'll get the idea): ##### sudo apt-get install horae Lecture des listes de paquets... Fait Construction de l'arbre des dépendances Lecture des informations d'état... Fait Certains paquets ne peuvent être installés. Ceci peut signifier que vous avez demandé l'impossible, ou bien, si vous utilisez la distribution unstable, que certains paquets n'ont pas encore été créés ou ne sont pas sortis d'Incoming. L'information suivante devrait vous aider à résoudre la situation : Les paquets suivants contiennent des dépendances non satisfaites : horae : Dépend: libifeffit-perl mais ne sera pas installé E: Impossible de corriger les problèmes, des paquets défectueux sont en mode « garder en l'état ». sudo apt-get install libifeffit-perl Lecture des listes de paquets... Fait Construction de l'arbre des dépendances Lecture des informations d'état... Fait Certains paquets ne peuvent être installés. Ceci peut signifier que vous avez demandé l'impossible, ou bien, si vous utilisez la distribution unstable, que certains paquets n'ont pas encore été créés ou ne sont pas sortis d'Incoming. L'information suivante devrait vous aider à résoudre la situation : Les paquets suivants contiennent des dépendances non satisfaites : libifeffit-perl : Dépend: perlapi-5.12.4 mais il n'est pas installable E: Impossible de corriger les problèmes, des paquets défectueux sont en mode « garder en l'état ». ##### So perlapi seems to be one problem. Any idea? Thanks for your help. Denis Denis Testemale Institut Néel - Département MCMF 25 avenue des Martyrs BP166 38042 Grenoble, France ph: +33 476 881 045 email: denis.testemale at grenoble.cnrs.fr

2 1

Postdoctoral position at the Synchrotron Catalysis Consortium
by Anatoly I Frenkel 11 Jun '12

11 Jun '12

Physics Department of Yeshiva University in New York City will have an opening for a postdoctoral research associate position, beginning September 2012. The postdoc will develop new experimental methods of investigations of thermal, structural and electronic properties of supported metal clusters. He or she will contribute to the ongoing research in heterogeneous catalysis in Anatoly Frenkel's group and will be stationed at Brookhaven National Laboratory. Required qualifications: expert knowledge of XAFS and its applications to nanomaterials, hands-on experience with vibrational spectroscopies, experience with in situ experiments. The research will be performed under the direction of Prof. Anatoly Frenkel primarily at the Synchrotron Catalysis Consortium at the NSLS but also at other synchrotrons as needed: APS, ESRF, SLS and, eventually, NSLS-II. Applicants should forward cover letter and CV to Prof. Frenkel at anatoly.frenkel(a)yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., 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, Email: anatoly.frenkel(a)yu.edu

1 0

Fitting pre-edge feature in Fe XANES
by shbone＠berkeley.edu 11 Jun '12

11 Jun '12

Dear All: I would like to attempt fits to the pre-edge features of a set of Fe K-edge XANES spectra for Fe(II) samples that show partial oxidation with the goal of determining whether Fe(III) exists in octahedral or tetrahedral coordination (e.g. Wilke et al., American Mineralogist, 2001). Broadly, the fitting procedure involves extracting the pre-edge feature from the edge using a spline function and then deconvoluting this feature using a set of pseudo-voigt functions. I believe that I can use the LCF module in Sixpack to fit the feature using the pseudo-voigt functions, but I'm having trouble extracting the pre-edge feature. I've tried using the spline function in Sixpack (and Athena), but I don't have enough options to modify the spline. It seems to me that I need to use a very rigid spline (for instance, one with only 3 or so knots), and that the options in Sixpack and Athena don't allow for this. I heard the program exafspak would allow me more freedom to control the spline function, but I haven't been able to successfully download the program, let alone use it. So, my questions are the following: (1) Is there a program other than exafspak that I could use to fit a spline to my data where I would have more control over the spline options? I would prefer not to use exafspak since my knowledge of unix is nil. (2) Has anyone used exafspak on a mac? I'm using OS 10.5.8 and I'd appreciate any tips you might be able to give me on installing the program. I followed the directions for installation provided on the website, but the command to install the program (i.e. "add_exafs") wasn't recognized. Thanks for your help! Sharon

3 2