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

Demeter Atoms & Vesta
by Andrew Korinda 22 Mar '12

22 Mar '12

Morning all, I finally decided to try using Demeter and this morning went to use Athena. Opening my data was all fine but importing the cif file into atoms got me in trouble. Upon selecting the file I got a pop-up saying "Choose a record from this CIF file" however there is nothing listed. If I click OK, the program crashes. This is also reproducible if I run stand-alone ATOMS. I have generated the CIF files from VESTA where I modify the crystal structure manually. This hasn't caused an issue in the past but with Demeter, perhaps there is a header I need to add? Attached is the CIF file I'm trying to use along with the error logs. Also I am using Windows 7 and the previous IFEFFIT is still installed. Thanks for the help and continued development, Andy Korinda Notestein Lab Chemical & Biological Engineering Northwestern University

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administrator privileges
by Henning Lichtenberg 21 Mar '12

21 Mar '12

Ladies and Gentlemen, we have been preparing a course about using Athena including some exercises (practical examples) for tomorrow, March 20th. For that course we reserved a computer pool in the computer science department of our university, and they created course accounts for the participants. They also installed the IFEFFIT package on that computer pool. Unfortunately it is not possible to run IFEFFIT on those computers (although it is installed) with a course account. It only works after administrator privileges have been added to the account. I was temporarily given such privileges, but just for troubleshooting. We cannot get those privileges for the course participants. Has anybody out there ever encountered a similar problem? Any idea how this could be fixed? (probably either by modifying the accounts or changing program settings) Thank you very much! Henning Lichtenberg Institute for Chemical Technology and Polymer Chemistry Karlsruhe Institute of Technology, Germany

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Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 17
by Alexander Riskin 21 Mar '12

21 Mar '12

Dear Bradley, I'm no IT expert but if a virtual machine exists composed of 4 CPU's, there should be 4 physical computers involved, or am I wrong and are you working with one of these QUAD-core cpu's? First thing I would check is the athena process in the task manager. right-click on the process line and increase the priority of the process (watch out since this might lead to system instabilities). If this does not help, maybe it is possible to run 4 instances of Athena and assign a separate cpu for every instance. Or maybe run Athena on the 4 separate computers making the VM (if they are available to you anyway...). This would cut your time in 4. Just a few suggestions, I hope they help, Alexander -- Alexander Riskin Universiteit Hasselt IMO - Inorganic and Physical Chemistry Agoralaan – Building D BE-3590 Diepenbeek / Belgium tel. +32.(0)11.26.83.94 fax. +32.(0)11.26.83.23 email:alexander.riskin@uhasselt.be On 21/03/2012 14:44, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Decrease LCF Fitting Computational Time in Athena
by BradleyW Miller 21 Mar '12

21 Mar '12

Hi, I have been given access to a Virtual Machine (VM) with 8 GB of RAM and 4 CPU's with the hopes of decreasing the time required to do LCF fittings. I have large set of environmental samples from different waste streams and/or contaminate sources. Currently I have 14 standards and I wanted to run a LCF model fitting up to 4 standards. This results in 1456 fits if I selected "fit all combinations". This takes about 100 mins. to run 1 samples (I have 60+ and more coming). It appears that Athena is constrained to using at most 25% of the available CPU and the physical memory is limited to 22% . 1) Is there a way I could change Athena's settings to take advantage of this VM's multiple CPU's and larger RAM? 2) Or if Athena can't handle multiple CPU's is there a way to increase the maximum percentage of the CPU being used? It appears that Athena is limited to accessing up to 25% of the CPU's. One CPU of the four appears to be processing a little more data than the other 3 CPU's (when viewed on the Task Manager, Performance tab). When more CPU's were added to the VM, computational time remained similar... if not worse. 3) Similarly the physical memory is limited to 22% of available memory (when viewed on the Task Manager, Performance tab) when Athena is running the LCF models as well. Could Athena's setting be changed to increase the % of RAM available for LCF fitting? 4) Any other suggestions? I spoke with my IT guy who said he believes the software is limiting my hopes of decreasing the computational time. I'd love to call it all contaminated dirt, rent some big equipment like D-9 dozers, big trucks, a couple barges and dump it into the ocean... but we don't have that much $$$ for remediation and my kids eat fish. That's is a joke of course... my kids don't eat fish :-) btw Thanks for your time and for use of the software! Respectfully, Bradley W. Miller, Ph.D. Post Doctoral Fellow Oak Ridge Institute for Science and Education U. S. Environmental Protection Agency National Risk Management Research Laboratory Land Remediation and Pollution Control Division 5995 Center Hill Avenue, Cincinnati, OH 45224-1702 www.tinyurl.com/bwmiller The great tragedy of Science—the slaying of beautiful hypothesis by an ugly fact.— Thomas H. Huxley Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency.

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Rh K edge XANES
by VITYUK, ARTEM 14 Mar '12

14 Mar '12

Dear ifeffit community, I think I have quite fundamental question regarding Rh K edge XANES modeling in feff and I would highly appreciate if somebody could help. I am trying to model K edge XANES spectra of organometallic rhodium complexes using feff. In particular, I am interested if there direct dependence between occupancy of the Rh p level (estimated by feff) and intensity of the main feature in XANES. If I understood it correctly, K edge XANES of transition metal organometallic complex probe not just metal empty p orbitals but empty molecular orbitals created by mixing of ligands orbitals of appropriate symmetry with p orbitals of metal. If it is so, does it mean that when feff calculates occupancy of the metal p level it takes into account those hybridization effects? Thank you so much! Artem Vityuk Ph.D. candidate Department of Chemical Engineering Swearingen Engineering Center University of South Carolina email: vityuk(a)email.sc.edu

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Learning IFEFFIT
by Krishnananda ShAsTri 11 Mar '12

11 Mar '12

Hi, I am a Physics student. I am new to IFEFFIT. I have installed IFEFFIT to windows and Athena was not so difficult to learn. But I am not getting how to add multiple paths in Artemis. I tried by taking one example but experimental and theoretical plots were not well matching. What may be the reason for that and also suggest me if any videos are there to learn.

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running ifeffit under 64-bit windows7
by Sameh Ibrahim Ahmed 10 Mar '12

10 Mar '12

Hi, I have used ARTEMIS to fit the EXAFS of a simple Cu foil with the two diffrent machines, a 32 bit and 64 bit ones, both running widows7, 32 ans 64 bit respectively. The results obtained are slightly different, I have appended the message with these results. the very low value of R-factor produced with the 64bit system is difficult to interpret. the questions are; 1- how to account for these differences? 2- if I to publish something, which measure of the quality should I present? and how can I interpret it? regards Sameh ============================================================ 32bit windows 7 Independent points = 12.172851562 Number of variables = 6.000000000 Chi-square = 53.001967099 Reduced Chi-square = 8.586301900 R-factor = 0.000163791 !!! Measurement uncertainty (k) = 0.000110566 Measurement uncertainty (R) = 0.057163282 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): amp = 0.9907500 +/- 0.0312520 (1.0000) enot = 5.6814210 +/- 0.3815760 (0.0000) delr1 = 0.0016460 +/- 0.0033990 (0.0000) ss1 = 0.0099820 +/- 0.0004090 (0.0030) w1 3rd cumulant = 0.0001710 +/- 0.0000340 (0.0000) p1 4th cumulant = 0.0000240 +/- 0.0000070 (0.0000) ============================================================ 64bit windows 7 Independent points = 12.172851562 Number of variables = 6.000000000 Chi-square = 54.036163164 Reduced Chi-square = 8.753841335 R-factor = 0.309664502E-06 !!! Measurement uncertainty (k) = 0.000097377 Measurement uncertainty (R) = 0.050344538 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): amp = 1.0029100 +/- 0.0296670 (1.0000) enot = 5.7522760 +/- 0.4614510 (0.0000) delr1 = 0.0024980 +/- 0.0040190 (0.0000) ss1 = 0.0101430 +/- 0.0003790 (0.0030) w1 3rd cumulant = 0.0001780 +/- 0.0000410 (0.0000) p1 4th cumulant = 0.0000260 +/- 0.0000070 (0.0000) ============================================================

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the 64-bit problem is already fixed
by Sameh Ibrahim Ahmed 10 Mar '12

10 Mar '12

Hi, Today, when I lunched artemis, it asked to download some update and I leted it updates automatically. Then, I tried running the already saved *.apj files saved before with the 32-bit system and, surprisingly, I have found them running normally and giving the same results as the old ones ... !!! Surely these updates are essential to run ifeffit properly under 64-bit systems. I suggest to integrate these updates in a newer version of ifeffit and make it available online as soon as possible. thanks Sameh Ibrahim Ahmed assistant professor of crystallography Ain-Shams University Egypt current institute XAFS beamline, ELETTRA Trieste, Italy.

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Re: [Ifeffit] how to built ATOM to obtian FEFF by using DFT model?
by winejar8324 10 Mar '12

10 Mar '12

Hi everyone! can u please help me? I was so glad that Prof. J F W Mosselmans gave me advice about EXAFS analysis of complex solution system in last time. Here i have an another question about how to bulit ATOM to obtain FEFF by using DFT model. When getting a reasonable zinc complex model caculated by Density Functional Theory, i wish use it to clarify the experimental EXAFS data. But i don't know how to bulit ATOM file using this model. Except for the coordinates in the DFT output file, i don't know how to get the other structure information including space, cell parameter etc. ********************************* title=name space=? a=? b=? c=? alpha=? beta=? gamma=? ( How to get these data? ) rmax = 8.0 core = Zn1 atom Zn 0 -0.25 -0.125 Zn1 1 (I can get the atom coordinates from the DFT output file) ....... ******************************* Is there any other methods to create the corresponding ATOM file? Thank you very much. winejar 2012-03-09 发件人： Takahide Yamaguchi 发送时间： 2012-03-08 16:00:36 收件人： ifeffit 抄送：主题： [Ifeffit] what is the reasonable arc-tan for edge jump Dear all, I was so glad that Bruce and Zajac gave me advice about MS path treatment in last time. Thank you very much. Now, I am working on analysis of Cu K edge by using EDG_FIT, following previous papers. I am wondering if someone gave me comment about current problem for me. And my question about XANES analysis is "what the reasonable arc-tan is as a back ground of XANES." In previous some papers, Cu K edge were deconvoluted by assuming arc-tan edge jump function. But I couldn't found the reasonable mention for the shape of arc-tan. For example of Cu(II), one paper (1), which has interest in the metalloproteins active site, the arc-tan were positioned around 8992 eV with 5 eV hwhm approximatly. 　 But in another paper (2), which reported about high valence Cu(III), the arc-tan for Cu(II) complex looks having narrow hwhm at higher positons (around at 8984 eV). (1) J. Phys. Chem. B 2000, 104,10814-10819 (2) JACS 2000, 122, 5775-5787 Are there any reason which can explain these difference? I hope any comment and advice. Takahide

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Re: [Ifeffit] inquire for the EXAFS of the mixture of species
by Carmelo Prestipino 09 Mar '12

09 Mar '12

Hi Here an another routine for itfa (PCA_GUI executable). http://code.google.com/p/prestopronto/ You can use athena to create the input file (a file with one energy column and the rest of column are spectra). All the best Carmelo > > Message: 1 > Date: Thu, 08 Mar 2012 17:00:15 +0900 > From: Takahide Yamaguchi <11nm023s(a)mcs.ibaraki.ac.jp> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] what is the reasonable arc-tan for edge jump > Message-ID: <4F58670F.5020600(a)mcs.ibaraki.ac.jp> > Content-Type: text/plain; charset="iso-2022-jp" > Message: 2 > Date: Thu, 8 Mar 2012 08:13:08 +0000 > From: <fred.mosselmans(a)diamond.ac.uk> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] inquire for the EXAFS of the mixture of species > Message-ID: > <CF65047C5B0562499EAFF9FBBC542D6426591B88(a)EXCHMBX01.fed.cclrc.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > > Hi Winejia, > > I think your problem may well be harder than an LC approach as suggest by Darius will solve, as it is possible (probable) that the reaction intermediates are not known structurally so you don't have model spectrum of them. Complex solution equilibrium mixtures are about as tough as it gets for soluble EXAFS problems. The methods that tend to work are Principal component analysis (which is available in sixpack and Athena) > This will probably tell you how many species you have in your reactant spectra, and will also tell you by target transformation if a spectrum of a model you have is one of those species. However to identify the unknowns you may need to use a more advanced approach like iterative transformation factor analysis (ITFA) . there is an itfa package available from the RoBL esrf beamline http://www.esrf.eu/UsersAndScience/Experiments/CRG/BM20/Software/ > This should be able to give you the spectra of the separate solution spectra which then you can analyse with Artemis. > > The key things you need to have is more spectra representing in different ratios of the solution species than the total no of solution species, otherwise your problem is underdetermined, preferably quite a lot more. > > Regards > Fred > > Prof. J F W Mosselmans > Principal Beamline Scientist I18 > Diamond Light Source > Diamond House > Harwell Campus > Didcot > Oxon > OX11 ODE > UK > > > > > > -- > > This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. > > Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. > > Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. > > Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > > > > > >

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