March 2012 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 23
by Carmelo Prestipino 31 Mar '12

31 Mar '12

Hi if I can add my two cent...(of EURO) At the ESRF for this kind of studies some work has been done. There is the module XAID of the code XOP wrote by Manuel Sanchez del Rio http://www.esrf.eu/computing/scientific/xop2.1/documentation.html It is written in IDL from scratch. It have normalization and linear combination fit features, it is fully graphically interfaced and in terms of performances is quite impressive. However, the program has a complicate structure that could difficult at the first approach (but Manuel is very kind, don't hesitate to contact him ). Otherwise there is the code PrestoPronto. code.google.com/p/*prestopronto*/ It is mainly a fully graphic python wrapping of ifeffit for sequential analysis. In terms of speed is very similar to Athena but it do automatically the tricks of cleaning memory But it is still a very young code...... It still has not any interface to linear combination analysis. We never tested for more than 1000.. spectra Probably Mark Newton could give you some more suggestions Regards Lello On Sat, Mar 31, 2012 at 7:00 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Ifeffit Digest, Vol 109, Issue 21 (KONG Quingyu) > 2. Re: Ifeffit Digest, Vol 109, Issue 21 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 Mar 2012 18:32:49 +0000 > From: KONG Quingyu <kong(a)synchrotron-soleil.fr> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 21 > Message-ID: > < > 30F62EE734A9EA45A3F211513CB6200324BD1922(a)SUN-DAG1.synchrotron-soleil.fr> > > Content-Type: text/plain; charset="iso-8859-1" > > Thank you for all your helpful suggestions. > > Actually, our beamline has recently installed a fast detector with a > repetation of 20KHz, which could collected data in a time resolution of few > tens of microsecond and could easily produce a large amount of data. We > have already accepted three users for microsecond time resolved studies, > each of them collected millions of spectra. > > Together with the company that provide the detector and our software > engineer we started to write a Python program to treat the data from > November last year, however our engineer quitted recently, this make us to > look for other solutions. > > If Demeter would works well for large amount of data treatment, it would > be great. As I know ID24 at ESRF has also installed the same detector and > would probably have similar demanding for such a program. > > Probably due to the limited memory of my pc, I can only open around 200 > spectra simultanously with Athena. > > Best, > Qingyu Kong > > > Beamline ODE > Soci?t? civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr > > ________________________________________ > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ > ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of > ifeffit-request(a)millenia.cars.aps.anl.gov [ > ifeffit-request(a)millenia.cars.aps.anl.gov] > Sent: Friday, March 30, 2012 3:29 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 109, Issue 21 > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. delr and ss parameterization (Ebrahim Rezaei) > 2. program (KONG Quingyu) > 3. Re: program (Carlo Segre) > 4. Re: program (Matt Newville) > 5. Re: delr and ss parameterization (Bruce Ravel) > 6. Re: program (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 29 Mar 2012 21:57:21 -0700 (PDT) > From: Ebrahim Rezaei <e_rezaei24(a)yahoo.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] delr and ss parameterization > Message-ID: > <1333083441.66190.YahooMailClassic(a)web120501.mail.ne1.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > > I am working with bulk and nano structures of MnO, MnO2 > and Mn2O3. I have two questions regarding how to > parameterize delr and ss in Artemis. > > > It is recommended to > use either delr=alfa*Reff or relate it to unit cell structure. Can anybody > tell > me how to do the second approach? > > > Also is that a good idea to let all ss to float? Or it should > be constrained based on type and distance of atoms? I have seen an example > about ZnO just letting the first two shell?s ss to float and let the rest > to be > the same. I would appreciate it very much if anybody could help me with > this too. > > > Regards, > > > Ebrahim Rezaei > > PhD Candidate, Chem. Eng. Dep., University of Saskatchewan > > Saskatoon, SK, Canada >

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Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 21
by KONG Quingyu 30 Mar '12

30 Mar '12

Thank you for all your helpful suggestions. Actually, our beamline has recently installed a fast detector with a repetation of 20KHz, which could collected data in a time resolution of few tens of microsecond and could easily produce a large amount of data. We have already accepted three users for microsecond time resolved studies, each of them collected millions of spectra. Together with the company that provide the detector and our software engineer we started to write a Python program to treat the data from November last year, however our engineer quitted recently, this make us to look for other solutions. If Demeter would works well for large amount of data treatment, it would be great. As I know ID24 at ESRF has also installed the same detector and would probably have similar demanding for such a program. Probably due to the limited memory of my pc, I can only open around 200 spectra simultanously with Athena. Best, Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Friday, March 30, 2012 3:29 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 109, Issue 21 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. delr and ss parameterization (Ebrahim Rezaei) 2. program (KONG Quingyu) 3. Re: program (Carlo Segre) 4. Re: program (Matt Newville) 5. Re: delr and ss parameterization (Bruce Ravel) 6. Re: program (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 29 Mar 2012 21:57:21 -0700 (PDT) From: Ebrahim Rezaei <e_rezaei24(a)yahoo.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] delr and ss parameterization Message-ID: <1333083441.66190.YahooMailClassic(a)web120501.mail.ne1.yahoo.com> Content-Type: text/plain; charset="utf-8" Hi everyone, I am working with bulk and nano structures of MnO, MnO2 and Mn2O3. I have two questions regarding how to parameterize delr and ss in Artemis. It is recommended to use either delr=alfa*Reff or relate it to unit cell structure. Can anybody tell me how to do the second approach? Also is that a good idea to let all ss to float? Or it should be constrained based on type and distance of atoms? I have seen an example about ZnO just letting the first two shell?s ss to float and let the rest to be the same. I would appreciate it very much if anybody could help me with this too. Regards, Ebrahim Rezaei PhD Candidate, Chem. Eng. Dep., University of Saskatchewan Saskatoon, SK, Canada

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program
by KONG Quingyu 30 Mar '12

30 Mar '12

We recently collected 3000 EXAFS spectra to follow a chemical reaction process, we would like to fit the experimental data with reference spectra using linear combination fitting. Does anyone know there are available or commercial program to normalize the data and make linear combination fitting. We tried to do it with Athena manually, but 3000 spectra take a long time for us and it is not a practical way. Thanks a lot. Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr

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delr and ss parameterization
by Ebrahim Rezaei 30 Mar '12

30 Mar '12

Hi everyone, I am working with bulk and nano structures of MnO, MnO2 and Mn2O3. I have two questions regarding how to parameterize delr and ss in Artemis. It is recommended to use either delr=alfa*Reff or relate it to unit cell structure. Can anybody tell me how to do the second approach? Also is that a good idea to let all ss to float? Or it should be constrained based on type and distance of atoms? I have seen an example about ZnO just letting the first two shell’s ss to float and let the rest to be the same. I would appreciate it very much if anybody could help me with this too. Regards, Ebrahim Rezaei PhD Candidate, Chem. Eng. Dep., University of Saskatchewan Saskatoon, SK, Canada

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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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