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

Re: [Ifeffit] Ifeffit Digest, Vol 117, Issue 13
by Zack Gainsforth 27 Nov '12

27 Nov '12

Kyler, you and Tsu-Chien are terrific! iXAFS is working for me again! Cheers, Zack Gainsforth Space Sciences Laboratory, UC Berkeley 7 Gauss Way Berkeley, CA 94720 510-642-9733 zackg(a)ssl.berkeley.edu On Nov 15, 2012, at 10:00 AM, 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: Launching Athena on Mountain Lion (Mac OS 10.8) (Kyler Carroll) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Nov 2012 09:32:34 -0800 From: Kyler Carroll <kyler.carroll(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8) Message-ID: <CAN+rEib3FNvmTE0x8BPgCBN2TRytRE+1CG2aN6A=mEEWxS6NcA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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Help: some operation using Athena and Artemis
by Bingjie Ouyang 26 Nov '12

26 Nov '12

Hi, I just joined the mailing list recommended by a friend, I hear this is a really good place to communicate and learn. So I'm here, actually I need help for some basic questions on Iffeffit software: 1, In Athena, how to make a fourier transform draft? 2, In Artemis, since I was told that each shell in R-space can be fitted separatly, is it OK to fit each shell in the R-range respectively, and then join up the fitted curve and just ignore the not match part in other R-ranges? And can a shell be comprised of several different paths (like Fe-O and Fe-S)? Thank you. Best wishes, Bingjie -- Bingjie Ouyang School of Earth Sciences and Engineering Nanjing University 22nd Hankou Road, Nanjing, Jiangsu, 210093 P. R. China Email: jessicaoy89(a)gmail.com

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Re: [Ifeffit] FOLP card
by Joshua Kas 26 Nov '12

26 Nov '12

Hi Enyuan, I don't really know a rule of thumb for ionic bond v.s. covalent bond, but by default, the FEFF code will automatically choose reasonable muffin tins in most cases, and most of the time it overlaps them by ~15%, i.e. FOLP 1.15. In many cases, the overlap doesn't change the structure in the XANES a lot until you get far from FOLP 1.0. However, there are some special cases. For example, we have found that using FOLP 0.8 for hydrogen atoms seem's to work reasonably well in the XANES. This is because of the short bond lengths of H. In addition, there are cases where one atom is fairly isolated from the others, i.e., cage like structures, where FEFF can't overlap the potentials, and setting FOLP to something smaller than 1.0 is essential to make the code run. I would start by letting the code choose the muffin tins automatically, then change them and see how the results change. If the changes in the XANES are small, you probably don't have to worry about FOLP. Otherwise, this is probably a limitation of the spherical muffin tin potential. The best thing to do in that case, is to compare the DOS (LDOS) with a calculation from a full potential electronic structure code, i.e., WIEN2K, ABINIT, QUANTUM ESPRESSO, etc. This can give you confidence in the FEFF calculation, or lead you to the best values for FOLP. You could also use the FOLP values to get the best comparison to experiment, but in some cases you may be fitting many-body effects, which can lead you to the wrong conclusions about your system. Cheers, Josh Kas On Mon, Nov 26, 2012 at 7:53 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Re:

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Plot multiple fits in (D)Artemis and statistical errors
by Nilmar Camilo 26 Nov '12

26 Nov '12

Dear Bruce, I am new in the list and really don't know if the points raised below were already discussed. In the (D)Artemis (Demeter version 0.9.13) how may I: - Plot different fits with the experimental data (to visually compare the results) - I don't know if this is a (new) bug of the program but when I try to restore a fit the program closes. In the log file the following line is written: "Can't use an undefined value as a HASH reference at C:/Strawberry/perl/site/lib/Demeter/Fit.pm line 1558." Obs.: I am running Demeter in Windows 7 (Pro). Another problem is related to the statistical errors when constraining the S0^2 parameter to float between two limits. The program doesn't return the error for all others parameters (but just zero as the error value) as you can see below: guess parameters: amp = 0.79284158 # +/- 0.00000000 [0.95] enot = 5.29826510 # +/- 0.00000000 [0] delrIn11 = 0.00235278 # +/- 0.00000000 [0] ssIn11 = 0.00155959 # +/- 0.00000000 [0.00300] delrCe1 = -0.00231455 # +/- 0.00000000 [0] ssCe1 = 0.00192778 # +/- 0.00000000 [0.00300] delrIn11In11 = 0.02070081 # +/- 0.00000000 [0] delrIr1 = -0.00435502 # +/- 0.00000000 [0] ssIr1 = 0.00386517 # +/- 0.00000000 [0.00300] delrIn31 = 0.00648507 # +/- 0.00000000 [0] ssIn31 = 0.00669602 # +/- 0.00000000 [0.00300] delrIn12 = 0.00255704 # +/- 0.00000000 [0] ssIn12 = 0.00305432 # +/- 0.00000000 [0.00300] def parameters: b = 0.80000000 # [min(max(0.8,amp),1.0)] Thanks so much in advance. Nilmar

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Re: [Ifeffit] Ifeffit Digest, Vol 117, Issue 21
by Enyuan Hu 25 Nov '12

25 Nov '12

Hi Joshua, Thank you for your answer. So you're saying that we can simultaneously define FOLP for each potential type in the way you showed, right? Then is there any rule of thumb on what appropriate numbers should be used, like what are for anions and what are for cations, what are for ionic bond and what are for covalent bond? thanks. best, Enyuan On Sun, Nov 25, 2012 at 1:00 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. error function in Athena's peak analysis module (Linda Lim) > 2. Re: error function in Athena's peak analysis module > (Chris Patridge) > 3. Re: FOLP card (Joshua Kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Nov 2012 12:24:08 -0800 > From: Linda Lim <ywllim(a)stanford.edu> > To: Ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] error function in Athena's peak analysis module > Message-ID: > <CALPaxYDOUGa7_NMkLmDS31gnk6MFR9RRp4wda+Ji3= > xRdHW5hQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi every one > > I am trying to do peak fitting on Athena. Whenever I choose the error > function and click "fit" the software crashes, but it works fine when I > choose arctangent. > > Just wondering if anyone encounter the same issue too, and whether I'm > missing something during the fitting process. Thanks! > > Regards > Linda >

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Re: [Ifeffit] FOLP card
by Joshua Kas 25 Nov '12

25 Nov '12

Hi Enyuan, You can define the folp options separately for each unique potential, i.e., FOLP 0 1.0 FOLP 1 0.8 FOLP 2 1.2 Will give you touching muffin tins for the 0 potential (absorber), and an overlap of 0.8 and 1.2 for the atoms with potential types 1 and 2 respectively. Note that the 0 potential will have not necessarily have "touching" muffin tin, since the 2 potential is larger than touching and could overlap the 0 potential. The third number gives the ratio of the muffin tin size to the touching muffin tin size that the cod would use if all FOLP radii were set to 1.0. Cheers, Josh Kas Cheers, Josh Kas On Sat, Nov 24, 2012 at 10:00 AM, <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. FOLP card (Enyuan Hu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Nov 2012 08:55:58 -0500 > From: Enyuan Hu <bearcharge(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] FOLP card > Message-ID: > < > CAJud35MQx-zvbvpPH1zbPitFXaUj9qm8TgoqEWsH9yCnwawRNA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I'm trying to see the impact of using FOLP card on my simulation results in > Feff9. As far as I understand it, FOLP is defining the overlapping of > muffin-tin radii. The first parameter defines the the position where this > card will be used (expressed as potential type), right? so should I do the > simulation for all potentials, that is going from 0 to the last number in > my potential list, or I just do it for some specific positions (potential > types)? thanks. > > Enyuan >

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FOLP card
by Enyuan Hu 24 Nov '12

24 Nov '12

Dear all, I'm trying to see the impact of using FOLP card on my simulation results in Feff9. As far as I understand it, FOLP is defining the overlapping of muffin-tin radii. The first parameter defines the the position where this card will be used (expressed as potential type), right? so should I do the simulation for all potentials, that is going from 0 to the last number in my potential list, or I just do it for some specific positions (potential types)? thanks. Enyuan

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iXAFS on Mountain Lion
by Weng, Tsu-Chien 22 Nov '12

22 Nov '12

Hi, I had problem launching iXAFS on Mountain Lion after the OS upgrade. It seems the path to X11 might be hard wired in the program. Here is my workaround solution by creating a symbolic link to XQuartz. It might be worth sharing the trick. 1. Install XQuartz 2.7.4 from <http://xquartz.macosforge.org/landing/> 2. Launch Terminal.app and issue the following commands: 2.1) cd /Applications/Utilities 2.2) sudo mkdir X11.app 2.3) cd X11.app 2.4) sudo ln -s ../XQuartz.app/Contents 3. Now either double-click on iXAFS.app or command line `open -a ixafs` should work -- Tsu-Chien WENG Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Road, Mail Stop 69 Menlo Park, CA 94025, USA +1-650-926-4107 (office) +1-650-926-4100 (fax)

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(no subject)
by Pooja Gupta 19 Nov '12

19 Nov '12

-- "A Ship is always safe at the shore - but that is NOT what it is built for" *********************************************** Dr. Pooja Gupta Scientific Officer Material research Lab Raja Ramanna Center for Advanced Technology, Indore-452013. (M.P.) INDIA. Ph. No. (O): +91-731-2442123 (M): +91 8435718320 Fax No. (O): +91 7312442140 E-mail ID: pooja(a)rrcat.gov.in

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Calculation of a XANES spectrum
by Wei Li 18 Nov '12

18 Nov '12

Dear colleagues, If I have a structural model with geometry optimised by DFT, how do I obtain a theoretical XANES spectrum based on that model? Second questions is how to calculation the projected density of states (PDOS). Thanks! best regards Wei -- Wei Li Postdoc researcher Environmental Soil Chemistry Group Delaware Environmental Institute University of Delaware, Newark,19713 Tel:631-949-0663 http://ag.udel.edu/soilchem/li.html <http://ag.udel.edu/soilchem/>

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