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

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 05 Dec '14

05 Dec '14

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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Fwd: Re: Use of feff8 with D-artemis?
by Bruce Ravel 20 Feb '13

20 Feb '13

On Thursday, July 12, 2012 05:31:19 PM you wrote: > > I wonder why the new Artemis (from Demeter) is limited to feff6 or feff7 as > the old ifeffit can deals with feff8 and feff9. > > Is it a wish? When you published data using feff7, the reviewers first note > that you should have used more actual version. I would challenge a reviewer to come up with a reliable study demonstrating that Feff8 or Feff9 provides a statistically significant improvement to EXAFS analysis. Obviously, I am not saying that full multiple scattering, self-consistency, and the various potential improvements in Feff9 are not relevant to XANES calculations or to Feff's treatment of other spectroscopies. What I am saying is that it has not been rigorously demonstrated that those things have an impact on the calculation of the extended EXAFS such that the analysis is improved in a statistically meaningful way. In short, I find that such arguments from reviewers boil down to "Feff8 is 33% better than Feff6 because 8 is 33% bigger than 6!" > Is it planned that D-Artemis will work with feff8 too? > > I am using the other programs of Demeter but still have to stick to the old > Artemis as none of my files can be read by D-Artemis (always error due to > feff8 or feff9 files by importing old project) That said, there is no good reason that artemis should not be able to use Feff8 or 9 if you want to do so. I suppose that laziness is the best explanation for why it doesn't yet. The Atoms portion of Demeter writes Feff8 files. The Atoms portion of Artemis simply has the line of code for using that part of Demeter commented out. That's trivial to fix. Getting Demeter to use Feff8 instead of Feff6 is not a lot of work, but it is also not a trivial amount of work. I will put this at the top of my to do list. Given that I will soon be leaving for conferences in distant places on the globe, I probably won't be able to release a version of Demeter that uses Feff8 effectively until Spetember. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ----------------------------------------- -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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dathena cannot import data
by Huynh Khuong 05 Dec '12

05 Dec '12

Dear Everyone, I am a complete beginner to this field and to this software, so please forgive me if I ask something stupid. I am using Ubuntu 12.10 64 bit. Demeter was built from source following the guidance here: http://bruceravel.github.com/demeter/pods/installation.pod.html Ifeffit was also built from source before the installation of Demeter. I tried to run dathena from a terminal and import a data file download from here: http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/examples/data.html <http://cars9.uchicago.edu/%7Eravel/software/doc/Athena/html/examples/data.h…> Dathena said that the data file is not readable (see the attached screenshot). No output text appeared on the terminal. If I use the old version of Athena installed from the repository of Ubuntu, the data file can be read easily. The data file is also attach. Could you please explain me about this issue ? Thank you very much in advance. Best, Khuong Huynh

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Demeter plotting problem in 64-bit Windows 7
by Leon Clarke 05 Dec '12

05 Dec '12

I've just installed the latest version of Demeter on my laptop running 64-bit Windows 7. While I can get the programs to start and run, e.g. Athena, no plots are generated. I'm actually sat in the Diamond XAS workshop and Fred M is stumped by this issue. Are there any known conflicts with the latest version of Demeter, specifically plotting data, running on 64-bit Windows 7 and any solutions? Many thanks, Leon ----- Dr Leon J. Clarke Lecturer in Environmental Analytical Chemistry Division of Chemistry and Environmental Sciences School of Science and the Environment Faculty of Science and Engineering Manchester Metropolitan University John Dalton East Oxford Road Manchester M1 5GD E-mail: l.clarke(a)mmu.ac.uk<mailto:l.clarke@mmu.ac.uk> WWW: http://www.sste.mmu.ac.uk/ Tel: +44 (0)161 247 1412 "Before acting on this email or opening any attachments you should read the Manchester Metropolitan University email disclaimer available on its website http://www.mmu.ac.uk/emaildisclaimer "

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error function in Athena's peak analysis module
by Linda Lim 03 Dec '12

03 Dec '12

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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Help to run Demeter on Windows XP (So. Muru)
by Andrei Shiryaev 30 Nov '12

30 Nov '12

Dear All, I have a similar problem running Demeter on Windows 7 64 bit. It simply makes nothing. I remember that several years ago there was a problem to run IFEFFIT on XP windows machines which were operating under non-unicode settings (in those cases it was Brazilian (i.e. Portugese) and Russian versions). Bruce had solved the problem using another compilation of Perl, if I am correct. Is is possible that the same "non-unicode" problem persists in Demeter? All the best, A.Shiryaev

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Help to run Demeter on Windows XP
by So. Muru 28 Nov '12

28 Nov '12

Dear all, greetings from Murugesan, recently I downloaded the latest version of Demeter for windows and installed it on my windows xp (32bit) environment. I try to run the programs by shortcuts in the desktop, but the programs didn't run. what was the problem, kindly give your suggestions to run the Demeter package successfully on windows xp environment. with thanks and regards S Murugesan -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr S Murugesan Kalpakkam, Tamil Nadu India Email : muruges(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [Ifeffit] FOLP
by Joshua Kas 27 Nov '12

27 Nov '12

Hi Enyuan, It is very strange that FOLP 1.3 is causing the code to take longer. There really should be almost no difference in timing between different values of FOLP. This has to be a bug. Would you mind sending your input file? As for the CRITERIA card, this effects the filtering of the path expansion. The path expansion should only be used for EXAFS calculations, which is why the CRITERIA card is greyed out for XANES calculations (which use full multiple scattering). If you really want to run XANES with path expansion, you can still do that using the text based input and running the code from the command line. If you don't know how to do this, I can explain. Just let me know what operating system you are using. Cheers, Josh > > Hi Joshua, > > Thank you for your comment. Like you said, I tried FOLP with value from 1 > to 1.3 and it didn't change the calculated spectrum much. It's very > time-consuming when FOLP reached 1.3, taking more than 3 hours to finish > the calculation on my laptop. On using 0.8 for hydrogen, actually I'm going > to calculated a sample with lots of Li in it. Do you suggest using a > similarly small number of FOLP for Li, in an analogy to H? The other thing > I want to ask is the CRITERIA card in Feff9. It seemed that once I asked > the program to calculate XANES, the CRITERIA card in the software cannot be > checked. It can only be checked if I selected EXAFS calculation mode. Is > there any way to solve this? thanks again for all your answers. > > Enyuan > > > On Mon, Nov 26, 2012 at 5:33 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: FOLP card (Joshua Kas) > > 2. Question on Glitch in FEFF for Ru EXAFS measurements > > (Dooshaye Moonshiram) > > 3. Re: Question on Glitch in FEFF for Ru EXAFS measurements > > (Bruce Ravel) > > 4. Re: Question on Glitch in FEFF for Ru EXAFS measurements > > (Bobrik, Michael) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 26 Nov 2012 10:56:19 -0800 > > From: Joshua Kas <joshua.j.kas(a)gmail.com> > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: Re: [Ifeffit] FOLP card > > Message-ID: > > < > > CAHuhYRkW5R6iSLjSc03aNnfVRmX+YWvUiNB4HDF7CDEJLNNSjw(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > 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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Re: [Ifeffit] Ifeffit Digest, Vol 117, Issue 24
by Enyuan Hu 27 Nov '12

27 Nov '12

Hi Joshua, Thank you for your comment. Like you said, I tried FOLP with value from 1 to 1.3 and it didn't change the calculated spectrum much. It's very time-consuming when FOLP reached 1.3, taking more than 3 hours to finish the calculation on my laptop. On using 0.8 for hydrogen, actually I'm going to calculated a sample with lots of Li in it. Do you suggest using a similarly small number of FOLP for Li, in an analogy to H? The other thing I want to ask is the CRITERIA card in Feff9. It seemed that once I asked the program to calculate XANES, the CRITERIA card in the software cannot be checked. It can only be checked if I selected EXAFS calculation mode. Is there any way to solve this? thanks again for all your answers. Enyuan On Mon, Nov 26, 2012 at 5:33 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: FOLP card (Joshua Kas) > 2. Question on Glitch in FEFF for Ru EXAFS measurements > (Dooshaye Moonshiram) > 3. Re: Question on Glitch in FEFF for Ru EXAFS measurements > (Bruce Ravel) > 4. Re: Question on Glitch in FEFF for Ru EXAFS measurements > (Bobrik, Michael) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 26 Nov 2012 10:56:19 -0800 > From: Joshua Kas <joshua.j.kas(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] FOLP card > Message-ID: > < > CAHuhYRkW5R6iSLjSc03aNnfVRmX+YWvUiNB4HDF7CDEJLNNSjw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > 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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Question on Glitch in FEFF for Ru EXAFS measurements
by Dooshaye Moonshiram 27 Nov '12

27 Nov '12

Dear Bruce, I recently collected EXAFS data on the *Tris(bipyridine)ruthenium(II) dichloride Ru 2 compound-photosensitizer in solution form. In order to compare EXAFS data to XRD data, I uploaded the XRD coordinates of this crystal structure from cambridge database in a FEFF calculation page in ARTEMIS. I ran FEFF on the x,y and z coordinates of this standard compound in Artemis and summed all paths to compare with my experimental data(collected in solution form in fluorescence mode)* *I have 2 problems* *1) I found a glitch when running FEFF in ARTEMIS. In order to compare XRD coordinates to EXAFS data, I upload the XRD coordinates in a FEFF calculation page, run FEFF and sum all paths. Now* *a) **f I upload the XRD coordinates in a FEFF calculation page without having the EXAFS artemis file present, I get different fits compared to* *b) if I first upload the EXAFS experimental file and then run FEFF on the XRD cartesian coordinates. It seems that **the sum of all paths from the FEFF calculation page tend to mimic the experimental EXAFS file which has first been uploaded and is not a true presentation of how the FT should be.* * * *-Please let me know if this is unclear and I can send you my EXAFS file as well as the XRD coordinates which I obtained from Cambridge structural databse* * * *2) Another problem which I have with my EXAFS data is that I have a peak at 2.5 Angstrom which does not match XRD coordinates and is not present if I run FEFF on XRD coordinates only(true comparison as I don't add the the experimental file in Artemis). Could this peak be due to the Ru standard somehow? All measurements were done in fluorescence mode (F/Io) at 20 K in cryostat using a germanium detector. I simultaneously collected EXAFS measurements on Ru metal standard between Iref and IT ionization chambers.* * * *Thank you for your help,* *Sincerely* *Best Regards* *Dooshaye Moonshiram*

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