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

Fwd: Icosahedral cluster coordinates
by Scott Calvin 27 Jun '11

27 Jun '11

Hi Zohair, I'm posting this back to the list, because I couldn't solve the problem. I did experiment with your file for a bit; it works fine for the atoms up to 4 angstroms, but ones much past that make feff fail. Maybe someone else can suggest why feff is choking on what appears on inspection to be a valid file. (Note to others on the list: the attached feff.inp file is the one that doesn't work; the pasted one is my original, and does work.) As for atoms being able to work with icosahedral structures, that will probably never be possible. Atoms is designed to work with crystal structures, and icosahedral clusters are not crystals; i.e. they don't have translational symmetry. A separate helper application would have to be written for this kind of cluster. --Scott Calvin Sarah Lawrence College Begin forwarded message: > From: <Zohair.Hussain(a)csiro.au> > Date: June 27, 2011 1:12:06 AM PDT > To: <dr.scott.calvin(a)gmail.com> > Subject: Re: [Ifeffit] Icosahedral cluster coordinates > > Dear Scott, > > I came across an e-mail exchange from 2005 between you and Patrick > Kluth regarding icosahedral clusters and feff files as below. > > I’m trying to fit data collected at the Cu k-edge for Mg65Cu25Gd10 > bulk metallic glass(BMG). It has been reported that BMGs have an > icosahedral structure. A recent paper (attached) gives a > demonstration of that. What I’ve tried to do is to modify the feff > file you made for Patrick to my MgCuGd structure. I attach the > feff.inp file I made for that. > > The problem I’m running into is that when I try and run this > modified feff file through artemis I get an error message (file > attached). I should point out that when I run your feff file for Fe > it runs without any errors. > > I’m wondering if you can either tell me what I’m doing wrong or > guide me to make a feff file from an atoms input file for the MgCuGd > material. > > In the long run, it would be good to know how to make Feff files for > icosahedral structures starting from an atoms input file (I usually > use webatoms for this) as I would be working with various BMG > materials (Al, Ti and Mg based) that should potentially have this > structure. > > I’d be grateful for your help. > > Kind Regards, > > > > Zohair Hussain > Postdoctoral Fellow > > CPSE - CSIRO > Private Bag 33 > Clayton South MDC > Clayton VIC 3169 > Australia > e-mail: zohair.hussain(a)csiro.au > Phone +61 3 9545 7891 > Fax +61 3 9544 1128 > > > > > > [Ifeffit] Icosahedral cluster coordinates > > Scott Calvin SCalvin at slc.edu > Tue Jul 19 19:06:17 CDT 2005 > Previous message: [Ifeffit] Icosahedral cluster coordinates > Next message: [Ifeffit] Icosahedral cluster coordinates > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > Hi Patrick, > > Hopefully this will do it. A disclaimer: I never actually tested this > on an icosahedral material, and I did the coordinates by hand, so I > can't guarantee it. > > --Scott Calvin > Sarah Lawrence College > > > > > > >I am working with metal clusters and would like to do some FEFF > >calculations on icosahedral clusters. Is there anyone out there who > >has a FEFF input file (or equivalently a list of coordinates) for an > >icosahedral cluster (147 atoms is probably sufficient for my > >purpuses). >

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system iXAFS3.0.3.dmg, cant open arthena project
by diya lee 27 Jun '11

27 Jun '11

Hi, I have a Macbook pro, and I have the iXAFS3.0.3.dmg system installed. But the artemis program could not open arthena project. when i choose open file and select the file ( arthena project), there system either does not respond or only show the first data in the entire project. How could I fix this?Thanks

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Align spectra in Athena
by Dave 23 Jun '11

23 Jun '11

Hi list, Doing my first steps in your world, I am trying to model my data. I am following Kelly's helpful review from 2008 and stuck on apparently simple issue: In order to reduce my deltaE0 (now 9.2), following her advise, I am trying to recall the theoretical spectrum from Artemis to Athena; this was produced by filtering and fitting my data according to the first shell, then fixing all parameters to their best fit, except for enot set to zero, making a sum of all paths under these conditions, saving it as a chi(k) and take it to Athena. Here, to my understanding, I suppose to introduce the 'new-made' chi(k) as a standard and align my data accordingly, save it as a chi(k) and take it back to Artemis to complete the fitting. Unfortunately I cannot make it a standard in Athena, since the whole background options are not available when a chi file is called in. Can someone give a hint? Suggest other ways to better choose E0? Best, Dave

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an error message " You have not used any memory yet"
by Mike Zhu 23 Jun '11

23 Jun '11

Hi All, I had been using Athena for couple of months and had not problem. But recently, I cannot load any new data although I am still able to open project files (*.prj) previously created. Then this error message shows up at the bottom of the Athena window. I tried to reinstall Ifeffit and to install different version of Ifeffit but all failed. I saw a message posted couple of years ago on a similar problem in this email list but it seemed no answer for it. My operating system is Window XP Professional 2000 Service Pack 3. Anyone have a clue how to fix it? Thanks. Best, Mengqiang Zhu

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Averaging of spectra for multiple configurations in Artemis
by Srinivas Tulishetti 22 Jun '11

22 Jun '11

Dear All, I am working on MD - EXAFS for ionic solvation system. I was doing MD-EXAFS for multiple configurations. Each configuration gives different spectrum. So would like get average of all spectra for those multiple configurations. Is it possible to do this in Artemis or iFEFFIT. If it is then, please give your valuable suggestions. Thanking you all. Best, Srinivas Tulishetti

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lfms1
by Francisco Garcia 21 Jun '11

21 Jun '11

Dear users, I have a question about the value lfms1 is the SCF card. What difference does it make if lfms1=0 (solid) versus lfms1=1 (molecule) for hydrated metal ion clusters? My understanding from the manual is that if the metal is the absorber and I am working with cluster, then lfms1=1. However, if the cluster is sufficiently large (radius=6 Ang--8 Ang), then should it be treated as a solid or molecule? Also, how crucial are the hydrogen atoms in the scattering process? Can the EXAFS spectra be computed with only the metal ion and oxygen positions or the hydrogen positions must be included as well? Thank you.

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Fwd: problem with horae installation on ubuntu 11.04
by Bruce Ravel 21 Jun '11

21 Jun '11

Samuel, As you can see, I am forwarding this to the mailing list. It seems to me that you do not have pgplot installed. On ubuntu this package is called "pgplot5". Have you installed it? I would have thought that the pgplot package would have been a dependency of the ifeffit package. Carlo: can you shed any light on Samuel's problem? Rgeards, B ---------- Forwarded Message ---------- Subject: problem with horae installation on ubuntu 11.04 Date: Tuesday, June 21, 2011, 08:19:46 am From: Bickel Sämi <bickels(a)student.ethz.ch> To: "bravel(a)anl.gov" <bravel(a)anl.gov> hi this is probably a stupid question but i'm quite stuck here. i need the athena software but it doesen't load. it termines with the error: > bickels@bickels-laptop:/$ athena > /usr/bin/perl: symbol lookup error: /usr/local/lib/perl/5.10.1/auto/Ifeffit/Ifeffit.so: undefined symbol: pgqndt_ > i tried compiling the ifeffit-perl but it did not work. also i don't know if i got another version of perl.. but i installed ifeffit trough synaptic. im a newbie and this is probably no big issue.. thanks and have a nice day samuel bickel ----------------------------------------- -- 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] SS and MS contributions to EXAFS
by Scott Calvin 18 Jun '11

18 Jun '11

Hi Francisco, Following up on Matt's comment, a FEFF calculation with default option assigns sigma2 to be 0, and that probably won't result in relative contributions between SS and MS that look much like what happens in the real material. A better strategy would be to read the calculation into Artemis, as Matt suggests, and use a Debye model for the sigma2 for the paths, trying a few different Debye temperatures to get a sense of how it affects the relative contributions. While the Debye model is not an appropriate model for quantitatively fitting most materials, at least it takes a stab at how sigma2 might depend on R, which will help with understanding how important the MS paths are to chi(k). --Scott Calvin Sarah Lawrence College On Jun 17, 2011, at 7:21 PM, Matt Newville wrote: > Hi Francisco, > > On Fri, Jun 17, 2011 at 7:34 PM, Francisco Garcia > <garcia.ff.000(a)gmail.com> wrote: >> Dear users, >> >> I would like to quantify the single scattering (SS) and multiple >> scattering (MS) contributions to the EXAFS spectra over a range of k >> values. I adopted the following approach and I would like ask >> experienced users if my approach is sound: >> >> (1) Run a regular EXAFS (default NLEG=8); I assume this includes all >> possible scattering paths. Call the chi(k) data chi.dat >> (2) Run another EXAFS but this time I set NLEG=2. I assume this is >> for >> all SS contributions. Call the chi(k) data chi_ss.dat >> (3) To obtain the MS contribution, I subtracted chi_ss.dat from >> chi.dat >> >> If my approach is faulty, can you tell me how to remedy it? >> >> Thank you. > > That approach would work under the assumption that the atomic > coordinates in the feff.inp file fully described the distribution of > atoms in the system. If, on the other hand, the feff.inp had an > idealized structure, then the approach would model the MS > contributions for that structure. For example, a feff.inp file often > assumes no static or thermal disorder in the system. In that case, > the MS contributions would have no disorder terms (eg, sigma^2) > applied to them. > > An equivalent approach that may be somewhat simpler would be to use > Artemis to run the Feff calculation with NLEG=8 (4 is probably good > enough below 6Ang in most structures), read in all the paths, and sum > the paths with NLEG>2. > > --Matt

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SS and MS contributions to EXAFS
by Francisco Garcia 17 Jun '11

17 Jun '11

Dear users, I would like to quantify the single scattering (SS) and multiple scattering (MS) contributions to the EXAFS spectra over a range of k values. I adopted the following approach and I would like ask experienced users if my approach is sound: (1) Run a regular EXAFS (default NLEG=8); I assume this includes all possible scattering paths. Call the chi(k) data chi.dat (2) Run another EXAFS but this time I set NLEG=2. I assume this is for all SS contributions. Call the chi(k) data chi_ss.dat (3) To obtain the MS contribution, I subtracted chi_ss.dat from chi.dat If my approach is faulty, can you tell me how to remedy it? Thank you.

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Temp effect
by Hana 17 Jun '11

17 Jun '11

Dear EXAFS experts, I am quite a beginner, and that's might be an ignorant question but really important to my work, so I would be happy to get a direction: what would be the right way to weigh in the effect of temperature in soils samples, since solutions like Debye models will not fit to my understanding? specifically, I am trying to compare my measurements(collected at 10K) to literature data of these metals adsorbed on iron oxides (collected at room temperature). I would appreciate any advise, Hana

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