June 2011 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Scripting - Python
by Andrew Korinda 21 Jul '11

21 Jul '11

Thanks for the help. Sorry it took so long to report back but I can only do must of my work on this on weekends. The corrected code worked great and I'm moving forward again. No message was given when the code wasn't working. Andy Korinda On Nov 1, 2010 1:55 PM, "Matt Newville" <newville(a)cars.uchicago.edu> wrote: Hi Andrew, On Mon, Nov 1, 2010 at 12:01 PM, Andrew Korinda <a-korinda(a)northwestern.edu> wrote: > I'm looking t... This is almost certainly due to space in the filename, and is really more of a problem with the fortran than python (or perl for that matter). That is, with a space in the file name, you should explicitly use read_data(file=...., group=...) This should work better:: import Ifeffit iff = Ifeffit.Ifeffit() ret = iff.ifeffit("read_data(file=C:\Program Files\Ifeffit\examples\Ifeffit\data\cu.xmu, group=c)") If it doesn't, let use know. > >From this experience I have some questions: > > ~First does anyone have some debugging tips for ... There should have been a printed message that might have altered you that the file hadn't been read in correctly: *** read_data: no file name given! was that message not given? > ~Secondly, Does anyone have any example Python scripts for Ifeffit > that they would like to shar... I sort of deliberately have left the base Ifeffit python module bare-bones. It would certainly be possible to add more functionality to that, or distribute add-on packages. It sort of depends what people would find desirable. I have many example scripts using Ifeffit + Python, mostly scripts, not documented, reliable code. Of course, there is also sixpack. I had some older GUIs as well. Would it be helpful to add some small examples on a wiki page? > ~Finally, would I be better off coding in Perl and using Demeter? That's a difficult question. The relative merits of Perl v Python are sort of a topic all on their own. For what it's worth, I believe (far) more people have used Python than Perl, but several very notable Ifeffit programs are written in Perl ;). --Matt PS: The next version of Ifeffit will be in python. Progress is slow, and when it will start to look like an EXAFS analysis program is a fair question. It probably shouldn't sway your decision much. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.g...

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Re: [Ifeffit] E0 issues
by Scott Calvin 28 Jun '11

28 Jun '11

Hi again, > > Thanks Scott, > I think it is a mistake done by many beginners. To be confident that > I understood you well: so basically the reproducibility of E0 > between samples while fitting to FEFF files mainly depends on the > quality of my calibration. For reproducibility, yes. > Actually, if there is no clear feature in my edges and they are > different in ‘slopes’, I must have either a calibration foil, or a > known standard, measured at the same time; otherwise there is no > good way to get comparable data? Some beamlines are more stable in energy than others. Sometimes it suffices to measure a standard occasionally between measuring data. If the calibration does not drift, or drifts in a predictable way, then you're OK. But if the calibration jumps around by an eV or two, as is not uncommon, then your data inherits that uncertainty unless you measure a reference material at the same time. > Is that right, or the fitting, considering all spectra’s components > will finally lead to a good fit, even with relatively poor > calibration (I will definitely be more careful in the future; but > asking for a set of samples that were mistakenly measured for me > without a standard). This is a different question. If you are fitting to FEFF, then it doesn't matter if the E0's were defined consistently for each sample, or if the calibration drifted. You will most likely float E0 as a free parameter anyway, so the fitting process will adjust for the differences. You do lose the ability to compare the E0's of your different samples, and you lose the ability to constrain them to be the same, but the rest of the fitting process is fine. --Scott Calvin Sarah Lawrence College P.S. Also note that if ifeffit returns an E0 shift of more than about 10 eV, that's a warning sign. Check if that would correspond to an E0 still on or near the rising portion of the edge (a bit past the white line is still OK). If it's not, then the fit is not a good one. If it is, then it's best to choose a new E0 in Athena (or SixPack) that is closer to to where ifeffit wants it; FEFF loses accuracy when the E0 has to be shifted by that much.

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Re: [Ifeffit] E0 issues
by Scott Calvin 27 Jun '11

27 Jun '11

Hi Hana, On Jun 27, 2011, at 2:04 PM, Hana wrote: > I guess my question is obvious to most of you, but after some > practice and reading, the following is still unclear to me > (hopefully some other beginners will benefit): Normally I have > calibrated my spectra using a calibration foil – so energy shift > was done according to that companion standard. Doing a simple > linear combination fit, I have set all spectra to the same E0 value, > somewhere on the edge, above the first derivative maxima (was it a > good practice?). That is a good practice, in my opinion. If you're going to do a linear combination fit, it doesn't really matter how you choose E0, as long as: 1) The spectra are all aligned on the same energy scale 2) The choice of E0 is in some way consistent By using a calibration foil, you have assured #1, and then by simply making E0 the same for all spectra, you have assured #2. > Recently, I found myself actually confused about E0; since my > samples inherently have a phase difference (which is the base to my > ability to differentiate them), how a certain reference point on the > spectrum can be determined? "Reference point" is indeed the correct term. As such, it is somewhat arbitrary, and just needs to be consistent for all spectra being compared. > What can be done when I do not have the calibration foil (especially > for these heavy elements that do not have specific sharp feature)? Consistency is the only requirement. There are many ways to align consistently. If you've got really noisy reference data for some reason, you could even fit some kind of function to the edge and use that, but for reference data that's not usually necessary. > And further, now that I am starting to work on the structural model; > how actually IFEFFIT determined the energy shift when there is no > specific reference point? If you float E0 when fitting to feff files, the reported value is a shift relative to wherever you initially picked it. Thus if you change the initial choice of E0 by 2 eV upward, the shift ifeffit reports should be 2 eV less. Hope that helps... --Scott Calvin Sarah Lawrence College

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E0 issues
by Hana 27 Jun '11

27 Jun '11

I guess my question is obvious to most of you, but after some practice and reading, the following is still unclear to me (hopefully some other beginners will benefit): Normally I have calibrated my spectra using a calibration foil – so energy shift was done according to that companion standard. Doing a simple linear combination fit, I have set all spectra to the same E0 value, somewhere on the edge, above the first derivative maxima (was it a good practice?). Recently, I found myself actually confused about E0; since my samples inherently have a phase difference (which is the base to my ability to differentiate them), how a certain reference point on the spectrum can be determined? What can be done when I do not have the calibration foil (especially for these heavy elements that do not have specific sharp feature)? And further, now that I am starting to work on the structural model; how actually IFEFFIT determined the energy shift when there is no specific reference point? I would be happy to get a better insight.

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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 24 Jun '11

24 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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