August 2005 - Ifeffit - millenia.cars.aps.anl.gov

Athena, Artemis, Hephaestus
by Seth Mueller 26 Aug '05

26 Aug '05

Please Help, I just installed, using the windows installer, the latest version of Ifeffit onto my computer (Windows XP). I can run all the programs but not the graphical user interfaces Athena, Artemis, and Hephaestus. When I try to run these programs, I get a DOS with a lot of gibberish that opens and closes in 30 seconds. I have no idea what is going on. Can anyone suggest a fix or workaround? ___________________________ Seth Mueller U.S. Geological Survey Box 25046 MS 973 BLDG 20 Denver Federal Center Denver, CO 80225-0046 phone 303.236.1882 fax 303.236.3200

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RE: [Ifeffit] A basic question about data collection
by Kropf, Arthur Jeremy 25 Aug '05

25 Aug '05

Scott, One often overlooked advantage of scanning in small energy steps is that it is much easier to see if a small interfering absorption edge is contaminating the data. Other than that, I agree with everything Matt wrote. In the end it comes down to what is best for your particular experiment; stepping through a fine energy grid may take prohibitively long, if you must wait for the monochromator to settle for 1 second between data points. Jeremy Kropf Chemical Engineering Division Argonne National Laboratory Argonne, IL 60439 Ph: 630.252.9398 Fx: 630.252.9373 kropf(a)cmt.anl.gov > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Newville, Matthew G. > Sent: Thursday, August 25, 2005 3:34 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] A basic question about data collection > > Hi Scott, > > Yep, collecting with an even energy grid is essentially > k-weighting the collection by k^1. It's not quite that simple > -- see below -- but it's close. Of course, you can also step > evenly in k and increase the count time at each point. A > common approach when usig solid-state fluorescence detectors > and/or dilute samples is to k-weight the collection time by > k, k^2, or k^3, and count for, say, 2sec per point at low-k > and ramp up to 10sec per point at high-k (looking at a random > recent scan). > It does definitely help cut down the total collection time to > get reasonably clean spectra on dilute systems. > > The challenge with using data that's on a fine energy grid is > that the routine converting energy to k has to know to use > all that data and also know *how* to use all that data. > Typically (at least, in ifeffit), data is interpolated from E > to an evenly-spaced k grid with a fairly simple interpolation > scheme. > If the energy data are too finely spaced, some data may > actually get ignored. Collecting out to k=18A^-1 with 0.5 eV > steps might not work at smoothing out the data as well as > you'd hope. > Since k=18 -> E=1234.4 and k=18.05 -> 1241.3, there ~6eV > between adjacent k-points (assuming ifeffit's delta_k = 0.05). > > This is important for QEXAFS (which typically does sample at > a very fine energy grid). I've been told by people doing > QEXAFS that a simple box-car average is good enough for > binnning QEXAFS data. That's what Ifeffit's rebin() function > does. I'd think that a more sophisticated rolling average > (convolution) would be better (and not screw up energy > resolution), but apparantly it's not an issue. > > --Matt > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Re: [Ifeffit] Athena, Artemis, Hephaestus
by Michel Schlegel 25 Aug '05

25 Aug '05

Seth, Some accuracy in any bug repport is always welcome. For example, you may want to give at least the name of the Window installe you used (i.e., Ifeffit 1.2.6). That may help avoid potential misundestranding about "latest") >I just installed, using the windows installer, the latest version of >Ifeffit onto my computer (Windows XP). Did you instal it as an administrator/user? are you using it as an administrator/usor? >I can run all the programs but not >the graphical user interfaces Athena, Artemis, and Hephaestus. What do you mean by "all the programs"? can you run, for instance, ifeffit from the shell? Best regards, Michel Schlegel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/DPC/SCP/LRSI Bat 391 - Piece 205B F91 191 Gif-sur-Yvette Cedex, France Ph: +33 (0)1 69 08 93 84 Fax: +33 (0)1 69 08 54 11

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RE: [Ifeffit] Athena, Artemis, Hephaestus
by Jensen, Mark P. 25 Aug '05

25 Aug '05

Seth, As usual, it depends on the gibberish in the DOS window. You might need to tell us more. However, I experienced a similar problem in the past when there was not enough memory for the programs. On Windows Anthena and Artemis (I don't know about Hephaestus) use a considerable amount of memory, 300+ MB. You might need to close some other programs or increase the amount of virtual memory available. Mark Jensen ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Mueller, Seth H. > Sent: Thursday, August 25, 2005 9:11 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Athena, Artemis, Hephaestus > > Please Help, > > I just installed, using the windows installer, the latest > version of Ifeffit onto my computer (Windows XP). I can run > all the programs but not the graphical user interfaces > Athena, Artemis, and Hephaestus. When I try to run these > programs, I get a DOS with a lot of gibberish that opens and > closes in 30 seconds. I have no idea what is going on. Can > anyone suggest a fix or workaround? > > > ___________________________ > Seth Mueller > U.S. Geological Survey > Box 25046 MS 973 BLDG 20 > Denver Federal Center > Denver, CO 80225-0046 > > phone 303.236.1882 > fax 303.236.3200 > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Fwd: Re: UO2 and U3O8 XANES SPECTRA
by Bruce Ravel 22 Aug '05

22 Aug '05

On Monday 22 August 2005 17:58, you wrote: > Hi: > > Does anybody have, or know where to find, L-edge XANES spectra of UO2 > and U3O8, that can easily be read into Athena? > > I'm asking as there they are not the easiest items to rapidly find. Oh look! Another example of why we need a good reference spectrum data base! Here: http://leonardo.phys.washington.edu/~ravel/misc/UO2_data.zip is a zip file full of UO2 data taken by the folks in my current research group. This dates from before my time on this job, so I cannot personally vouch for the data. But I examined it and it looks good AND it looks like UO2 ;-) According to the header, it is UO2 powder with SiO2 used a dispersant. The column labeled mcs3 is I0, mcs4 is It. An pin diode and scattered radiation was used for the reference, which is in column mcs5. Hydrated uranyl phosphate is the reference material. I included the project file that I made in the course of checking out the data. You'll probably wish to further play around with the data processing -- I spent all of about 3 minutes at it. I see that there is some U3O8 data on our beamline computer, but I'll have to ask the person who measured it before I swipe it and send it to you. I'll look into that. HTH, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu *** My cell phone number has changed. Please ask if you need the new number Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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RE: [Ifeffit] database
by Michel Schlegel 22 Aug '05

22 Aug '05

Le 21:18 19/08/2005, vous avez écrit: >Carlo, Thanks for the offer of help! > >Dave, thanks for the suggestions, I think those are all good. > >In fact, I think none of this is that hard to do, but it will >take some time. For what it's worth, I think the data should be >stored in a 'proper' relational database, if for no other reason >than to make it easier and faster to search. It will also make >many of the 'fancier' features (user comments) easier to >implement. I may be just a nuisance, but wouldn't it be interesting to contact people currently developping mineralogical databases (e.g., from the Mineralogical Society of America) to have some insight on how their database is organized? That may save a lot of time. >At this point, I think the most immediate need is (as Dave >mentioned yesterday) to identify a reasonable format for the >data at both upload time and at download time. For upload, we'd >certainly want a web form where fields could be filled in or >parsed from a file following a 'Standard Data File Format'. I think the simplest way is to separate the "general information" field from the "data field". The general information may be entered as a standard fill-in submission page, and this information would then be entered as commented lines (e;g., startting with "#") at the beginning of the download files (pardon me if you think this is obvious!). Among the information to be added, I suggest a few more technical hints, like: - Synchrotron/beamline/station (or "calculated") - Crystal (e;g., Si(111)) - detection mode - raw spectrum/average of xxx spectra Other questions: - Is it advisable to accept only "raw" data (including glitches), or will some kind of preprocessing be allowed? - Would it be advisable to rank the spectra according to their quality (as for the powder diffraction files)? Best regards, Michel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/DPC/SCP/LRSI Bat 391 - Piece 205B F91 191 Gif-sur-Yvette Cedex, France Ph: +33 (0)1 69 08 93 84 Fax: +33 (0)1 69 08 54 11

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RE: [Ifeffit] Cu oxides spectra
by Barton, David (DG) 22 Aug '05

22 Aug '05

Matt, As you know I am a strong supporter of such a model compound database. I am fairly certain that most people that have collected an XAFS spectra have at some point wanted to compare their data with a model compound or two that they didn't have on hand when they collected their data at the beamline. Not only would such a database help those that need a spectra that they didn't collect, but it would also help those that are attempting to collect model spectra and would like a comparison of data quality with others that have collected spectra on the same compound. > I think there are a few important features for such a database: > - through-the-web uploading and annotating of data, probably > after 'logging on' (as with the FAQ). > - simple visualization, even if just plotting mu(E). > - link to crystallographic info. Say, an atoms.inp. > - easy searching. > - either "user comments" added by others (aka Amazon-style > reviews) or some way to indicate that the data is "good". These are all excellent features to add to the database. I especially like the "user comments"/rating feature, this would be very helpful as the database grows and some spectra are collected on similar compounds. This would help users find the spectra with the highest data quality as determined by the community. Other fields that I believe would be of some value in your current model database would be: - add separate fields for compound name and elemental composition (should make searching easier for elements) - add fields for source of model compound (i.e. purchased from vendor {vendor name, purity, etc} or if synthesized {give journal reference to synthesis procedure}) - add check box if phase purity has been checked by other analytical methods and add a text field where the user could describe what other techniques were used. - add field for which edge was collected (k-edge, L1-edge, etc). - under link to crystallographic info you could add a field for Journal Reference to crystal structure. Hope this helps, Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Matt Newville > Sent: Friday, August 19, 2005 12:04 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Cu oxides spectra > > > Hi Dave, > > > Excellent start to a Model compounds XAFS library. > > Well, actually it's close to a decade old. But it *is* still > only a start. ;) > > > How can I add data to this collection? I have collected > ~50 reference > > spectra and would like to donate them to the world. > > I believe everyone in the XAFS community could benefit by > > sharing of reference spectra with one another and I would like > > to do my part. > > > Do you have a page that I could enter the spectra info and > upload the > > data? Or would it be better to create a spreadsheet with > the spectra > > info and zip up all raw spectra data? I am willing to format it in > > any form that works for you. > > Right now, you can just mail me the spectra and any > information you have on them. I'd prefer them as column data > of energy, xmu, and any other channels you might have (i0, a > reference foil, etc), and in individual files rather than a > spreadsheet. > > I think it's definitely worth looking into re-implementing > this Model Data database. Looking at the code and data I > have, I think this is definitely possible, and it does seem > like it is time to revisit this idea. > > I think there are a few important features for such a database: > - through-the-web uploading and annotaing of data, probably > after 'logging on' (as with the FAQ). > - simple visualization, even if just plotting mu(E). > - link to crystallographic info. Say, an atoms.inp. > - easy searching. > - either "user comments" added by others (aka Amazon-style > reviews) or some way to indicate that the data is "good". > > Does anyone else have thoughts or suggestions for such a > database of model compound data? Is a database like this > worth doing? > > Thanks, > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] Cu oxides spectra
by Barton, David (DG) 19 Aug '05

19 Aug '05

Matt, Excellent start to a Model compounds XAFS library. How can I add data to this collection? I have collected ~50 reference spectra and would like to donate them to the world. I believe everyone in the XAFS community could benefit by sharing of reference spectra with one another and I would like to do my part. Do you have a page that I could enter the spectra info and upload the data? Or would it be better to create a spreadsheet with the spectra info and zip up all raw spectra data? I am willing to format it in any form that works for you. Regards, Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Matt Newville > Sent: Wednesday, August 17, 2005 10:27 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Cu oxides spectra > > > Marco (Scott), > > There's CuO and Cu2O (and azurite) data available: > http://cars9.uchicago.edu/~newville/ModelLib/search.html > > The Cu2O there is from the Lytle database. > > Reading data from the Lytle database is not always easy, > but there is a FAQ entry about how to do this: > > http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=show&file =faq03.004.htp Hope that helps, --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Cu oxides spectra
by marco antoni alsina corvalan 18 Aug '05

18 Aug '05

Hi all, My name is Marco, and I´m currently attempting to identify mixed phases of copper oxides through XANES. Searching for standards I visited the XAFS Database, however I was not able to read the Farrel Lytle database, and I mean I don't fully understand whow to extract the energy and absorption from the data (I also think that there is not a standard along with the data). If anyone knows how to read this Database or better yet, if anyone has measure copper oxides standards I would be very greatful if you would let me use that data for XANES comparisons. Thanks Marco Alsina Estudiante de Magister Departamento de Ingeniería Hidráulica y Ambiental Pontificia Universidad Católica de Chile

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Icosahedral cluster coordinates
by Patrick Kluth 17 Aug '05

17 Aug '05

Hi All, Since this is my first message to the mailing list, I`d like to say thanks very much to Bruce, Matt and everyone else who is involved for this great piece of software. It makes life in the EXAFS world so much easier. 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). Thanks Patrick --------------------------------------------------------------------------------- Dr. Patrick Kluth ARC Australian Postdoctoral Fellow Department of Electronic Materials Engineering Research School of Physical Sciences and Engineering The Australian National University Canberra, ACT 0200 AUSTRALIA Phone: +61 2 6125 0358 Fax: +61 2 6125 0511 Mobile: +61 408 66 31 04 Email: Patrick.Kluth(a)anu.edu.au http://www.rsphysse.anu.edu.au/eme ---------------------------------------------------------------------------------

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