Re: [Ifeffit] Effect of gradual thickness variation in beam
Hi Anatoly, Sorry, I meant to write 1000 um inner diameter. Energies will be V and Fe, 5465 & 7112 eV. Samples are roughly 1 absorption length thick for the metal (V, Fe) and about 2-2.5 absorption lengths for the entire sample. Bruce, I may just flip over the sample holder and have the sample tubes in plane with the storage ring to take advantage of the greater horizontal spread, rather than focusing on the vertical. Cutting the vertical slits down to 100-300 um while keeping the horizontal around 500 um ought to get me the most beam at the least variation in mu(E), especially if I go with 1500 um ID tubes. The samples are nice and concentrated so I can afford to give up a lot of photon flux. Bar-napkin calculations tell me with a 1500 um ID tube and 200 um V 750 um H slits I'll lose an acceptable amount of photon flux and have a <1% thickness variation. I'm fairly confident I've made pressed pellets with as much or more variation from one spot to another, without noticeable mu(E) changes from spot to spot, in the vicinity of this energy range. I'll go ahead and take your advice, and amend my setup procedure with some measurements of Io intensity and mu(E) reproducibility as a function of slit width. While a bit of a bother, it's still worth it to keep our sample prep simple and inexpensive. Thanks, Jason On Thu, Jan 28, 2016 at 9:12 AM, Bruce Ravel wrote: > On 01/27/2016 07:05 PM, Jason Gaudet wrote: > >> I'm planning on some transmission-mode XAS with smaller than usual >> sample tubes. I'm realizing I might be in danger of creating excessive >> non-uniformity in my samples by having the beam size on the same order >> of magnitude as the sample tube radius. >> >> For example, let's say I want to measure liquid in a sample tube with a >> 1000 micron outer diameter, with a beam 500 microns wide and centered on >> the sample tube. If the tube is orthogonal to the ring plane, the entire >> vertical portion of the beam will pass through the same length of >> liquid. But in the horizontal plane, the center of the beam will pass >> through 1000 microns of sample while the edges of the beam will pass >> through 866 microns of sample, due to the curvature of the sample cell >> across the horizontal plane. >> >> Most of what I know about the statistics of thickness effects are about >> leakage and pinholes - nonlinearity caused by a few spots having very >> low or negligible sample thickness. But I don't know how significant a >> "mild" thickness distribution might be. If this sort of thickness >> distribution is going to be an issue it would be great to know that >> beforehand and either go with larger samples, smaller beam size, or more >> creative orientation. >> > > > Jason, > > There may be some distortion to the data due to the varying thickness. > On the plus side, liquids tend to be very homogeneous. > > Probably the best solution to this situation, if it's available at the > beamline, is to focus the beam in the vertical, for example, using a > flat mirror on a bender. Focusing to a spot would also address the > thickness situation, but you need to be mindful that the intense beam > could generate radicals from the liquid, causing sample damage. > > If the sample is sufficiently concentrated, then you could simply slit > the beam down to 100 or 200 microns and still have enough for a > transmission measurement. In fact, that would be the way to decide if > you are seeing a big problem from the shape of the tube. Compare the > mu(E) with the slits at 500 to mu(E) with the slits at 100 (carefully > aligning the sample both times, of course). If they are the same, > then, then you're golden. > > B > > > -- > Bruce Ravel bra...@bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage:http://bruceravel.github.io/home/ > Software:https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] Effect of gradual thickness variation in beam
Sample cell Hi all, I'm planning on some transmission-mode XAS with smaller than usual sample tubes. I'm realizing I might be in danger of creating excessive non-uniformity in my samples by having the beam size on the same order of magnitude as the sample tube radius. For example, let's say I want to measure liquid in a sample tube with a 1000 micron outer diameter, with a beam 500 microns wide and centered on the sample tube. If the tube is orthogonal to the ring plane, the entire vertical portion of the beam will pass through the same length of liquid. But in the horizontal plane, the center of the beam will pass through 1000 microns of sample while the edges of the beam will pass through 866 microns of sample, due to the curvature of the sample cell across the horizontal plane. Most of what I know about the statistics of thickness effects are about leakage and pinholes - nonlinearity caused by a few spots having very low or negligible sample thickness. But I don't know how significant a "mild" thickness distribution might be. If this sort of thickness distribution is going to be an issue it would be great to know that beforehand and either go with larger samples, smaller beam size, or more creative orientation. Thanks, Jason ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Data being overwritten in Artemis history window
Some of us are blessed with Fourier eyes, others with QFS memory. :) Honestly, I remembered because the event gave me an aversion to ever using QFS in a large Artemis project, and when I saw a similar issue on the list I recalled why I avoid QFS. I think in the changelog you mentioned whatever you did to fix my problem had some effect on how the fit history was saved, breaking compatibility with earlier versions. It seems (although you likely know much better) that there's some quirk about how QFS path data is saved which can (perhaps still) generate errors that are different and not as well-handled as atoms-derived path data. On Mon, Mar 9, 2015 at 2:55 PM, Bruce Ravel wrote: > > Wow! Jason, that either impressive or really creepy! > > I concur that those seem really similar. And I don't see any evidence in > my change logs that I ever actually addressed that complaint. Apparently > patience is a virtue. :) > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Data being overwritten in Artemis history window
Ian, your post gave me a bit of deja vu. Bruce, that sounds very similar to a bug report I gave you (back when Demeter was in alpha?) on Nov 3 2011. You might want to check your personal Email, or I could forward a copy to the group. Even though it's many versions ago this might be a different facet of the same bug. Relevant text: "Take any of my "Ref" samples from the files I gave you and start a new file. (Alternatively, use any data you have.) Make a quick FS fit and let Artemis fill in the Path variables. (Although I see this on all types of fits, and when I write my own variables.) Make one fit with a "bad guess" for one parameter, like N*so2=1 for my FCC Pd, and for the next fit, make a proper guess of 12. (This is only to deliberately make fits with very different results; this may also work by varying the window, etc.) Copy the log for each result and set aside for a moment. Now, go to the GDS window and hit "Discard All." Go back to the History tabs and look at the fit parameters again. You should see the report from the last fit is unchanged, and the statistical parameters for the first fit are the same, but the guess parameters and everything below for the first fit are now overwritten by the values from the last fit." -Jason On Mon, Mar 9, 2015 at 9:18 AM, Bruce Ravel wrote: > On 03/09/2015 04:17 AM, Godfrey, Ian wrote: > >> >> In the history window some, but not all, data from previous fits seems >> to get overwritten when running a new fit. Specifically I've noticed >> this happening with the information in the "Data set" section. To >> reproduce run a QFS fit with some R-space fitting windows (say 2-4); at >> this point the log will be displayed correctly in the history window. >> Now change the R window (say 1.5-3.5) and run the fit again. When you go >> to the history window the R window information will be displayed >> correctly for the most recent fit but, for the previous fit it will have >> been overwritten by the newer fit. Some of the other info, such as >> R-factor by k-weight seems to get overwritten too. >> >> >> A video of this behaviour can be found here: >> https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state= >> pickup_info&id=29d3e5c2 password: >> 54c8545f >> >> >> System info: Win 8.1 Enterprise x64 running Demeter 0.9.22 pre release >> x64; log attached. >> >> > > Ian, > > First off, I really like your way of making a bug report. Your video > makes the problem completely clear. (I also rather like your > background image.) While all my worst days begin with email that > starts "Sorry ... another bug report!", an unambiguous explanation > makes me very happy. > > As for the problem you are reporting -- yikes! That's really > troubling. I'll look into it. > > Cheers, > B > > > -- > Bruce Ravel bra...@bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage:http://bruceravel.github.io/home/ > Software:https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Regarding a fit for Fe(OTf)2
So I did in fact run into an actual chemist with actual experience on this material not ten minutes ago, and she explained the structure is Fe hydride cations and triflate anions; without the water there is no structure. You can presumably replace water with ACN or something similar and get the same general structure, but if you took iron (II) triflate hexahydrate and attempted to remove water without substitution, you would've probably made iron nanoparticles or some other material. So it comes back to the question of what your material really is ... -Jason On Wed, Dec 3, 2014 at 2:39 PM, Jason Gaudet wrote: > Hi Pushkar, > > Do you have a reliable source that tells you what Fe-O and Fe-S bond > distances and coordination your iron triflate should have? > > I'm not familiar with iron triflate but I was under the impression Fe was > coordinated to the sulfonate through an oxygen? And if so, even if your > sample didn't absorb water, you're trying to measure a S second-shell on > the other side of an octahedral O shell? And apparently you're correctly > fitting that O shell? Am I visualizing the structure correctly? > > If your concentration of Fe was very low, or your setup was otherwise less > than ideal (which, for catalyst studies, is pretty common), I would not be > surprised if your data quality isn't sufficient to distinguish S scatterers > on the other side of six O scatterers from your noise level. > > But without knowing the structure, or your sample setup, or your spectra, > all I can really do is imagine these things ... > > (And yes, it is hygroscopic.) > > -Jason > > > On Tue, Dec 2, 2014 at 8:22 PM, pushkar shejwalkar < > pshejwalkar2...@gmail.com> wrote: > >> Dear All, >> I am experiencing problem during my fit for Fe(OTf)2 >> anhydrous. The problem is as follows. >> I collected the data and used a model to fit. The fitting values and >> other technical information is as below. The basic problem is Fe(OTf)2 in >> anhydrous condition is probably not cyrstalline because of which there are >> no crystal data available. Although .cif file is available for hexahydrate >> and tetra acetonitrile. But obviously it is not directly useful as I am >> looking for Fe(OTf)2 only. I used hexahydrate for fitting, and the fit >> information is given. Is this fit acceptable? >> >> *Now two questions* >> 1) Why do I not see any scattering or peak for Fe-S. I expected S to be a >> strong scatterer and would show a peak. Under given circumstances it looks >> like Fe is all surrounded by water and no triflate is present near Fe at >> all. Is this assumption even make sense (when the bottle said anhydrous) >> The bottle was not kept under inert condition (and its my fault), but does >> it mean Fe(OTf)2 is so hygroscopic and that it can actually form such >> hexahydrate to the full extent? >> OR there is some inherent problem with my fitting and collection itself. >> I used RBKG=1.0 >> >> 2) Is anybody working on Fe(OTf)2 and had such or any other problem >> indicating that Fe(OTf)2 by itself is a bad choice of precursor because of >> its reactivity. Also any comments on purification method etc. does anybody >> know if crystal structure is available for Fe(OTf)2 anhydrous? I could not >> find it on the quick search or on CCDC. Any other site where I can get >> crystal data and .cif information? >> >> Thank you very much for all the help, I hope the question is asked >> appropriately and all the other information is provided, however, if >> anybody needs any other information please let me know. >> Thank you in an anticipation >> Best >> Pushkar >> >> >> Independent points : 16.125 >> Number of variables : 4 >> Chi-square : 7324.9401796 >> Reduced chi-square : 604.118 >> >> R-factor: 0.0195782 >> >> Measurement uncertainty (k) : 0.0001264 >> Measurement uncertainty (R) : 0.0004142 >> Number of data sets : 1 >> >> guess parameters: >> >> SO = 1.06525455# +/- 0.05504541 [1.0] >> delE = -2.32587026# +/- 0.59606221 [-2.77870] >> delR = 0.00911122# +/- 0.00503027 [-0.02322] >> ss = 0.00706809# +/- 0.00071967 [0.00300] >> >> Correlations between variables: >> >> delr & dele --> 0.9154 >> ss & so --> 0.9023 >> All other correlations below 0.4 >> &
Re: [Ifeffit] Regarding a fit for Fe(OTf)2
Hi Pushkar, Do you have a reliable source that tells you what Fe-O and Fe-S bond distances and coordination your iron triflate should have? I'm not familiar with iron triflate but I was under the impression Fe was coordinated to the sulfonate through an oxygen? And if so, even if your sample didn't absorb water, you're trying to measure a S second-shell on the other side of an octahedral O shell? And apparently you're correctly fitting that O shell? Am I visualizing the structure correctly? If your concentration of Fe was very low, or your setup was otherwise less than ideal (which, for catalyst studies, is pretty common), I would not be surprised if your data quality isn't sufficient to distinguish S scatterers on the other side of six O scatterers from your noise level. But without knowing the structure, or your sample setup, or your spectra, all I can really do is imagine these things ... (And yes, it is hygroscopic.) -Jason On Tue, Dec 2, 2014 at 8:22 PM, pushkar shejwalkar < pshejwalkar2...@gmail.com> wrote: > Dear All, > I am experiencing problem during my fit for Fe(OTf)2 > anhydrous. The problem is as follows. > I collected the data and used a model to fit. The fitting values and other > technical information is as below. The basic problem is Fe(OTf)2 in > anhydrous condition is probably not cyrstalline because of which there are > no crystal data available. Although .cif file is available for hexahydrate > and tetra acetonitrile. But obviously it is not directly useful as I am > looking for Fe(OTf)2 only. I used hexahydrate for fitting, and the fit > information is given. Is this fit acceptable? > > *Now two questions* > 1) Why do I not see any scattering or peak for Fe-S. I expected S to be a > strong scatterer and would show a peak. Under given circumstances it looks > like Fe is all surrounded by water and no triflate is present near Fe at > all. Is this assumption even make sense (when the bottle said anhydrous) > The bottle was not kept under inert condition (and its my fault), but does > it mean Fe(OTf)2 is so hygroscopic and that it can actually form such > hexahydrate to the full extent? > OR there is some inherent problem with my fitting and collection itself. I > used RBKG=1.0 > > 2) Is anybody working on Fe(OTf)2 and had such or any other problem > indicating that Fe(OTf)2 by itself is a bad choice of precursor because of > its reactivity. Also any comments on purification method etc. does anybody > know if crystal structure is available for Fe(OTf)2 anhydrous? I could not > find it on the quick search or on CCDC. Any other site where I can get > crystal data and .cif information? > > Thank you very much for all the help, I hope the question is asked > appropriately and all the other information is provided, however, if > anybody needs any other information please let me know. > Thank you in an anticipation > Best > Pushkar > > > Independent points : 16.125 > Number of variables : 4 > Chi-square : 7324.9401796 > Reduced chi-square : 604.118 > > R-factor: 0.0195782 > > Measurement uncertainty (k) : 0.0001264 > Measurement uncertainty (R) : 0.0004142 > Number of data sets : 1 > > guess parameters: > > SO = 1.06525455# +/- 0.05504541 [1.0] > delE = -2.32587026# +/- 0.59606221 [-2.77870] > delR = 0.00911122# +/- 0.00503027 [-0.02322] > ss = 0.00706809# +/- 0.00071967 [0.00300] > > Correlations between variables: > > delr & dele --> 0.9154 > ss & so --> 0.9023 > All other correlations below 0.4 > > nameN S02 sigma^2 e0 delr Reff R > = > O1.1 6.000 1.065 0.00707 -2.326 0.00911 2.09150 2.10061 > > > -- > Best Regards, > Pushkar Shejwalkar. > Post-doctoral -Researcher,JSPS Fellow > Hokkaido University, > Sapporo, > Japan > [image: Inline image 3] > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Can the degeneracy (N) in Artemis be a variable?
I assume you mean you "can't assign a [variable] to N." It's a quirk of FEFF that the value of N for a path must be a number (perhaps even an integer?) but amplitude may be any number or a variable. For that reason it's typical (or at least common practice in my experience) to leave N as 1 and define the amplitude as some function of So2, degeneracy, percent of that phase, or whatever else is appropriate for your sample. -Jason On Sat, Jul 26, 2014 at 12:56 PM, Peng Liu wrote: > Hi all, > > When I model a standard, I know the degeneracy through the other data. But > for spectra of unknown material, I would like to set degeneracy as a > variable like the amplitude, deltE0, e.g.. However, I can assign a letter > to N and define it. Do you have any idea how I should do it? > > Thanks for your reply, > > Peng > > -- > Ph.D. Candidate > Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 > University of WaterlooPh: 519-888-4567 ext. 37232 > 200 University Avenue West > Waterloo, Ontario N2L 3G1Fax:519-746-3882 > p26...@uwaterloo.ca > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] LCF
It depends how you want to set up your guess-def-set parameters. For argument I'll describe a system of BCC Mo metal and MoO3, where you want to determine what fraction of Mo is in each. My usual method is just to set each path as N=1, SO2=amp_O for Mo-O, and N=1, SO2=amp_Mo for Mo-Mo. Then, in guess-def-set, I'd GUESS N_Mo = 8 N_O = 6 SET (SO2 as determined by my standards) so2=0.87 and DEFINE my amplitudes amp_Mo = N_Mo*so2 amp_O = N_O*so2 (And of course you want all the other parameters as well, I'm just showing the amplitude ones.) Then, once I get my N_Mo and N_O I can scale these to my expected coordination numbers and see if I get reasonable contributions for each. (Is N_Mo/8 + N_O/6 = 1?) If I had a really good reason to believe all Mo metal in my sample had an average Mo-Mo coordination of exactly 8 and all Mo oxide had an average Mo-O coordination of exactly 6, I could define things another way. SET N_Mo = 8 N_O = 6 so2=0.87 DEFINE amp_Mo = N_Mo*so2*Frac_metal amp_O = N_O*so2*(1-Frac_metal) GUESS Frac_metal=0.5 And that constrains all the amplitude parameters so the only result is what atomic fraction of Mo is present in the metal phase. Makes sense? -Jason On Thu, Nov 7, 2013 at 2:05 PM, KONG Qingyu < qingyu.k...@synchrotron-soleil.fr> wrote: > Hello Jason, > > Thanks a lot for your reply. > > What I can get from Artemis is the fitted parameters (amp, enot, ss^2, > delr) of each path, Mo-O, Mo-Mo, how can one get the percentage of Mo, x > from Li2MoO3 and 100-x from MoO3, from the fitted information. > > Best regards, > > > Qingyu > > Beamline ODE > Société civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: k...@synchrotron-soleil.fr > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] linear combination fitting
Hi Qingyu, Each Mo absorber contributes to the spectrum equally, so if you think you have a good analysis that indicates x% of Mo scatterers are most similar to Li2MoO3 and 100-x% are most similar to MoO3, those are simply atomic percentages. All you have to do is convert the atomic% to mass% using the formula weight of your components. -Jason On Wed, Nov 6, 2013 at 2:57 PM, KONG Qingyu < qingyu.k...@synchrotron-soleil.fr> wrote: > Hello, > > We measured EXAFS of a mixed sample of Li2MoO3 and MO3, with Artemis we > fitted the data with two FEFF calculations using the crystal structures of > Li2MoO3 and MO3, the fitting results are quite good. We would like to know > the weight of Li2MoO3 and MO3 in the sample, how can we get this value from > Artemis? > > Thanks a lot in advance. > > > Qingyu Kong > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Peak assignment and ionization potential with FEFF
Hi Ross, The impression I get from this question (and it might be wrong) is that you're very new to XAS and you're asking a question about a particular tool for x-ray absorption spectroscopy prior to understanding what an x-ray absorption spectrum actually is. If that's the case, this mailing list might not be very helpful to you right now, as there are many other resources for learning the basics of XAS. -Jason On Fri, Sep 13, 2013 at 3:38 PM, Ross Devol wrote: > Just to clarify, I'm working with XANES spectroscopy. > > Thanks > Ross > > On 09/13/13, Ross Devol wrote: > > Hi everyone, > > > > Does anyone know whether FEFF can be used to assign peaks? In other > words, is there a way to tell which peaks in a calcite O K-edge spectrum > are due to CO bonds and which to CaO bonds? > > Also, does FEFF calculate the ionization potential and if so, where does > it output this? > > > > Thanks! > > > > Ross DeVol > > University of Madison-Wisconsin > > ___ > > Ifeffit mailing list > > Ifeffit@millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Disable duplicate data group check
Hi all, Not a bug this time, but a feature that occasionally frustrates me. Artemis does a sanity check prior to fitting, and if it detects a project has two instances of the same Athena data group, it will refuse to fit the new data. IME this is not a particularly helpful warning, and a major hassle if I'm trying a couple different treatments of the same data to see how the FEFF fit is affected. (The message is "This data came from the the same source as another data group. You seem to be trying to increase your number of independent points by fitting the same data more than once in a multiple data set fit." But of course I'm not doing this; only one dupe is being fitted at a time.) I don't see any option in the Artemis preferences to disable this warning, which means I have to spend effort deleting and loading data sets, and keeping a "dummy" data set I don't really care about to collect all my paths in. Is the possibility of extremely novice users trying to fit multiple instances of the same data such a serious threat that this function needs to exist? Is there any possibility of disabling this check, or giving an option to disable it in the Preferences? It would save me from the occasional headache ... Thanks, Jason ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] plotting
This list of alternatives is pretty near exhaustive: http://alternativeto.net/software/originlab/ Although I personally use Origin. On Tue, Mar 26, 2013 at 5:07 PM, Scott Calvin wrote: > Hi Eva, > > Personally, I'm pretty happy with Pro Fit. It's a commercial product (like > Origin) but is much cheaper. It's also got the stupidest name imaginable, > since Google will assume you misspelled "profit." With that in mind the > website is http://www.quansoft.com . If you're willing to spend more, > Igor Pro is a good product. > > --Scott Calvin > Sarah Lawrence College > > P.S. Disclosure: I have no financial relationship with either software > producer. > > On Mar 26, 2013, at 4:50 PM, Eva Vanamee wrote: > > > Thanks everyone for the helpful comments! I'll go with exporting to > Origin. > > A final question. I am now a Mac user, is there a good alternative to > Origin? > > > > Best, > > > > - Eva > > > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] generating high res figures
And to do this, use the Artemis Plot dialog box to generate the chart you want (e.g. the data and fit in magnitude R-space), click the "Save Next Plot to File" button at the very bottom of the dialog box, and click the correct plot button at the top (e.g. R). This lets you save the plot as an ASCII file. -Jason On Tue, Mar 26, 2013 at 1:25 PM, Scott Calvin wrote: > Hi Eva, > > Demeter is not intended to be used to produce publication-quality figures. > It's best to export the data, fits, etc., and then use a proper graphing > program to generate figures. Even a spreadsheet will do in a pinch, > although most of us use dedicated scientific graphing software. > > --Scott Calvin > Sarah Lawrence College > > On Mar 26, 2013, at 1:13 PM, Eva Vanamee wrote: > > > Hi, > > > > I'm in the happy stages of making figures. > > I'd like to know how to change figure legends, make high resolution > figures from a fit, etc. > > > > For instance: > > I saved the session file. Can I go back to a particular fit to make a > figure or do I need to rerun it? > > Can I change the figure legends? I used sample 1 and I want to give it a > different name > > Can I use special characters (e.g. Greek letters)? > > Can I adjust the resolution for different formats (talk vs. publication)? > > > > I am running Demeter 0.9.9.9 under XP. > > > > Thanks in advance for the help! > > > > - Eva > > > > > > ___ > > Ifeffit mailing list > > Ifeffit@millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Different R-factor values
Perhaps next time I'll notice the attachment ... I don't see that "r factor for k-weight=..." in my old projects; I'm not sure if I just never used that version? I checked some Artemis 0.8.006 logfiles from 2009 and per-k-weight R-factors aren't in there, so that's a little weird. I'm still pretty sure, as you say, the overall R-factor is the statistically meaningful one. -Jason On Fri, Jan 25, 2013 at 11:01 AM, Jason Gaudet wrote: > Hi Chris, > > Might be helpful also to link to the archived thread you're talking about. > > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2006-June/007048.html > > Bruce might have to correct me on this, but if I remember right there were > individual-data-set R-factor and chi-square calculations at some point, > which come not from IFEFFIT but from Bruce's own post-fit calculations, and > these eventually were found to be pretty buggy and were dropped. > > I don't understand what "the average over the k weights" R factor is; > analyzing the same data set with multiple k weights (which is pretty > typical) still means a single fit result and a single statistical output in > IFEFFIT, as far back as I can remember, anyhow. The discussion about > multiple R-factors is for when you're simultaneously fitting multiple data > sets (i.e. trying to fit a couple different data sets to some shared or > partially shared set of guess variables). > > I think the overall residuals and chi-square are the more statistically > meaningful values, as they are actually calculated by the same algorithm > used to determine the guess variables - they're the quantities IFEFFIT is > attempting to reduce. I don't believe I've reported the per-data-set > residuals in my final results, as I only treated it as an internal check > for myself. (It would be nice to have again, though...) > > -Jason > > On Thu, Jan 24, 2013 at 10:12 AM, Christopher Patridge < > patri...@buffalo.edu> wrote: > >> I am reviewing some older analysis projects from artemis and just wanted >> to know which R-factor more accurately describes the misfit? I suspect the >> average over the k weights values since this was adopted in Demeter? >> >> Thanks, >> >> Chris Patridge >> >> -- >> >> Christopher J. Patridge, PhD >> NRC Post Doctoral Research Associate >> Naval Research Laboratory >> Washington, DC 20375 >> Cell: 315-529-0501 >> >> >> ___ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Different R-factor values
Hi Chris, Might be helpful also to link to the archived thread you're talking about. http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2006-June/007048.html Bruce might have to correct me on this, but if I remember right there were individual-data-set R-factor and chi-square calculations at some point, which come not from IFEFFIT but from Bruce's own post-fit calculations, and these eventually were found to be pretty buggy and were dropped. I don't understand what "the average over the k weights" R factor is; analyzing the same data set with multiple k weights (which is pretty typical) still means a single fit result and a single statistical output in IFEFFIT, as far back as I can remember, anyhow. The discussion about multiple R-factors is for when you're simultaneously fitting multiple data sets (i.e. trying to fit a couple different data sets to some shared or partially shared set of guess variables). I think the overall residuals and chi-square are the more statistically meaningful values, as they are actually calculated by the same algorithm used to determine the guess variables - they're the quantities IFEFFIT is attempting to reduce. I don't believe I've reported the per-data-set residuals in my final results, as I only treated it as an internal check for myself. (It would be nice to have again, though...) -Jason On Thu, Jan 24, 2013 at 10:12 AM, Christopher Patridge wrote: > I am reviewing some older analysis projects from artemis and just wanted > to know which R-factor more accurately describes the misfit? I suspect the > average over the k weights values since this was adopted in Demeter? > > Thanks, > > Chris Patridge > > -- > > Christopher J. Patridge, PhD > NRC Post Doctoral Research Associate > Naval Research Laboratory > Washington, DC 20375 > Cell: 315-529-0501 > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] references
Hi Soma! Google "S02 transferability site:http://millenia.cars.aps.anl.gov/"; and you'll find lots of messages on the subject if you haven't already. There's a post from Bruce on May 4 2010 where he writes: Recent work from John Rehr's group has elaborated on this, demonstrating that S02 is, in the strictest sense, neither transferable nor constant in energy. However, these effects are small such that chemical transferability remains a useful and defensible practice in many EXAFS analyses. http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2010-May/009378.html I don't know what specific work he's referring to but that might be a good direction. -Jason On Tue, Jan 22, 2013 at 1:15 PM, Matt Newville wrote: > Hi Soma, > > On Tue, Jan 22, 2013 at 11:11 AM, Soma Chattopadhyay > wrote: > > > > > 2) A lot of times we find So2 from the respective metal foil and fix it > > when we fit the sample data for the same element. Is there any reference > for > > this one? > > > > I know about the book by Shelly, Hesterberg and Ravel. > > Would appreciate if I get some more references. > > I'm not aware of a truly thorough study of this convention. Several of > the early UWXAFS papers mention using this approach. Probably the > clearest statement is from > > E A Stern, et al "The UWXAFS Analysis Package - Philosophy and Details", > Physica B208 pp 117-120 (1995) > [DOI: 10.1016/0921-4526(94)00826-H] > > which states (full paragraph): > > The set of parameters that most frequently have a strong > enough correlation to give difficulty in obtaining their > values separately are S02, the passive electron overlap > constant[13], sigma^2, the disorder about the optimal > distance, and N, the number of atoms in a particular > coordination shell. The most reliable way to separate out > sigma^2 from the other two parameters is to measure the > temperature dependence of sigma^2 and vary the product S02*N > so as to obtain a fit to an Einstein oscillator, particularly > the zero point value. Since S02 is dependent essentially on > only the center atom, it can be found in known structures and > N determined from the S02*N value. > > Here Reference 13 is to Stern and Heald's chapter in the Handbook of > Synchrotron Radiation Vol 1 (1983). > > Cheers, > > --Matt > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Determining errors in R_fit
Since R_eff is constant, surely all you need to do is multiply R_eff by the uncertainty in alpha? That will be the uncertainty in delta_R and R_fit. The program is only giving you statistically-derived uncertainty for the values it fits; the user needs to determine how to propagate or otherwise deal with this uncertainty. -Jason On Fri, Nov 16, 2012 at 1:33 PM, Rana, Jatinkumar Kantilal < jatinkumar.r...@helmholtz-berlin.de> wrote: > Dear Ifeffit users, > > > > I have a very simple doubt about reporting the uncertainties in R_fit. > > > > In the fit, I have assumed that a bond length changes by a constant > fraction, **alpha** such that > > > > Delta R = R_effective * alpha > > > > and, > > > > R_fit = R_effective +/- Delta R > > > > I can get uncertainties in the fitted value of **alpha** from artemis. > But the question is how to work out the uncertainties in the R_fit. Will > it be same as that of **alpha** ?? > > > > Thanks in advance !!! > > > > With best regards, > > Jatin > > > > -- > > Helmholtz-Zentrum Berlin für Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher > Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. > Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Demeter will not start without admin permissions
Thanks Matt, this was helpful in directing my troubleshooting. Somehow, the problem seemed to resolve itself today without my intervention. So I'm again stumped, but I'm stumped with a perfectly functional version of Demter again. Maybe recent Java updates changed something, or some other software update I'm too lazy to track down ... So, trouble issue resolved, as mysteriously as it began. Gremlins, clearly. -Jason On Fri, Aug 31, 2012 at 1:24 PM, Matt Newville wrote: > > One question would be whether you can run the codes from the older > Ifeffit installation? > > For what it's worth, Ifeffit has been built with MinGW for awhile now. > Still, as you suggest, a recent install of MSVC2008 might be causing > the conflict. You might try grabbing the MS*71.dll files from the > older Ifeffit installation and making sure they are put somewhere > early in the path when running strawberry perl. > > As far as I can tell, Bruce built the file > C:/strawberry/perl/site/lib/auto/Ifeffit/Ifeffit.dll separately from > ifeffit_12.dll, (probably) also with MinGW, but in a way that depends > on the ifeffit_12.dll (I don't see any other obvious dlls around). I > don't know what dlls this Ifeffit.dll will try to load, but that is > probably what is causing the trouble. > > Hope that helps, > > --Matt > > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] How to write feff.inp file for CO adsorbed Cu?
Tian, Thanks for these articles, although I think they (kind of) confirm what I was saying before. As you say, the Phys Rev article was taken at the O K edge, not the Cu K edge, so of course it's going to probe O-C-Cu structure much more effectively than using a Cu absorber. (Although that's not to say SEXAFS is easy!) I have no experience in this method so I can't say if O K edge would be an appropriate technique for you or not. The J Am Chem Soc article concerns a Ru catalyst that was atomically disperse or nearly so under at least one condition, allowing C,O scatterers to be more clearly observed. I'm extremely suspicious about the peak assignments in Fig 5a; they look to me like Ru-O and Ru-Ru paths, and without good curve fits to that plot I find the assignments speculative. If I were a reviewer I would ask for such fits, but since this is a 22 year old paper I would simply suggest caution about that one specific aspect, as by itself, it may not be as convincing today as it was when it was published. Perhaps one of their citations makes a solid case. Interestingly, I'm running an experiment right now on that same model of Nicolet FTIR. Those things last forever! IME, every time I'm at a beamline, I set aside at least a few hours for exploratory experiments. These exploratory experiments let me get an idea of the type of data I can get from new samples, and allow me to try out a handful of completely new techniques. If something works, I'll plan a big experiment around it for the next trip. If nothing works, I don't feel too bad about those few hours of beamtime not leading to anything of immediate. In suggesting you exercise caution, I don't mean to say don't run these experiments, I mean to say be prepared for difficulty, and don't let this be your one and only plan. My personal experience is this: I've run some in situ experiments with Pt, Pd, Cu catalysts, under NO and CO and although I can see secondary effects of adsorption - changes in oxidation state, metal-oxide and metal-metal bonding - I've yet to actually observe the adsorbed species in EXAFS, even when the catalysts are very disperse. Ribeiro does a lot of operando EXAFS and his recent paper on Cu/SSZ-13, where the Cu is in fact atomically disperse within the lattice, does not directly observe Cu-N paths ( dx.doi.org/10.1016/j.cattod.2011.11.037). In situations similar to yours, I have used XAS simultaneous with FTIR, because that's the best way to observe the metal oxidation state and the adsorbates at the same time. This is not an easy task but it might be the appropriate one for you. And if you're lucky, and can see Cu-C paths, you have that same data confirmed with IR. This of course means compromises; an experiment ideal for both techniques is going to be less than ideal for either one separately. In summary: metal edge XAS is really useful in catalysis because we can observe all sorts of changes in oxidation state and morphology. But it is not the best tool for observing adsorbates, because it averages the contribution of adsorbing sites with the very large number of non-adsorbing sites. You cannot see Cu-C in CO adsorbed to a small particle or flat surface of Cu as easily as you can see Cu-C in copper cyanide, because in the adsorbed case the Cu-Cu contributions are many and strong while the Cu-C contributions are few and weak. Even if you can see Cu-C paths in your samples (and I hope you do!) that still does not mean that you're going to get a quantification of Cu-CO adsorption sites anywhere near as good as you could by IR and TPD. -Jason On Wed, Sep 5, 2012 at 11:12 PM, Zhaomo Tian wrote: > Hi,Jason! > I think you are really professional and pointed out the most important > point at the beginning ! > > Actually I am really worried about my experiment too, I also have a doubt > about whether I can see C or O contributions to the EXAFS in my sample.But > I think maybe no one can give the answer for sure. So at least I need to > try first and see. Actually the originality of my work is to study the > electrochemical reduction of CO2 on metal electrodes. Since CO is noticed > as an important adsorbed intermediate in the multistep reaction and only > copper has been found to be unique among the metals in its ability to > produce a high quantities of hydrocarbon fuels, i start to first > investigate the interaction between adsorbed CO and copper.Thats why I > believe that using EXAFS to study the chemisorbed CO gas-copper system will > contribute to some reasonable explanation. > > I sent you two references, in the first one there is evidence for CO > adsorbed Ru taken at Ru k-edge,where CO is observed in EXAFS, and the > second one SEXAFS study on CO adsorbed on Cu, but it is taken at oxygen K > edge.I think even if there is not exact the same evidence with my system > which is EXAFS on Cu k-edge of CO adsorbed Cu, but it may still work. Why > do you think my experiment is not promising? Could you please e
[Ifeffit] Demeter will not start without admin permissions
Hi all, I came across another Demeter startup issue that seems different from the mingw and perl conflicts previously discussed, and I'm pretty stumped. System: Demeter 0.9.10 on Windows 7 32bit Issue: All Demeter apps (dathena.bat, dartemis.bat, etc.) will no longer run as a user. Apps will only run when opened as an administrator. Trying to open as a user causes cmd window and splash screen to pop up and instantly disappear. No "compatibility mode" seems to help. The problem seemed to pop up sometime between August 2 and August 8, after upgrading to 0.9.10, but I downgraded to 0.9.0 and the problem persisted, so (likely) something changed in my Windows environment and not Bruce's software. The log: Can't load 'C:/strawberry/perl/site/lib/ auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/strawberry/perl/lib/DynaLoader.pm line 200. at C:/strawberry/perl/site/lib/Demeter.pm line 36 Compilation failed in require at C:/strawberry/perl/site/lib/Demeter.pm line 36. BEGIN failed--compilation aborted at C:/strawberry/perl/site/lib/Demeter.pm line 36. Compilation failed in require at C:/strawberry/perl/site/lib/Demeter/UI/Athena.pm line 5. BEGIN failed--compilation aborted at C:/strawberry/perl/site/lib/Demeter/UI/Athena.pm line 5. Compilation failed in require at C:\strawberry\perl\site\bin\dathena.bat line 25. BEGIN failed--compilation aborted at C:\strawberry\perl\site\bin\dathena.bat line 25. I exchanged a few Emails with Bruce before realizing this is a bit more complex than I thought. We've thus figured out (I think) - Explicitly giving myself full permissions to C:/strawberry/perl/site/lib/auto/Ifeffit/ and %APPDATA%/demeter has no effect. - Although I have a cygwin version of perl, demeter is calling up the right one each time. Invoking perl with the full path in e.g. dathena.bat has no effect. I suspect the problem might not be in perl or any of Bruce's code, but in some behavior of ifeffit that was previously condoned by Windows but now requires elevated permissions. I understand ifeffit is written in fortran90 but I don't know if there's any aspect of it that might be affected by recent MS Visual C++ updates I've done on my laptop. (MS Visual C++ 2008 x86 9.0.30729.17 and MS Visual C++ 2010 x86 10.0.30319). I'm pretty sure MSVC2008 coincides with the time Demeter stopped working but it could just be a coincidence. There are also of course various security updates I can't easily sort through. I was hoping Matt might be able to point me in the right direction here; I don't know the inner workings of IFEFFIT and I might be far off track already. Thanks, Jason ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Importing data to Athena crashes on WinXP
Hi Bradley, I'm using 0.9.10 on Win7 and I'm seeing the same thing. The problem might be related to initializing the plot window with the "Athena: Column Selection" dialog when the file being read has a large number of columns. I can load this file into an already-existing project without a problem, when that project already has the plot window initialized and displaying earlier data prior to loading your raw data. But if I have an empty Athena project, I can load this file if I cut it down to 2 or 4 or 12 columns, with more columns making the plot window display respond slower and slower. With all 29 columns the program just hangs. Can you take some project with data in it, and load this raw data into that project without crashing? That might be a useful workaround for the moment. -Jason If so, you might temporarily get around the problem by loading data into On Mon, Aug 13, 2012 at 4:59 PM, BradleyW Miller < miller.bradl...@epamail.epa.gov> wrote: > > New Demeter Athena 0.9.10 > Old Athena 0.8.061 > > Matt I tried everything you suggested in addition I tried removing > everything except the columns. Nothing worked. > > Thanks for your time. > > Respectfully, > Bradley W. Miller, Ph.D. > Post Doctoral Fellow > Oak Ridge Institute for Science and Education > U. S. Environmental Protection Agency > National Risk Management Research Laboratory > Land Remediation and Pollution Control Division > 5995 Center Hill Avenue, Cincinnati, OH 45224-1702 > > Office: (513) 487-2889miller.bradl...@epa.gov > Fax: (513) 569-7879www.epa.gov > > www.tinyurl.com/bwmiller > > The great tragedy of Science—the slaying of beautiful hypothesis by an > ugly fact.— Thomas H. Huxley > > > Views or Opinions expressed in this email is solely representative of the > sender and does not represents those of the EPA or any other agency. > > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] problem with Demeter- Artemis/Atoms
Attaching the CIF would make it much easier to help. Is the CIF supposed to have partial occupancy? (In which case the old version would only work if it ignored one all but one partial occupancy site.) -Jason On Wed, May 23, 2012 at 6:33 PM, Matt Frith wrote: > I was attempting to import a .cif file into Artemis to use for a FEFF > calculation and I am getting the following error message: > > "Atoms is currently unable to use crystal data which has sites of partial > occupancy. Sorry." > > These .cif files work fine with the old version of Artemis/Atoms. Is > there currently a way around this problem, or is this something that will > be addresses in later version. > > Thank you for your help. > > Sincerely, > > Matt Frith > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] AuPd CIF
I don't think the CIF can be described any way other than as fractional occupancy of the Au (or Pd) site, which ATOMS is not designed for. For Au L3 fitting of FCC alloys like this I would usually use ATOMS to make a FEFF input file for Au, substitute every scatterer in the FEFF input with Pd, and carefully combine the paths from the resulting FEFF calculations to fit the data. This has worked fairly well for my Pt and Pd catalysts (reasonable results, useful accuracy). Bruce wrote a workaround for dopants and alloys that should help you edit the FEFF input correctly; from your message I'm not clear if you've already seen it and/or that's what you're doing already. http://cars9.uchicago.edu/ifeffit/Doped -Jason On Thu, Feb 23, 2012 at 8:39 AM, Kaiser, Julian < julian.kai...@helmholtz-berlin.de> wrote: > Hi Sven, > > thank's a lot. I think at the ICSD there are no cif files free available, > right? I couldn't find some. The structure of Au and Pd is quite similar. > I've already created a CIF by changing Au to Pd atoms in the CIF but I > don't know if I did it right, so I'm just looking for another official CIF > to check it . > > Best regards, > Julian > > -- > *Von:* ifeffit-boun...@millenia.cars.aps.anl.gov [ > ifeffit-boun...@millenia.cars.aps.anl.gov]" im Auftrag von "Sven L. M. > Schroeder [sven.schroe...@gnomikos.com] > *Gesendet:* Mittwoch, 22. Februar 2012 17:50 > *Bis:* 'XAFS Analysis using Ifeffit' > *Betreff:* Re: [Ifeffit] AuPd CIF > > Hi Julian > > > > There are several (Au)x(Pd)y alloy structures in the ICSD (Inorganic > Crystal Structure Database) of FIZ Karlsruhe… If I remember correctly the > space group for AuPd (x =1 and y = 1) is FM3-M, so you may in fact be able > to generate a file by yourself… > > > > *From:* ifeffit-boun...@millenia.cars.aps.anl.gov [mailto: > ifeffit-boun...@millenia.cars.aps.anl.gov] *On Behalf Of *Kaiser, Julian > *Sent:* 22 February 2012 16:32 > *To:* ifeffit@millenia.cars.aps.anl.gov > *Subject:* [Ifeffit] AuPd CIF > > > > Dear ifeffit-list members, > > I'm looking for an AuPd CIF (crystal information file). I couldn't find > one at the Crystallography Oben Database (www.crystallography.net) or at > the mailing-list archive. I've seen measurements at AuPd-foil published, so > I think there meight also exist an CIF. Would be nice, if someone could > give me a hint. > > Thanks for your kind help, > Julian > > > -- > > > Helmholtz-Zentrum Berlin für Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher > Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. > Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Geschäftsführerin: Prof. Dr. Anke Rita Kaysser-Pyzalla > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > -- > > Helmholtz-Zentrum Berlin für Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher > Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. > Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Geschäftsführerin: Prof. Dr. Anke Rita Kaysser-Pyzalla > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] PdO reference
Excellent, thanks! On Thu, Nov 3, 2011 at 1:35 PM, David Sprouster wrote: > Jason: > > The famous "Lytle database" actually has a couple of PdO sample spectra > (link below). I think they can also be opened in the newest version of > Athena as-well. > > http://ixs.iit.edu/database/data/Farrel_Lytle_data/RAW/Pd/index.html > > Hope that helps > > Dave > > -- > David Sprouster PhD > Postdoctoral Research Fellow > Department of Electronic Materials > Engineering > Research School of Physics and > Engineering > The Australian National University > Canberra ACT 0200, Australia > Currently at Hysitron Inc. > T: +612 612 50868 > F: +612 612 50511 > M: +1 612 600 1286 > W: http://physics.anu.edu.au/eme/ > -- > > > > > > On 3/11/11 12:00 PM, "ifeffit-requ...@millenia.cars.aps.anl.gov" > wrote: > > >PdO reference > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] PdO reference
Hello! I've recently written an atoms input file for palladium (II) oxide (PdO) that fits well to some experimental data. Unfortunately, I do not have access to a PdO reference to validate the structure. We will probably run PdO on the same beamline in the near future, but until then it'd be nice to know how close my structure is to a standard. Does anyone have a PdO multicolumn file they are able to share? I will of course send the structure to the atoms.inp archive if it fits well. Thanks! -Jason ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] atoms.inp files
If I might add to Dr. Ravel's response: if you're just starting with EXAFS (apologies if you're not) you might not realize that writing a crystallographic reference in atoms.inp syntax is actually pretty trivial. Here's how to do that: http://cars9.uchicago.edu/~newville/adb/#input -Jason On 5/10/2010 10:29 AM, csr...@latech.edu wrote: Thanks for responding Mohamed. I previously had looked at the website that you mentioned (http://cars9.uchicago.edu/~newville/adb/search.html) but did not see either files (TiAl or TiAl3) on there. Do you or anyone else know of another place I can look? ~Corisma Robinson This message was sent using IMP, the Internet Messaging Program. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Jason Gaudet Environmental Catalysis and Nanomaterials Laboratory Department of Chemical Engineering Virginia Tech 147B Randolph Hall Blacksburg, VA 24061 540-231-9371 jgau...@vt.edu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fwd: Mg k-edge and Athena Questions
The Photon Factory at KEK, Tsukuba, Japan has two beamlines (BL7A, BL2C) that cover 250-1500 eV at around 10^9 photons/s. Bruce Ravel wrote: > > There are some other options if you are willing to look farther afield > than NSLS. The XAS beamline at CAMD is one option. I believe that > there are beamlines at the ALS that can do XAS in that energy range. > Examples from even farther afield would inlcude the Lucia beamline at > Soleil and beamline 8 at the Thai synchrotron. > > Perhaps some of the folks on this mailing list can suggest some other > options for that energy range. > > -- Jason Gaudet Environmental Catalysis and Nanomaterials Laboratory Department of Chemical Engineering Virginia Tech 147B Randolph Hall Blacksburg, VA 24061 540-231-9371 jgau...@vt.edu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fwd: Athena troubleshooting
Bruce Ravel wrote: > See my comment below on the value of attaching a small project file >> Also, this is more of a software question. I'm not sure why, but about >> half of the samples flip their orientation 180 degrees (from positive y to >> negative y) when "normalizing" them. But when I'm trying to display >> several samples at once about half are showing positive peaks and half are >> negative peaks. For instance, samples 10, 3 and 1 don't flip when >> normalized, however all of the other samples do. >> > > I don't really know what you are talking about, but I suspect that you > have poorly chosen values for the pre-edge or nromalization > parameters: > I think I might go back a few steps first and make sure the data files and experimental setup are/were such that I0/If/It are properly labeled and selected so that the pre-edge/norm parameters *can* be properly chosen. -- Jason Gaudet Environmental Catalysis and Nanomaterials Laboratory Department of Chemical Engineering Virginia Tech 147B Randolph Hall Blacksburg, VA 24061 540-231-9371 jgau...@vt.edu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] 8 coordination crystal
When trying to do ab initio fits of a material it's best to determine the actual crystal structure and generate an ATOMS input file from that. CeO2 structure: http://cst-www.nrl.navy.mil/lattice/struk/c1.html -Jason mohamed sobhy wrote: > Dear > I am trying to simulate CeO2 crystal lattice but I found that in > Artemis documentations the following > > *Currently the following coordination geomatries are available:* > ** 4-coordinate crystal* > ** 6-coordinate crystal* > ** octahedral molecule* > ** tetrahedral molecule* > ** square-planar molecule* > ** > CeO2 has coordination no of 8, so what is the meaning of that > > Also is there any manual or working examples for Artemis > > Thnaks > > Mohamed > > > > > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > -- Jason Gaudet Environmental Catalysis and Nanomaterials Laboratory Department of Chemical Engineering Virginia Tech 147B Randolph Hall Blacksburg, VA 24061 540-231-9371 jgau...@vt.edu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] a question
Are you determining bond length from the magnitude of chi(R) or are you fitting ab initio data to the curves? In my experience the |chi(R)| peaks are usually closer than the actual bond distances due to phase shift. Dr Somaditya Sen wrote: > Hi All > I am having problems in comparing the real bond length as obtained > from EXAFS data and Reitveld analysis of XRD data of te same sample. > The bond lengths as observed from the XAFS data seems to be much > smaller that that from XRD. Is there some multiplication factor known > in literature to address this issue? > > S Sen > > > > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > -- Jason Gaudet Environmental Catalysis and Nanomaterials Laboratory Department of Chemical Engineering Virginia Tech 147B Randolph Hall Blacksburg, VA 24061 540-231-9371 jgau...@vt.edu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
