July 2010 - Ifeffit - millenia.cars.aps.anl.gov

Large Amplitude Values
by Gavin Garside 31 Jul '10

31 Jul '10

Fellow X-Ray Absorption Enthusiasts, I have recently compiled a model that gives excellent visual fits in R, q, and k space for bond spacing in a BCC structure. This model gives bond spacings that make sense, and are very close to what would be expected from this set. The R factors are very low, and the enot values correspond quite well to the edge. However, our amplitude values are much larger than typically expected. They come in at the range of 1.8 up to 5.0, but only on a few data sets. On all the rest the amplitude values are 0.4 to 1.0. Could this increase in amplitude be attributed to the fact that we ran florescence measurements instead of transmission, and have a weaker signal coming to the detector? What else could be causing this in only one data set? All samples used in this model have the same structure. Thanks in advance to any replies, your help and time is appreciated. Gavin gavin_garside(a)yahoo.com

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Large Amplitude Values
by Gavin Garside 30 Jul '10

30 Jul '10

Group, I have recently compiled a model that gives excellent visual fits in R, q, and k space. This model also bond spacings that make sense, and are very close to what would be expected from this set. The R factors are very low, and the enot values correspond quite well to the edge. However, our amplitude values are much larger than typically expected. They come in at the range of 1.8 up to 5.0, but only on a few data sets. On all the rest the amplitude values are 0.4 to 1.0. Could this increase in amplitude be attributed to the fact that we ran florescence measurements instead of transmission? What else could be causing this in only one data set, where they all have the same structure. Thanks in advance to any replies, your help and time is appreciated. Gavin gavin_garside(a)yahoo.com

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Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of absorbing atoms"
by Jatinkumar Rana 29 Jul '10

29 Jul '10

Dear Matt, Dear Scott, Thank you very much for the detailed explanation on Delta E0 and S02. Now, things are becoming more clear to me. Best regards, Rana On 28.07.2010 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Case of "nonequivalent multiple atomic sites of absorbing > atoms" (Matt Newville) > 2. Re: Case of "nonequivalent multiple atomic sites of absorbing > atoms" (Scott Calvin) > 3. Re: updating Athena in Windows 7 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Jul 2010 06:46:24 -0500 > From: Matt Newville<newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of > absorbing atoms" > Message-ID: > <AANLkTikm-ufMHua8Tpoq3ja7Xr0Bc+XxFPWfSh75RZgO(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Rana, > > Delta E0 is a shift in the Energy origin of k, that is where k=0. For > the experimental data, this was chosen empirically (and so somewhat > arbitrarily) from the measured data. For the FEFF calculation, it was > chosen at the calculated absorption threshold (lowest available > electronic level), but is known to not be perfect at this, especially > in Feff6. > > Though E0 is meant to be the absorption threshold, it is more > important that the FEFF calculation and measured data agree. Because > of this, Delta E0 is best left as an adjustable parameter in the > analysis. > > It is generally found that a single Delta E0 parameter is needed *per > measured data set and per FEFF calculation*, because measured data can > be shifted in energy and because each calculation can have a different > definition of E0. It is possible to read the FEFF outputs and try to > figure out how different these energies are and so set (not allow to > float) the different E0 values. I believe this can work well, but it > is not automated, and so not often used. In addition, usually one > uses a different Delta E0 for each data set, but well-aligned data > that re-use a FEFF calculation (say, data taken on the same system at > different external conditions) can often get by with sharing a single > Delta E0 parameter. > > S02 is meant to express the incomplete overlap of the "passive > electrons" in the absorbing atom. Removing the deep core electron can > allow the other (L, M, N, O) electrons to relax slightly from their > ground state. That relaxation reduces the overlap of the "initial" > and "final" states of the transition that gives rise to XAFS, and so > reduces the full effect. FEFF6 does not do a very good job of > estimating this effect. > > In practice, S02 can also mask other "amplitude issues", some > theoretical (the inelastic losses that fold into the mean-free-path > are not perfect) and some experimental (it is easier to mis-measure > the amplitude than the phase of an oscillation). For XAFS, these > experimental problems all tend to spoil the amplitude of the > meaurement more than the phase: pin-holes in the sample, slight > misalignment of the sample, over-absorption for fluorescence > measurements, energy bandwidth of the incident beam and harmonic > content of the incident beam. > > The rule of thumb is that it is OK to use the same S02 for all samples > of a particular absorbing atom. Many would add "measured at the same > beamline" to that rule, so that effects of energy bandwidth and > harmonic content are compensated. > > Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Wed, 28 Jul 2010 08:05:23 -0400 > From: Scott Calvin<SCalvin(a)slc.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of > absorbing atoms" > Message-ID:<8295E519-0FC0-4D2C-8C33-944E9BF0F53D(a)slc.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Rana, > > Currently, S02 is usually described as being due to the relaxation of > the other electrons in an atom when a core electron is removed, > resulting in incomplete overlap of initial and final states. This > appears to be a fairly good description, as careful experiments show > good agreement with theoretical calculations based on this idea. > > Note, however, that there could be some other contributors to S02. A > photon could, in addition to exciting the core electron at the edge, > also excite a valence electron. > > There's a small thread on the transferability of S02 here: > > http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg01626.html > > E0 is a tricky concept, in my opinion: it is the energy origin in the > EXAFS equation. Perhaps a theorist can give me a pithy physical > interpretation of what happens at that energy, but I don't know there > needs to be anything; at k near 0, the path expansion is not > convergent, so I'm not sure we should expect anything special to > happen exactly at 0. In other words, it's not exactly the Fermi level > or any other special energy. > > E0 is dependent on oxidation state; it can shift by an electron volt > or two when oxidation states vary. > > Note that oxidation state is a simplistic measure of what's happening > with the electron distribution in a material. Suppose fluorine is > substituted for iodine in some material. Formally, the oxidation state > of the atom they are bonded to is not changed by the substitution. But > in reality, the electron distribution is different, and a small E0 > shift would not be surprising. > > I think the bottom line, then, is this: > > S02 is completely transferable for the same element at multiple > absorbing sites. > > Delta E0 is transferable with some caution for the same element at > multiple absorbing sites if the oxidation state is the same. > > One other note: there's no rule that when trying constraints, you have > to start unconstrained and add constraints to see the effect on the > fit. With complicated systems like yours, it often pays to start with > unrealistically simple constrains (not only E0's and S02's the same, > but also sigma2's), and see if you're on the right track. Then look at > the effect of relaxing constraints. > > --Scott Calvin > Sarah Lawrence College > > > > On Jul 28, 2010, at 4:00 AM, Jatinkumar Rana wrote: > > >> Dear Users, >> >> Since long, i was trying to understand the physical meaning of term >> "Delta E0" and "S02" in EXAFS equation. I have little bit of idea >> about both of them. for example, S02 is element specific and it is >> transferable between samples (if we consider same absorbing atom). >> >> However, I am not able to realize their importance in terms of their >> "physical meaning" as far as interaction of photoelectron is >> concerned. Therefore, it is difficult for me to understand their >> influence on EXAFS. >> >> I am dealing with a case of "nonequivalent multiple atomic sites of >> absorbing atoms". It is quite obvious that in such kind of case no. >> of variables are more than no. of independent points and there is a >> need to constrain the parameters to solve such problems. >> >> I have following questions : >> >> How do i understand "Delta E0" and "S02" theoretically (in terms of >> photoelectron interaction) ? >> >> Can i constrain "Delta E0" for all absorbing atomic site as same ? >> (my assumption : all absorbing atoms are at same oxidation level) >> >> your comments and suggestions would be highly appreciated... >> >> Best regards, >> Rana >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> > > > ------------------------------ > > Message: 3 > Date: Wed, 28 Jul 2010 07:37:52 -0500 > From: Matt Newville<newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] updating Athena in Windows 7 > Message-ID: > <AANLkTinxBX3aCXUGdN5XZCajMuK5gWCyftb9N-6YvpVz(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Todd, > > On Mon, Jul 26, 2010 at 3:39 PM, Monson, Todd<tmonson(a)sandia.gov> wrote: > >> On Saturday, while starting up Athena, I was informed that there was an >> update to Athena available.? I tried installing the update but failed.? I am >> afraid this is due to some user permission issue in windows 7.? How can I >> try to reinstall the update and ensure that it works? >> > You can change the file current.dat in C:\Program > Files\Ifeffit\config. It probably reads > > 013 > > right now, and you could change that to 012 or even lower. That will > cause an update the next time ifeffit looks for updates, which only > happens when one of the programs starts and if the time in > Ifeffit\config\updater.ini is past. To force a check for updates the > next time ifeffit runs, change updater.ini to read > > timestamp = 0 > > In general, I believe this should work for Windows 7 (I have access to > two Windows 7 64-bit machines, and all seems to be working on them, > though I admit to not stressing them too much). So, as you say, I > would also guess that the trouble you had was "only" permission > issues. But, please let us know how it goes, > > Sorry for the trouble, > > --Matt > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 89, Issue 19 > *************************************** > > >

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updating Athena in Windows 7
by Monson, Todd 28 Jul '10

28 Jul '10

On Saturday, while starting up Athena, I was informed that there was an update to Athena available. I tried installing the update but failed. I am afraid this is due to some user permission issue in windows 7. How can I try to reinstall the update and ensure that it works? Thanks, Todd Todd Monson Sandia National Labs Nanomaterials Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

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Case of "nonequivalent multiple atomic sites of absorbing atoms"
by Jatinkumar Rana 28 Jul '10

28 Jul '10

Dear Users, Since long, i was trying to understand the physical meaning of term "Delta E0" and "S02" in EXAFS equation. I have little bit of idea about both of them. for example, S02 is element specific and it is transferable between samples (if we consider same absorbing atom). However, I am not able to realize their importance in terms of their "physical meaning" as far as interaction of photoelectron is concerned. Therefore, it is difficult for me to understand their influence on EXAFS. I am dealing with a case of "nonequivalent multiple atomic sites of absorbing atoms". It is quite obvious that in such kind of case no. of variables are more than no. of independent points and there is a need to constrain the parameters to solve such problems. I have following questions : How do i understand "Delta E0" and "S02" theoretically (in terms of photoelectron interaction) ? Can i constrain "Delta E0" for all absorbing atomic site as same ? (my assumption : all absorbing atoms are at same oxidation level) your comments and suggestions would be highly appreciated... Best regards, Rana

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Re: [Ifeffit] Ifeffit Digest, Vol 89, Issue 17
by Jatinkumar Rana 28 Jul '10

28 Jul '10

Hello Darek, Thank you so much for your reply. Yes, i can rely on model, we have performed reitveld refinement to get the crystallographic data. To my knowledge, there should not be any other phases. Your suggestion is quite right. Somehow, i have to constrain my parameters (to reduce the no. of parameters) and try to fit it. However, I would like to ask you following questions. I am confused about the term "Delta E0" what is the theoretical meaning of that in terms of photoelectron interactions ? If you have multiple atomic sites of absorbing atom, should "Delta E0" be same for all of them (assuming all absorbing atoms are at same oxidizing state) ? I am looking forward to your comments.. Best regards, Rana On 27.07.2010 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. updating Athena in Windows 7 (Monson, Todd) > 2. ODP: Ifeffit Digest, Vol 88, Issue 12 (Zajac, Dariusz A.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 26 Jul 2010 14:39:00 -0600 > From: "Monson, Todd"<tmonson(a)sandia.gov> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] updating Athena in Windows 7 > Message-ID: > <AC050BA7EAC9A34E9A05BC31C3AA2E8B183C0D11B5(a)ES02SNLNT.srn.sandia.gov> > Content-Type: text/plain; charset="us-ascii" > > On Saturday, while starting up Athena, I was informed that there was an update to Athena available. I tried installing the update but failed. I am afraid this is due to some user permission issue in windows 7. How can I try to reinstall the update and ensure that it works? > Thanks, > Todd > > Todd Monson > Sandia National Labs > Nanomaterials Sciences > P.O. Box 5800, MS 1415 > Albuquerque, NM 87185-1415 > (505) 845-2129 > Fax: (505) 844-5470 > >

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Re: [Ifeffit] Ifeffit Digest, Vol 88, Issue 12
by Jatinkumar Rana 27 Jul '10

27 Jul '10

Dear Darek, Sorry for the late response. To fit the "first shell" the No.of independent points and No.of variables which i use are as follows: I use deltaK=11, deltaR = 1.1 so No.of independent points are 8 and No.of variables are 4 (i.e. N, e0, delr, and ss2) I set s02=0.9. Best regards, Rana On 14.06.2010 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. XAFS fitting with multiple atomic sites of absorbing atom > (Jatinkumar Rana) > 2. ODP: XAFS fitting with multiple atomic sites of absorbing > atom (Zajac, Dariusz A.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 14 Jun 2010 12:00:27 +0200 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: Ifeffit users<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] XAFS fitting with multiple atomic sites of > absorbing atom > Message-ID:<4C15FDBB.1050203(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear users, > > I have measured XAFS spectra on Mn and Fe edge on my material. The > material contains 3 different atomic positions for Mn and 4 different > atomic positions for Fe. > > Initially, I tried fitting Fe-edge/Mn-edge spectra using indiviual Fe/Mn > atomic position one-by-one (i.e. first take one Fe/Mn position, > calculate Feff paths, consider certain paths to fit specific R-range, > then take another Fe/Mn position and do the same) but the fit was not > good visually and in terms of goodness of fit parameters. > > Then, i tried fitting Fe-edge/Mn-edge spectra, taking into account all > Fe/Mn atomic position together i.e. I separately calulated Feff paths > for each Fe/Mn atomic position and summed up related paths from each > Feff calculation for fitting a specific R-range. (The assumption being, > the experimental Fe-edge/Mn-edge XAFS spectra has varying contribution > from all Fe/Mn atomic position in crystal structure). > > Anybody in the group could comment about my approach to fit such problem ? > > Is there any specific strategy to fit such problem ? > > I would be thankful if you could suggest some literature available on > such problems. > > Thanks in advance. > > Best regards, > Rana > > > ------------------------------ > > Message: 2 > Date: Mon, 14 Jun 2010 13:34:18 +0200 > From: "Zajac, Dariusz A."<dariusz.zajac(a)desy.de> > To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] ODP: XAFS fitting with multiple atomic sites of > absorbing atom > Message-ID: > <35E004AD6290A7438FCA34BBF325F41601206741(a)ADXV2.win.desy.de> > Content-Type: text/plain; charset="iso-8859-2" > > > Dear Rana, > could you specify how many independent data points and variables you have and you use for fitting? > thnx > darek > > -----Wiadomo?? oryginalna----- > Od: ifeffit-bounces(a)millenia.cars.aps.anl.gov w imieniu Jatinkumar Rana > Wys?ano: Pn 2010-06-14 12:00 > Do: Ifeffit users > Temat: [Ifeffit] XAFS fitting with multiple atomic sites of absorbing atom > > Dear users, > > I have measured XAFS spectra on Mn and Fe edge on my material. The > material contains 3 different atomic positions for Mn and 4 different > atomic positions for Fe. > > Initially, I tried fitting Fe-edge/Mn-edge spectra using indiviual Fe/Mn > atomic position one-by-one (i.e. first take one Fe/Mn position, > calculate Feff paths, consider certain paths to fit specific R-range, > then take another Fe/Mn position and do the same) but the fit was not > good visually and in terms of goodness of fit parameters. > > Then, i tried fitting Fe-edge/Mn-edge spectra, taking into account all > Fe/Mn atomic position together i.e. I separately calulated Feff paths > for each Fe/Mn atomic position and summed up related paths from each > Feff calculation for fitting a specific R-range. (The assumption being, > the experimental Fe-edge/Mn-edge XAFS spectra has varying contribution > from all Fe/Mn atomic position in crystal structure). > > Anybody in the group could comment about my approach to fit such problem ? > > Is there any specific strategy to fit such problem ? > > I would be thankful if you could suggest some literature available on > such problems. > > Thanks in advance. > > Best regards, > Rana > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 88, Issue 12 > *************************************** > > >

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Re: [Ifeffit] ATHENA: \\\"you have not used any memory yet\\\"
by Claire Gervais 23 Jul '10

23 Jul '10

Hello, You are right, this is exactly by googling that I have found that I was not alone to have this problem! I did change the fonts to have all windows entirely visible, but it did not improve. Still stuck with no OK in view. Indeed, it seems that the application waits for me. I am in Gnome, but I don't think it's the point, otherwise it would work under Windows in Virtualbox, no...? I am not an expert in GUI however. Claire ------------------------------------- > > Claire, > > Please use the mailing list. That way, others can find solutions to problems > by doing a google search. > > Is your problem related to question 13 at > http://cars9.uchicago.edu/ifeffit/FAQ/HoraeQuestions > > Are you a KDE user? The "everything is grey" could be a kwin visual cue that > the application is waiting for input that you cannot find because the column > selection dialog is off the bottom of the screen. > > B ------------------------------------

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Ei component
by Abhijeet Gaur 17 Jul '10

17 Jul '10

Hi all My question is about Ei component taken for the problem of poor energy resolution. How it can be calculated using measured energy resolution ? How Ei can be calculated using a known sample, such as a foil for which we have comparable spectra on a beamline with better energy resolution ? With regards Abhijeet Gaur Vikram University Ujjain, India

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Re: [Ifeffit] Neg SS
by Abhijeet Gaur 16 Jul '10

16 Jul '10

Hi Thanks for the quick response. As per the data collection range is concerned, we have limitation of 300eV above the edge. I think I had done data processing in Athena right. I know that the peak at position less than 1 Angs can not be real but I am unable to remove it by data processing in Athena. As per the model is concerned I am attaching herewith feff calculation result and the XRD results for different bondlengths of the sample. By comparing them it seems that model is right. On the other hand poor energy resolution is also one of the reasons for this kind of results. I had alraedy read about this Ei component earlier in papers, but I am unable to follow the procedure like how to calculate it using a known standard. From where I can get literature related to this? It will be really helpfull. With regards Abhijeet Gaur

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