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

How to analyze this data
by Elsa E. Sileo 10 Aug '10

10 Aug '10

I have some measurements at the As edge of As(V) adsorbed onto pure goethite (alfa-FeOOH), Mn partially substituted Goethite (alfa-Mn,Fe.OOH), Al substituted goethite (alfa-Al,FeOOH) and Mn and Al goethite (alfa-Al,Mn,FeOOH) The EXAFS signals change from one spectrum to another. I have refined the distances As-Fe on pure goethite, but when I try to refine Mn-FeOOH or Al,FeOOH, the analysis gets more difficult because As forms different complexes with Al and Fe. Unfortunately for me is almost impossible to have the pure phases alfa-MnOOH or alfa-AlOOH, and measured the As adsorbed. How can I analyze the spectra and have some knowledge about the As-surface complexes formed? Thanks, Elsa Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: sileo(a)qi.fcen.uba.ar

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Re: [Ifeffit] Physical meaning of POLARIZATION card 0 0 1
by Joshua Kas 06 Aug '10

06 Aug '10

Does this POL card > setting mean that the electric vector is along the z/c axis of the > crystal axis? Not quite. FEFF doesn't really know about crystal symmetry. The coordinates in the POLARIZATION card are the same as those in the feff.inp file under the ATOMS card. If the c axis of the crystal happens to be along the z direction, then POLARIZATION 0 0 1 sets the electric field vector along the c axis. You will have to look at the coordinates in the feff.inp to figure out which direction the c axis is. I may be wrong, but I think atoms/webatoms puts the c-axis in the z direction by default. Cheers, Josh Kas > I did read the Feff manual and the POL card but I am > still confused how to relate these to the crystal structure and > orientation. > > Thank you all in advance, > > -- > Chris Patridge > PhD. Candidate > Dept. of Chemistry > SUNY University at Buffalo > Buffalo, NY 14260 > Contact: 315-529-0501 > >

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Physical meaning of POLARIZATION card 0 0 1
by Chris Patridge 06 Aug '10

06 Aug '10

Hello everyone, I am working on modeling HfO2 using L3 Hf edge data. Using the default Feff input generated in Artemis, there is some significant mismatch between the data and theory so I augmented the Feff file by adding the POLARIZATION card setting the values of x y z to (0 0 1). Summing the theoretical paths in this calculation looked much closer and fitting the theory gives the results pasted in the text file. Does this POL card setting mean that the electric vector is along the z/c axis of the crystal axis? I did read the Feff manual and the POL card but I am still confused how to relate these to the crystal structure and orientation. Thank you all in advance, -- Chris Patridge PhD. Candidate Dept. of Chemistry SUNY University at Buffalo Buffalo, NY 14260 Contact: 315-529-0501

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Stoichiometry from EXAFS data
by Peter Zalden 02 Aug '10

02 Aug '10

Dear Feff users, lately, we measured a sample containing Sb and Te at EXAFS beamline CEMO, Hasylab and are wondering whether one can determine the stoichiometry from the height of the different K edges´ steps, if one normalizes the values on the edge steps of the elements (cf. http://physics.nist.gov/PhysRefData/XrayMassCoef/tab3.html) The absorption gases and the specimen were not changed for the different K edges. Of course, I have already tried doing so and from statistical reproducibility and from the resulting values compared to the expected ones I would estimate an error of this method of about 1%. A source of error that I could imagine originates from the different beam position at different energies combined with a slight inhomogenity in the pressed sample powder. Now my question is: Are there any other sources of error that I should take into accout? Is there any reference on this method from a more experienced user that I could cite? Kind regards, Peter --- Dipl.-Phys. Peter Zalden I. Physikalisches Institut IA, RWTH Aachen, 52056 Aachen EMAIL: zalden(a)physik.rwth-aachen.de

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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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