Re: [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences
[Ifeffit] Artemis fitting using FEFF paths plus experimentalreferencesOf course I tried PCA! Over a certain range of temperatures, one component looks tolerably like magnetite. The other is sort of, but not exactly, maghemite. However, if I go below that restricted range, it's not pseudobinary anymore. Also, I still don't know what the "maghemite-like" end-member actually is. Still, for the purposes of the ALS user-meeting poster I have to hang in a week or so, I'll probably take the PCA analysis plus a FEFF fit to the one end-member, and try to do a more thorough job when I have time. No, it doesn't fit well to a combo of the references I have, which does include maghemite. To be fair, what I have is not an isothermal series but an isochronal series at different temperatures, so there's less reason for expecting simple kinetics than in an isothermal series. mam ----- Original Message ----- From: Anatoly Frenkel To: MAMarcus@lbl.gov Sent: Monday, September 24, 2007 6:59 PM Subject: RE: [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences Matthew - please forward my reply to the list if you consider it appropriate. I am spammed out. Anatoly ************************* Matthew, May be it is not relevant, since I do not know if you have a series of EXAFS data at different stages of the oxidation, or just the initial and the final stages. If you do have several stages, including the starting (unoxidized) and final (oxidized, or a sum of oxidized and unoxidized, depending where you stopped at) ones, the principal component analysis seems to match your needs well. I assume you also have access to EXAFS data in bulk magnetite and maghemite references. PCA analysis may tell you (if you are lucky and your system is similar to those where such information was previously obtained): 1) The volume fractions of intermediate species at each stage of the oxidation: 2) Identities of each intermediate species The first part is entirely model-independent. The second part is not, but a reasonable selection of standard compounds (e.g., magnetite or maghemite) may help you isolating the intermediates. The good thing is that you do not need to fit a Fe-Fe and Fe-O bonds to the spectrum of the entire heterogeneous sample, where these contributions may be present in different species, and you have a large number of fitting parameters that describe such a model. Instead, you may end up obtaining that your species are identical with their bulk reference compounds (and thus no fit is required since the only thing you need to know is the volume fraction of this species) or, you may have to fit a couple of FEFF paths to that unknown species, after you deconvolute it from the mixture knowing what the rest of the phases are (it is doable in the case of one intermediate, but can be done in the case of a larger number of intermediates as well). Anatoly -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Matthew Sent: Monday, September 24, 2007 7:05 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences I have a system in which Fe:C alloy nanoparticles are being oxidized. I have the EXAFS of the unoxidized nanoparticles, and I'd like to use that as a reference for fitting as in: Fe_EXAFS(oxidation_stage) = x*(unox_particles)+(1-x)*(Fe->O paths + Fe->Fe paths +...) where the Fe->O and Fe->Fe are based on magnetite and maghemite, which seem to be products of the oxidation. It's not just a linear fit to unoxidized+magnetite+maghemite because the oxide is somewhat disordered. If I do Artemis fits to the shells from the two oxides alone, I find I lose some Fe atoms (sum of fractions < 1), a result which is echoed in linear-combo fits to the oxides alone. Thus, I really want to do a hybrid fit. The unoxidized particles are highly disordered to the point where they don't fit well with reasonable shells, so I'd rather not have to represent them as FEFF shells. How can I do this hybrid fit? mam _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Matthew, It sounds like you have a problem caused by the finite size of the nanoparticles, which results in lower than expected amplitude of the shells in comparison to the amplitude of the shells generated from the xtal structures of maghemite and magnetite. If this is the case and you have a good idea how large the nanoparticles are, you can use Scott Calvin's formula for the amplitude of a scattering shell in a nanoparticle: APPLIED PHYSICS LETTERS 87 (23): Art. No. 233102 DEC 5 2005. This works very well for metallic nanoparticles, but I have never tried it on oxide nanoparticles. Maybe you could try using Scott's formula for the amplitudes and the distances from the crystal structures. If I recall correctly, Scott uses 3 Debye-Waller parameters as variables: one each for the first two shells and one for all other shells. The other possibility is to fit the XANES and low k portion of the EXAFS, but I assume that you have already tried that. Sincerely, Wayne Matthew wrote:
Of course I tried PCA! Over a certain range of temperatures, one component looks tolerably like magnetite. The other is sort of, but not exactly, maghemite. However, if I go below that restricted range, it's not pseudobinary anymore. Also, I still don't know what the "maghemite-like" end-member actually is. Still, for the purposes of the ALS user-meeting poster I have to hang in a week or so, I'll probably take the PCA analysis plus a FEFF fit to the one end-member, and try to do a more thorough job when I have time. No, it doesn't fit well to a combo of the references I have, which does include maghemite.
To be fair, what I have is not an isothermal series but an isochronal series at different temperatures, so there's less reason for expecting simple kinetics than in an isothermal series. mam
----- Original Message ----- *From:* Anatoly Frenkel mailto:frenkel@bnl.gov *To:* MAMarcus@lbl.gov mailto:MAMarcus@lbl.gov *Sent:* Monday, September 24, 2007 6:59 PM *Subject:* RE: [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences
Matthew - please forward my reply to the list if you consider it appropriate. I am spammed out. Anatoly
*************************
Matthew,
May be it is not relevant, since I do not know if you have a series of EXAFS data at different stages of the oxidation, or just the initial and the final stages. If you do have several stages, including the starting (unoxidized) and final (oxidized, or a sum of oxidized and unoxidized, depending where you stopped at) ones, the principal component analysis seems to match your needs well. I assume you also have access to EXAFS data in bulk magnetite and maghemite references.
PCA analysis may tell you (if you are lucky and your system is similar to those where such information was previously obtained):
1) The volume fractions of intermediate species at each stage of the oxidation: 2) Identities of each intermediate species
The first part is entirely model-independent. The second part is not, but a reasonable selection of standard compounds (e.g., magnetite or maghemite) may help you isolating the intermediates. The good thing is that you do not need to fit a Fe-Fe and Fe-O bonds to the spectrum of the entire heterogeneous sample, where these contributions may be present in different species, and you have a large number of fitting parameters that describe such a model. Instead, you may end up obtaining that your species are identical with their bulk reference compounds (and thus no fit is required since the only thing you need to know is the volume fraction of this species) or, you may have to fit a couple of FEFF paths to that unknown species, after you deconvolute it from the mixture knowing what the rest of the phases are (it is doable in the case of one intermediate, but can be done in the case of a larger number of intermediates as well).
Anatoly
-----Original Message----- *From:* ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]*On Behalf Of *Matthew *Sent:* Monday, September 24, 2007 7:05 PM *To:* XAFS Analysis using Ifeffit *Subject:* [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences
I have a system in which Fe:C alloy nanoparticles are being oxidized. I have the EXAFS of the unoxidized nanoparticles, and I'd like to use that as a reference for fitting as in:
Fe_EXAFS(oxidation_stage) = x*(unox_particles)+(1-x)*(Fe->O paths + Fe->Fe paths +...)
where the Fe->O and Fe->Fe are based on magnetite and maghemite, which seem to be products of the oxidation. It's not just a linear fit to unoxidized+magnetite+maghemite because the oxide is somewhat disordered. If I do Artemis fits to the shells from the two oxides alone, I find I lose some Fe atoms (sum of fractions < 1), a result which is echoed in linear-combo fits to the oxides alone. Thus, I really want to do a hybrid fit. The unoxidized particles are highly disordered to the point where they don't fit well with reasonable shells, so I'd rather not have to represent them as FEFF shells.
How can I do this hybrid fit? mam
_______________________________________________ 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
The particles are ~8nm diameter, and the distances involved are 0.3-0.34nm, so that's only a 6% effect. Also, the
fitted Fe-Fe coordinations vary with oxidation temperature, with the biggest deficits at the lowest temps. The particles
actually hollow more at the higher temperature, so one would expect it to go the other way. It actually makes some sense that
there be vacancies because these particles are known to become hollow via a Kirkendall mechanism, and the structure of maghemite
shows that some vacancies are possible even in equilibrium.
Naturally, I did do XANES linear-combo fits. I assume that's what you meant?
mam
----- Original Message -----
From: "Wayne Lukens"
Hi Matthew,
It sounds like you have a problem caused by the finite size of the nanoparticles, which results in lower than expected amplitude of the shells in comparison to the amplitude of the shells generated from the xtal structures of maghemite and magnetite. If this is the case and you have a good idea how large the nanoparticles are, you can use Scott Calvin's formula for the amplitude of a scattering shell in a nanoparticle:
APPLIED PHYSICS LETTERS 87 (23): Art. No. 233102 DEC 5 2005.
This works very well for metallic nanoparticles, but I have never tried it on oxide nanoparticles.
Maybe you could try using Scott's formula for the amplitudes and the distances from the crystal structures. If I recall correctly, Scott uses 3 Debye-Waller parameters as variables: one each for the first two shells and one for all other shells.
The other possibility is to fit the XANES and low k portion of the EXAFS, but I assume that you have already tried that.
Sincerely,
Wayne
participants (3)
-
Matthew -
Matthew Marcus
-
Wayne Lukens