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

Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 6
by Enyuan Hu 09 Aug '12

09 Aug '12

Hi Matthew, It's so exciting to see your response in here because I've been reading your paper! It's very recent paper and I couldn't be found in Google Scholar yesterday, but I was lucky to find it in your website. In fact, seeing your response makes me feel, ah, I've come to the right place! Anyway, I'll continue my information-digging and see what I can find. Andrew, thanks for your input. I also tried in OriginLab like you did, but no good fitting was achieved. I'll see if I can try some other ways... Enyuan On Thu, Aug 9, 2012 at 11:06 AM, <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: pre-edge centroid (Andrew Korinda) > 2. Re: Ifeffit Digest, Vol 114, Issue 5 (Enyuan Hu) > 3. Re: Ifeffit Digest, Vol 114, Issue 5 - Mn XANES (Matthew Marcus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 9 Aug 2012 08:26:32 -0500 > From: Andrew Korinda <a-korinda(a)northwestern.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] pre-edge centroid > Message-ID: > <CA+JhC7wgLFQR3F8Gaqnbp=hrz0tMb+HDoirMZAoLm_jdC= > 4Ayw(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Enyuan, > > I've had trouble with fitting in Athena as well and just used Excel > and a Gaussian function for the peak. As Domink stated, fitting the > edge as an arctan function simultaneously is a large help. I had tried > extracting the pre-edge and fitting the peak in Origin as a > pseudo-Voight function; however, I couldn't get a reliable fit of the > edge alone. > > In summary, it's a bit of all or nothing. When fitting the arctan > function, I typically stopped at 2 eV below the edge. > > Andy Korinda > > On Thu, Aug 9, 2012 at 8:11 AM, Dominik Samuelis <d.samuelis(a)fkf.mpg.de> > wrote: > > Dear Enyuan, > > > > in my experience, peak fitting works very well with Athena. Try not to > fit > > only the prepeak, but maybe include an arctan describing the edge (see > > attached pdf, the fit was made using athena). This makes isolating the > > prepeak much more reliable. > > > > Best regards, > > Dominik > > > > > > On 09.08.2012 06:21, Enyuan Hu wrote: > >> > >> Dear all, > >> > >> I was wondering if anyone could comment on how to get the centroid of > >> pre-edge by fitting the pre-edge peak by pseudo-Voigt functions. I tried > >> to do that in Athena, but it seemed that peaking fitting part is the > >> relatively less developed function in the software. Any comment would be > >> appreciated. > >> > >> Enyuan > >> > >> > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > > > > > -- > > Dr. Dominik Samuelis > > d.samuelis(a)fkf.mpg.de > > Max-Planck-Institut f?r Festk?rperforschung > > Max Planck Institute for Solid State Research > > Heisenbergstr. 1 > > 70569 Stuttgart > > Germany > > Phone +49-711-689-1769 > > Fax +49-711-689-1722 > > Web http://www.fkf.mpg.de/maier/ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 9 Aug 2012 10:53:32 -0400 > From: Enyuan Hu <bearcharge(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 5 > Message-ID: > < > CAJud35PZaf7HDS4digfUZk8RkDsXxLR06i1FqB_ugeRtDXJXnA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Dominik, > > Thank you so much for your quick response. Indeed, it's really nice fitting > according to your result. But my situation seems a little bit different as > I'm dealing with the Mn XANES data and there're doublets and sometimes > triplets in the pre-edge. Actually, I might as well explain my interest of > doing such fitting. I read in the paper *(F Farges, PHYSICAL REVIEW B 71, > 155109 (2005))* that the centroid of pre-edge peak is a more accurate > measurement of the oxidation state of the element of interest, compared to > the more conventional inflection point or half-way method. So I was trying > to follow the paper and see if it also works for my samples. Anyway, thanks > again for your help! > > Enyuan > > On Thu, Aug 9, 2012 at 9:11 AM, > <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: question for ifeffit mailing list - ATHENA NORMALIZATION > > (Marie Zwetsloot) > > 2. Re: question for ifeffit mailing list - ATHENA NORMALIZATION > > (Scott Calvin) > > 3. pre-edge centroid (Enyuan Hu) > > 4. Re: pre-edge centroid (Dominik Samuelis) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 8 Aug 2012 13:17:59 -0400 > > From: Marie Zwetsloot <mjz56(a)cornell.edu> > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: Re: [Ifeffit] question for ifeffit mailing list - ATHENA > > NORMALIZATION > > Message-ID: > > <CALtZdD54= > > 1-w4U3vk7DdNU_CUkGpK-1vJ3ioOR_CSvkj4UeCXw(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi Scott Calvin, > > > > Thanks for your help. Yes, this is as far as my pre- and post-edge range > > go. I realized I should have made them longer; it was my first time doing > > this and wasnt aware that i should lengthen my pre and post-edge for > later > > on analysis. This will be good lesson for the future. > > > > So you would not recommend doing linear combination fitting? I was > planning > > on trying it out.. But I wouldnt want to do it if with my pre- and > > post-edge range, I am bound to derive wrong conclusions from the data. > > > > Best, > > Marie > >

1 0

pre-edge centroid
by Enyuan Hu 09 Aug '12

09 Aug '12

Dear all, I was wondering if anyone could comment on how to get the centroid of pre-edge by fitting the pre-edge peak by pseudo-Voigt functions. I tried to do that in Athena, but it seemed that peaking fitting part is the relatively less developed function in the software. Any comment would be appreciated. Enyuan

3 2

Re: [Ifeffit] question for ifeffit mailing list - ATHENA NORMALIZATION
by Marie Zwetsloot 08 Aug '12

08 Aug '12

Hi Scott Calvin, Thanks for your help. Yes, this is as far as my pre- and post-edge range go. I realized I should have made them longer; it was my first time doing this and wasnt aware that i should lengthen my pre and post-edge for later on analysis. This will be good lesson for the future. So you would not recommend doing linear combination fitting? I was planning on trying it out.. But I wouldnt want to do it if with my pre- and post-edge range, I am bound to derive wrong conclusions from the data. Best, Marie

2 1

Re: [Ifeffit] question for ifeffit mailing list - ATHENA NORMALIZATION
by Marie Zwetsloot 07 Aug '12

07 Aug '12

Dear Ifeffit community, Thanks for your questions. I am very new to this field (M.Sc. student in soil science), so I really appreciate that you are taking the time to give me some advice. I have attached a picture of some of the normalized spectra I am working with as well as mu(E) spectra (I am sorry for attaching the picture, for some reason my email did not allow me to copy it into this message). I am doing Xanes analysis on phosphorus in bone char. My normalization range is from 15-60 eV and pre-edge range is from -13.5 to -6.75. Maybe my normalized spectra looked actually fine; they are not that far above 1 (more or less around 0.3 above). I just thought they looked a little strange/skewed. Let me know what you think. Thanks, Marie

2 1

[IFEFFIT] question about chemically unordered systems
by Meutzner, Falk 07 Aug '12

07 Aug '12

Dear IFEFFIT Community, is there a way to calculate the spectrum for chemically disordered systems? We have a simple binary bcc structure. It crystallises either in superstructure (CsCl) or chemically disordered (W type) with both atoms randomly taking part of either (0,0,0) or (0.5,0.5,0.5). It is easy to get the superstructured model for artemis, but we have no clue how to model the disordered system... Thanks a lot for your help, we really appreciate it. Best regards Falk

4 4

question for ifeffit mailing list - ATHENA NORMALIZATION
by Marie Zwetsloot 07 Aug '12

07 Aug '12

* Is there a way through which I can control that my norm(E) only has a range from 0-1? Right now, some of my scans go from 0 - 3 after having normalized them. It seems that most people publish their data only ranging from 0-1..? . Is there a difference between the two?*

3 2

Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 18
by Michael Weir 30 Jul '12

30 Jul '12

Hello Branko, I've worked a little bit with small Pt nanoparticles and I think I may see a problem. In the project file you sent us, you choose an Rbkg of 1.6 for your nanoparticles but 1.0 for the foil. The Pt-O bonds at ~ 2 A end up at about 1.5/1.55 A in the Fourier Transform, so your choice of Rbkg is suppressing the real signal in that region. I'd look again with a lower Rbkg if you haven't already (1.2 is a good starting point). I didn't see your Pt-O standards in the project. Also keep in mind that Artemis will plot individual paths from the FEFF calculation, which is really useful for determining if a specific path has a strong contribution to your fit or if a pair of paths will be difficult to distinguish. I hope that helps! Michael Weir On Mon, Jul 30, 2012 at 9:01 AM, <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: Ifeffit Digest, Vol 113, Issue 17 (Branko Zugic) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Jul 2012 12:00:37 -0400 > From: Branko Zugic <brankozugic(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 17 > Message-ID: > <CAOJ5_YxOhbiN8zJfi_xG8+NSVuhnfTydyR== > xc61Uov-CwdhMw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Anatoly, > > I've only tried approximating using the short bond at 2 A up until now. > Below are the spectra that I'm trying to interpret. These are merged QEXAFS > data taken at increasing temperature under WGS conditions. Perhaps I > haven't processed them well enough? There certainly seem to be changes > taking place during the course of reaction, which I'm trying to interpret. > > Given that the material starts out very well dispersed (I've observed many > sub-nm Pt clusters via ac-STEM) and grow to 1-2 nm particles during > reaction, I would expect to observe corresponding structural changes during > reaction. I also observe significant changes in the EXAFS spectra when > alternating between WGS gas and He - hence my thought to including some > kind of Pt-C and Pt-O paths, similar to those used in the Ir4(CO)12 work. > > Thanks for any help! > > > Branko > > > > On Sat, Jul 28, 2012 at 1:00 PM, > <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: Modeling Pt/C Catalyst Under WGS Conditions > > (Anatoly I Frenkel) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sat, 28 Jul 2012 01:02:23 +0000 > > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions > > Message-ID: <98fc47e6-bd47-4c56-8fb2-3385fa7dbbbe@blur> > > Content-Type: text/plain; charset="utf-8" > > > > Maybe your system is more complex? Have you included a long Pt-O bond at > > around 2.5 A or just a short one at around 2A? Hard to help without > seeing > > what the problem is. > > > > Anatoly > > > > > > > > Sent from my mobile phone, please forgive typos > > > > > > -----Original message----- > > From: Branko Zugic <Branko.Zugic(a)tufts.edu> > > To: "ifeffit(a)millenia.cars.aps.anl.gov" < > ifeffit(a)millenia.cars.aps.anl.gov > > > > > Sent: Fri, Jul 27, 2012 15:28:37 GMT+00:00 > > Subject: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions > > > > Hello, > > > > I am trying to interpret some in-situ Quick-EXAFS and EXAFS data that I > > took under water-gas shift conditions (CO + H2O diluted in He) on some > Pt/C > > catalysts. I'm finding that the Pt-Pt and Pt-O fits using foil data, Pt-O > > standards, and quick 1st shell approximations for Pt-O aren't that great. > > After looking through the literature I came across some papers (i.e. > > http://pubs.acs.org/doi/abs/10.1021/jp983283e) that use the Ir-O and > Ir-C > > interactions from Ir4(CO)12 to approximate Pt-O and Pt-C interactions. I > > then found some crystallographic tables for Ir4(CO)12 (below), but it's > > unclear to me whether I can use this to create an atoms inp file (and > > whether the data is for the structure I'm looking for or the referenced > > Ir(CO)3). So far I've had no luck. > > > > Is this a reasonable approach to this problem? Is the information I have > > enough to do this? Any suggestions as to where I may be able to find the > > crystallographic data I am looking for? > > > > > > Branko Zugic > > > > > > -- > > PhD Candidate > > Tufts University, Chemical and Biological Engineering > > 4 Colby Street, Room 226 > > Medford, MA 02155 > > Ph: (O) 617 627 2267 (H) 508 414 8555 > > Email: Branko.Zugic(a)tufts.edu<mailto:Branko.Zugic@tufts.edu>, > > brankozugic(a)gmail.com<mailto:brankozugic@gmail.com><mailto: > > brankozugic(a)gmail.com> > >

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 17
by Branko Zugic 30 Jul '12

30 Jul '12

Hi Anatoly, I've only tried approximating using the short bond at 2 A up until now. Below are the spectra that I'm trying to interpret. These are merged QEXAFS data taken at increasing temperature under WGS conditions. Perhaps I haven't processed them well enough? There certainly seem to be changes taking place during the course of reaction, which I'm trying to interpret. Given that the material starts out very well dispersed (I've observed many sub-nm Pt clusters via ac-STEM) and grow to 1-2 nm particles during reaction, I would expect to observe corresponding structural changes during reaction. I also observe significant changes in the EXAFS spectra when alternating between WGS gas and He - hence my thought to including some kind of Pt-C and Pt-O paths, similar to those used in the Ir4(CO)12 work. Thanks for any help! Branko On Sat, Jul 28, 2012 at 1:00 PM, <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: Modeling Pt/C Catalyst Under WGS Conditions > (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 28 Jul 2012 01:02:23 +0000 > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions > Message-ID: <98fc47e6-bd47-4c56-8fb2-3385fa7dbbbe@blur> > Content-Type: text/plain; charset="utf-8" > > Maybe your system is more complex? Have you included a long Pt-O bond at > around 2.5 A or just a short one at around 2A? Hard to help without seeing > what the problem is. > > Anatoly > > > > Sent from my mobile phone, please forgive typos > > > -----Original message----- > From: Branko Zugic <Branko.Zugic(a)tufts.edu> > To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov > > > Sent: Fri, Jul 27, 2012 15:28:37 GMT+00:00 > Subject: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions > > Hello, > > I am trying to interpret some in-situ Quick-EXAFS and EXAFS data that I > took under water-gas shift conditions (CO + H2O diluted in He) on some Pt/C > catalysts. I'm finding that the Pt-Pt and Pt-O fits using foil data, Pt-O > standards, and quick 1st shell approximations for Pt-O aren't that great. > After looking through the literature I came across some papers (i.e. > http://pubs.acs.org/doi/abs/10.1021/jp983283e) that use the Ir-O and Ir-C > interactions from Ir4(CO)12 to approximate Pt-O and Pt-C interactions. I > then found some crystallographic tables for Ir4(CO)12 (below), but it's > unclear to me whether I can use this to create an atoms inp file (and > whether the data is for the structure I'm looking for or the referenced > Ir(CO)3). So far I've had no luck. > > Is this a reasonable approach to this problem? Is the information I have > enough to do this? Any suggestions as to where I may be able to find the > crystallographic data I am looking for? > > > Branko Zugic > > > -- > PhD Candidate > Tufts University, Chemical and Biological Engineering > 4 Colby Street, Room 226 > Medford, MA 02155 > Ph: (O) 617 627 2267 (H) 508 414 8555 > Email: Branko.Zugic(a)tufts.edu<mailto:Branko.Zugic@tufts.edu>, > brankozugic(a)gmail.com<mailto:brankozugic@gmail.com><mailto: > brankozugic(a)gmail.com> >

1 0

Re: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions
by Anatoly I Frenkel 28 Jul '12

28 Jul '12

Maybe your system is more complex? Have you included a long Pt-O bond at around 2.5 A or just a short one at around 2A? Hard to help without seeing what the problem is. Anatoly Sent from my mobile phone, please forgive typos -----Original message----- From: Branko Zugic <Branko.Zugic(a)tufts.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri, Jul 27, 2012 15:28:37 GMT+00:00 Subject: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions Hello, I am trying to interpret some in-situ Quick-EXAFS and EXAFS data that I took under water-gas shift conditions (CO + H2O diluted in He) on some Pt/C catalysts. I'm finding that the Pt-Pt and Pt-O fits using foil data, Pt-O standards, and quick 1st shell approximations for Pt-O aren't that great. After looking through the literature I came across some papers (i.e. http://pubs.acs.org/doi/abs/10.1021/jp983283e) that use the Ir-O and Ir-C interactions from Ir4(CO)12 to approximate Pt-O and Pt-C interactions. I then found some crystallographic tables for Ir4(CO)12 (below), but it's unclear to me whether I can use this to create an atoms inp file (and whether the data is for the structure I'm looking for or the referenced Ir(CO)3). So far I've had no luck. Is this a reasonable approach to this problem? Is the information I have enough to do this? Any suggestions as to where I may be able to find the crystallographic data I am looking for? Branko Zugic -- PhD Candidate Tufts University, Chemical and Biological Engineering 4 Colby Street, Room 226 Medford, MA 02155 Ph: (O) 617 627 2267 (H) 508 414 8555 Email: Branko.Zugic(a)tufts.edu<mailto:Branko.Zugic@tufts.edu>, brankozugic(a)gmail.com<mailto:brankozugic@gmail.com><mailto:brankozugic@gmail.com>

1 0

Modeling Pt/C Catalyst Under WGS Conditions
by Branko Zugic 27 Jul '12

27 Jul '12

Hello, I am trying to interpret some in-situ Quick-EXAFS and EXAFS data that I took under water-gas shift conditions (CO + H2O diluted in He) on some Pt/C catalysts. I'm finding that the Pt-Pt and Pt-O fits using foil data, Pt-O standards, and quick 1st shell approximations for Pt-O aren't that great. After looking through the literature I came across some papers (i.e. http://pubs.acs.org/doi/abs/10.1021/jp983283e) that use the Ir-O and Ir-C interactions from Ir4(CO)12 to approximate Pt-O and Pt-C interactions. I then found some crystallographic tables for Ir4(CO)12 (below), but it's unclear to me whether I can use this to create an atoms inp file (and whether the data is for the structure I'm looking for or the referenced Ir(CO)3). So far I've had no luck. Is this a reasonable approach to this problem? Is the information I have enough to do this? Any suggestions as to where I may be able to find the crystallographic data I am looking for? Branko Zugic -- PhD Candidate Tufts University, Chemical and Biological Engineering 4 Colby Street, Room 226 Medford, MA 02155 Ph: (O) 617 627 2267 (H) 508 414 8555 Email: Branko.Zugic(a)tufts.edu, brankozugic(a)gmail.com <brankozugic(a)gmail.com>

1 0