[Ifeffit] Ifeffit Digest, Vol 114, Issue 7
Enyuan Hu
bearcharge at gmail.com
Thu Aug 9 11:57:12 CDT 2012
Dear all,
Thank you so much for all your valuable input. I attached the fitting
result using ATHENA as pdf file. Seems that the fitting is not bad. Like
Dominik and Maria pointed out, it takes some caution to do the fitting. My
experience is, do not fit all parameters at the same time first. Approach
by a try-and-error method, manually adjusting the parameters based on
observation of difference between fitted data and experimental data. When
you think it's about the time, free all parameters (no including centroid)
for the final try. Good luck with that.
Here's another question, how do I compute the centroid of the fitted peaks?
ATHENA gives the centroid for each peak, do I just average them? thanks!
Enyuan
On Thu, Aug 9, 2012 at 11:26 AM,
<ifeffit-request at millenia.cars.aps.anl.gov>wrote:
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>
> Today's Topics:
>
> 1. Re: Ifeffit Digest, Vol 114, Issue 5 (Mar?a Elena Montero Cabrera)
> 2. Re: Ifeffit Digest, Vol 114, Issue 6 (Enyuan Hu)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 9 Aug 2012 09:19:13 -0600
> From: Mar?a Elena Montero Cabrera <elena.montero at cimav.edu.mx>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 5
> Message-ID:
> <CAKUL-=
> gGdfc9W_uQ015cyeVuPXbp3P-yfSnm-O18kV5-S6J2pA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello all,
> I have done pre-edge fitting of Ti in multiferroic ceramics with Athena. I
> have selected error function for the "background" and alternatively
> Lorenztian or Gaussian function for *several* peaks, and Athena has worked
> quite well. The point is to do it with some systematic procedure, and
> fixing some parameters, instead of letting them being free in each step.
> Certainly, Athena doesn't have the pseudo-Voigt function. Try to do this
> way, Enyuan. I think Bruce has commented something about this way sometime
> ago, but I am not sure.
> Regards
> Maria Elena
>
> 2012/8/9 Enyuan Hu <bearcharge at gmail.com>
>
> > 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 at millenia.cars.aps.anl.gov
> > > wrote:
> >
> >> Send Ifeffit mailing list submissions to
> >> ifeffit at 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 at millenia.cars.aps.anl.gov
> >>
> >> You can reach the person managing the list at
> >> ifeffit-owner at 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 at cornell.edu>
> >> To: ifeffit at millenia.cars.aps.anl.gov
> >> Subject: Re: [Ifeffit] question for ifeffit mailing list - ATHENA
> >> NORMALIZATION
> >> Message-ID:
> >> <CALtZdD54=
> >> 1-w4U3vk7DdNU_CUkGpK-1vJ3ioOR_CSvkj4UeCXw at 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
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL: <
> >>
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120808/819dffdb/attachment-0001.htm
> >> >
> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Wed, 8 Aug 2012 15:10:16 -0400
> >> From: Scott Calvin <scalvin at sarahlawrence.edu>
> >> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> >> Subject: Re: [Ifeffit] question for ifeffit mailing list - ATHENA
> >> NORMALIZATION
> >> Message-ID: <B36E3403-35BC-48BE-8E4D-AE2CB8556769 at slc.edu>
> >> Content-Type: text/plain; charset="iso-8859-1"
> >>
> >> Hi Marie,
> >>
> >> I think you can try linear combination fitting, but you'll have to build
> >> in the uncertainty in normalization in to your own estimates of
> uncertainty.
> >>
> >> If you don't check the box that says "force weights to sum to 1," then
> >> you can allow for normalization errors in your sample.
> >>
> >> If your standards also have only short energy ranges, then there's
> >> nothing you can do about that, though. As I said, you'll just have to
> build
> >> them in to your uncertainty. If you are unsure of the edge jump of a
> >> standard to 20%, then the contribution of that standard to the linear
> >> combination fit is uncertain by 20%.
> >>
> >> Uncertainty in normalization is one of the leading contributions to the
> >> uncertainty that should be associated with linear combination fitting,
> even
> >> when the energy ranges are sufficient. In a case like yours, they're
> bigger
> >> than they could have been, but it doesn't mean you can't use linear
> >> combination analysis at all.
> >>
> >> --Scott Calvin
> >> Sarah Lawrence College
> >>
> >> On Aug 8, 2012, at 1:17 PM, Marie Zwetsloot wrote:
> >>
> >> > 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
> >> > _______________________________________________
> >> > Ifeffit mailing list
> >> > Ifeffit at millenia.cars.aps.anl.gov
> >> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >>
> >>
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 3
> >> Date: Thu, 9 Aug 2012 00:21:14 -0400
> >> From: Enyuan Hu <bearcharge at gmail.com>
> >> To: ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> >> Subject: [Ifeffit] pre-edge centroid
> >> Message-ID:
> >> <CAJud35NRYb67J7xLATPHPJGjEyvOK_gUKZur+dL9T30x8k=
> >> UHA at mail.gmail.com>
> >> Content-Type: text/plain; charset="iso-8859-1"
> >>
> >> 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
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL: <
> >>
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/3a09d07c/attachment-0001.htm
> >> >
> >>
> >> ------------------------------
> >>
> >> Message: 4
> >> Date: Thu, 09 Aug 2012 15:11:31 +0200
> >> From: Dominik Samuelis <d.samuelis at fkf.mpg.de>
> >> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> >> Subject: Re: [Ifeffit] pre-edge centroid
> >> Message-ID: <5023B703.6020609 at fkf.mpg.de>
> >> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> >>
> >> 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 at millenia.cars.aps.anl.gov
> >> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >> >
> >>
> >>
> >> --
> >> Dr. Dominik Samuelis
> >> d.samuelis at 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/
> >> -------------- next part --------------
> >> A non-text attachment was scrubbed...
> >> Name: prepeak_fit.pdf
> >> Type: application/pdf
> >> Size: 108409 bytes
> >> Desc: not available
> >> URL: <
> >>
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/83335ed8/attachment.pdf
> >> >
> >> -------------- next part --------------
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> >> Desc: S/MIME Cryptographic Signature
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> >>
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/83335ed8/attachment.p7s
> >> >
> >>
> >> ------------------------------
> >>
> >> _______________________________________________
> >> Ifeffit mailing list
> >> Ifeffit at millenia.cars.aps.anl.gov
> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >>
> >>
> >> End of Ifeffit Digest, Vol 114, Issue 5
> >> ***************************************
> >>
> >
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> >
>
>
> --
> Mar?a Elena
>
> Dra. Mar?a Elena Montero Cabrera
> Centro de Investigaci?n en Materiales Avanzados (CIMAV)
> Miguel de Cervantes 120, Compl. Ind. Chihuahua
> Chihuahua CP 31109, Chih. M?xico
> Tel (614) 4391123
> -------------- next part --------------
> An HTML attachment was scrubbed...
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> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/010b2cc5/attachment-0001.htm
> >
>
> ------------------------------
>
> Message: 2
> Date: Thu, 9 Aug 2012 11:25:37 -0400
> From: Enyuan Hu <bearcharge at gmail.com>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 6
> Message-ID:
> <CAJud35Ow=Jnr3dyL=_WEHF=5+6Dn6VmY_xJBQ0QL+TXHK=
> F3ZA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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 at millenia.cars.aps.anl.gov>wrote:
>
> > Send Ifeffit mailing list submissions to
> > ifeffit at 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 at millenia.cars.aps.anl.gov
> >
> > You can reach the person managing the list at
> > ifeffit-owner at 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 at northwestern.edu>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: Re: [Ifeffit] pre-edge centroid
> > Message-ID:
> > <CA+JhC7wgLFQR3F8Gaqnbp=hrz0tMb+HDoirMZAoLm_jdC=
> > 4Ayw at 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 at 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 at millenia.cars.aps.anl.gov
> > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > >>
> > >
> > >
> > > --
> > > Dr. Dominik Samuelis
> > > d.samuelis at 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 at 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 at gmail.com>
> > To: ifeffit at millenia.cars.aps.anl.gov
> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 5
> > Message-ID:
> > <
> > CAJud35PZaf7HDS4digfUZk8RkDsXxLR06i1FqB_ugeRtDXJXnA at 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 at millenia.cars.aps.anl.gov>wrote:
> >
> > > Send Ifeffit mailing list submissions to
> > > ifeffit at 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 at millenia.cars.aps.anl.gov
> > >
> > > You can reach the person managing the list at
> > > ifeffit-owner at 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 at cornell.edu>
> > > To: ifeffit at millenia.cars.aps.anl.gov
> > > Subject: Re: [Ifeffit] question for ifeffit mailing list - ATHENA
> > > NORMALIZATION
> > > Message-ID:
> > > <CALtZdD54=
> > > 1-w4U3vk7DdNU_CUkGpK-1vJ3ioOR_CSvkj4UeCXw at 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
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> > >
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120808/819dffdb/attachment-0001.htm
> > > >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Wed, 8 Aug 2012 15:10:16 -0400
> > > From: Scott Calvin <scalvin at sarahlawrence.edu>
> > > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > > Subject: Re: [Ifeffit] question for ifeffit mailing list - ATHENA
> > > NORMALIZATION
> > > Message-ID: <B36E3403-35BC-48BE-8E4D-AE2CB8556769 at slc.edu>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Hi Marie,
> > >
> > > I think you can try linear combination fitting, but you'll have to
> build
> > > in the uncertainty in normalization in to your own estimates of
> > uncertainty.
> > >
> > > If you don't check the box that says "force weights to sum to 1," then
> > you
> > > can allow for normalization errors in your sample.
> > >
> > > If your standards also have only short energy ranges, then there's
> > nothing
> > > you can do about that, though. As I said, you'll just have to build
> them
> > in
> > > to your uncertainty. If you are unsure of the edge jump of a standard
> to
> > > 20%, then the contribution of that standard to the linear combination
> fit
> > > is uncertain by 20%.
> > >
> > > Uncertainty in normalization is one of the leading contributions to the
> > > uncertainty that should be associated with linear combination fitting,
> > even
> > > when the energy ranges are sufficient. In a case like yours, they're
> > bigger
> > > than they could have been, but it doesn't mean you can't use linear
> > > combination analysis at all.
> > >
> > > --Scott Calvin
> > > Sarah Lawrence College
> > >
> > > On Aug 8, 2012, at 1:17 PM, Marie Zwetsloot wrote:
> > >
> > > > 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
> > > > _______________________________________________
> > > > Ifeffit mailing list
> > > > Ifeffit at millenia.cars.aps.anl.gov
> > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > >
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 3
> > > Date: Thu, 9 Aug 2012 00:21:14 -0400
> > > From: Enyuan Hu <bearcharge at gmail.com>
> > > To: ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > > Subject: [Ifeffit] pre-edge centroid
> > > Message-ID:
> > > <CAJud35NRYb67J7xLATPHPJGjEyvOK_gUKZur+dL9T30x8k=
> > > UHA at mail.gmail.com>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > 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
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> > >
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/3a09d07c/attachment-0001.htm
> > > >
> > >
> > > ------------------------------
> > >
> > > Message: 4
> > > Date: Thu, 09 Aug 2012 15:11:31 +0200
> > > From: Dominik Samuelis <d.samuelis at fkf.mpg.de>
> > > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > > Subject: Re: [Ifeffit] pre-edge centroid
> > > Message-ID: <5023B703.6020609 at fkf.mpg.de>
> > > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> > >
> > > 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 at millenia.cars.aps.anl.gov
> > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > > >
> > >
> > >
> > > --
> > > Dr. Dominik Samuelis
> > > d.samuelis at 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/
> > > -------------- next part --------------
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> > > Type: application/pdf
> > > Size: 108409 bytes
> > > Desc: not available
> > > URL: <
> > >
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/83335ed8/attachment.pdf
> > > >
> > > -------------- next part --------------
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> > >
> >
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> > > >
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
> > > Ifeffit mailing list
> > > Ifeffit at millenia.cars.aps.anl.gov
> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > >
> > >
> > > End of Ifeffit Digest, Vol 114, Issue 5
> > > ***************************************
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/933169c1/attachment-0001.htm
> > >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 09 Aug 2012 08:05:53 -0700
> > From: Matthew Marcus <mamarcus at lbl.gov>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 5 - Mn XANES
> > Message-ID: <5023D1D1.8090600 at lbl.gov>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > You might also consider the method given in:
> > Manceau, A., Marcus, M. A., Grangeon, S. (2012) "Determination of Mn
> > valence states in mixed-valent magnanates by XANES spectroscopy",
> American
> > Mineralogist 97,816-827
> >
> > (not that I'm plugging my own work or anything :-) )
> > Marcus, M. A.
> >
> > On 8/9/2012 7:53 AM, Enyuan Hu wrote:
> > > 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 at millenia.cars.aps.anl.gov <mailto:
> > ifeffit-request at millenia.cars.aps.anl.gov>> wrote:
> > >
> > > Send Ifeffit mailing list submissions to
> > > ifeffit at millenia.cars.aps.anl.gov <mailto:
> > ifeffit at 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 at millenia.cars.aps.anl.gov <mailto:
> > ifeffit-request at millenia.cars.aps.anl.gov>
> > >
> > > You can reach the person managing the list at
> > > ifeffit-owner at millenia.cars.aps.anl.gov <mailto:
> > ifeffit-owner at 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 at cornell.edu <mailto:mjz56 at cornell.edu
> >>
> > > To: ifeffit at millenia.cars.aps.anl.gov <mailto:
> > ifeffit at millenia.cars.aps.anl.gov>
> > > Subject: Re: [Ifeffit] question for ifeffit mailing list - ATHENA
> > > NORMALIZATION
> > > Message-ID:
> > > <CALtZdD54=
> > 1-w4U3vk7DdNU_CUkGpK-1vJ3ioOR_CSvkj4UeCXw at mail.gmail.com <mailto:
> > 1-w4U3vk7DdNU_CUkGpK-1vJ3ioOR_CSvkj4UeCXw at 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
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120808/819dffdb/attachment-0001.htm
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Wed, 8 Aug 2012 15:10:16 -0400
> > > From: Scott Calvin <scalvin at sarahlawrence.edu <mailto:
> > scalvin at sarahlawrence.edu>>
> > > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov
> <mailto:
> > ifeffit at millenia.cars.aps.anl.gov>>
> > > Subject: Re: [Ifeffit] question for ifeffit mailing list -
> > ATHENA
> > > NORMALIZATION
> > > Message-ID: <B36E3403-35BC-48BE-8E4D-AE2CB8556769 at slc.edu <mailto:
> > B36E3403-35BC-48BE-8E4D-AE2CB8556769 at slc.edu>>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Hi Marie,
> > >
> > > I think you can try linear combination fitting, but you'll have to
> > build in the uncertainty in normalization in to your own estimates of
> > uncertainty.
> > >
> > > If you don't check the box that says "force weights to sum to 1,"
> > then you can allow for normalization errors in your sample.
> > >
> > > If your standards also have only short energy ranges, then there's
> > nothing you can do about that, though. As I said, you'll just have to
> build
> > them in to your uncertainty. If you are unsure of the edge jump of a
> > standard to 20%, then the contribution of that standard to the linear
> > combination fit is uncertain by 20%.
> > >
> > > Uncertainty in normalization is one of the leading contributions to
> > the uncertainty that should be associated with linear combination
> fitting,
> > even when the energy ranges are sufficient. In a case like yours, they're
> > bigger than they could have been, but it doesn't mean you can't use
> linear
> > combination analysis at all.
> > >
> > > --Scott Calvin
> > > Sarah Lawrence College
> > >
> > > On Aug 8, 2012, at 1:17 PM, Marie Zwetsloot wrote:
> > >
> > > > 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
> > > > _______________________________________________
> > > > Ifeffit mailing list
> > > > Ifeffit at millenia.cars.aps.anl.gov <mailto:
> > Ifeffit at millenia.cars.aps.anl.gov>
> > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > >
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 3
> > > Date: Thu, 9 Aug 2012 00:21:14 -0400
> > > From: Enyuan Hu <bearcharge at gmail.com <mailto:bearcharge at gmail.com
> >>
> > > To: ifeffit <ifeffit at millenia.cars.aps.anl.gov <mailto:
> > ifeffit at millenia.cars.aps.anl.gov>>
> > > Subject: [Ifeffit] pre-edge centroid
> > > Message-ID:
> > > <CAJud35NRYb67J7xLATPHPJGjEyvOK_gUKZur+dL9T30x8k=
> > UHA at mail.gmail.com <mailto:UHA at mail.gmail.com>>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > 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
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/3a09d07c/attachment-0001.htm
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 4
> > > Date: Thu, 09 Aug 2012 15:11:31 +0200
> > > From: Dominik Samuelis <d.samuelis at fkf.mpg.de <mailto:
> > d.samuelis at fkf.mpg.de>>
> > > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov
> <mailto:
> > ifeffit at millenia.cars.aps.anl.gov>>
> > > Subject: Re: [Ifeffit] pre-edge centroid
> > > Message-ID: <5023B703.6020609 at fkf.mpg.de <mailto:
> > 5023B703.6020609 at fkf.mpg.de>>
> > > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> > >
> > > 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 at millenia.cars.aps.anl.gov <mailto:
> > Ifeffit at millenia.cars.aps.anl.gov>
> > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > > >
> > >
> > >
> > > --
> > > Dr. Dominik Samuelis
> > > d.samuelis at fkf.mpg.de <mailto:d.samuelis at 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 <tel:%2B49-711-689-1769>
> > > Fax +49-711-689-1722 <tel:%2B49-711-689-1722>
> > > Web http://www.fkf.mpg.de/maier/
> > > -------------- next part --------------
> > > A non-text attachment was scrubbed...
> > > Name: prepeak_fit.pdf
> > > Type: application/pdf
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> > > Desc: not available
> > > URL: <
> >
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> > >
> > > -------------- next part --------------
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> >
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> > >
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
> > > Ifeffit mailing list
> > > Ifeffit at millenia.cars.aps.anl.gov <mailto:
> > Ifeffit at millenia.cars.aps.anl.gov>
> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > >
> > >
> > > End of Ifeffit Digest, Vol 114, Issue 5
> > > ***************************************
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Ifeffit mailing list
> > > Ifeffit at millenia.cars.aps.anl.gov
> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> >
> > End of Ifeffit Digest, Vol 114, Issue 6
> > ***************************************
> >
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>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 114, Issue 7
> ***************************************
>
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