[Ifeffit] Ifeffit Digest, Vol 114, Issue 7
Andrew Korinda
a-korinda at northwestern.edu
Thu Aug 9 12:23:12 CDT 2012
More specifically I report the weight average centroid, where the
weighting factor is the area of the peak.
WAC=(C1*A1)/(C1*A1+C2*A2)
Chalmin, E.; Farges, F.; Brown, G., Contrib. Mineral. Petrol. 2009,
157 (1), 111-126.
Andy K.
On Thu, Aug 9, 2012 at 11:57 AM, Enyuan Hu <bearcharge at gmail.com> wrote:
> 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:
>>
>> 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: 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 --------------
>> >> A non-text attachment was scrubbed...
>> >> Name: smime.p7s
>> >> Type: application/pkcs7-signature
>> >> Size: 4534 bytes
>> >> Desc: S/MIME Cryptographic Signature
>> >> URL: <
>> >>
>> >> 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...
>> URL:
>> <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 --------------
>> > > 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 --------------
>> > > A non-text attachment was scrubbed...
>> > > Name: smime.p7s
>> > > Type: application/pkcs7-signature
>> > > Size: 4534 bytes
>> > > Desc: S/MIME Cryptographic Signature
>> > > URL: <
>> > >
>> >
>> > 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
>> > > ***************************************
>> > >
>> > -------------- 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
>> > > Size: 108409 bytes
>> > > Desc: not available
>> > > URL: <
>> >
>> > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/83335ed8/attachment.pdf
>> > >
>> > > -------------- next part --------------
>> > > A non-text attachment was scrubbed...
>> > > Name: smime.p7s
>> > > Type: application/pkcs7-signature
>> > > Size: 4534 bytes
>> > > Desc: S/MIME Cryptographic Signature
>> > > URL: <
>> >
>> > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/83335ed8/attachment.p7s
>> > >
>> > >
>> > > ------------------------------
>> > >
>> > > _______________________________________________
>> > > 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
>> > ***************************************
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120809/5874f198/attachment.htm>
>>
>> ------------------------------
>>
>> _______________________________________________
>> 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
>> ***************************************
>
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
More information about the Ifeffit
mailing list