Re: [Ifeffit] Normalization of LCF coefficients when fitting experimental spectra with theoretical spectra
Dear Patricia, Linear combination fits are a nice tool, but one should handle them with great care - the background subtraction process can introduce significant errors. You have to fine tune the parameters by hand if you are using Athena to get reasonable results - sometimes PCA (principle component analysis) helps to find a reasonable number of components - Athena only shows the fitting errors: please keep in mind, that the error of the complete measurement and data evaluation process is much larger. It makes sense to test the process with known mixtures. - the variation of the of the sum of all components between 98 and 105 % (even with choosing -> sum coefficients to 1) is a problem somewhere inside of Athena. I think only Bruce Ravel can help you there. best regards Stefan > Am 08.03.2021 um 19:27 schrieb Patricia Poths : > > Hi, > > I am a theoretical chemistry PhD student working on fitting experimental > spectra with computed spectra in order to get a better understanding of the > composition. In the LCF process with athena, I have found that when I allow > "sum coefficients to 1", I get an unphysical negative coefficient of the last > standard- after reading through the mailing list I understood why, and so no > longer use that. The sum of my coefficients during the fitting now is close > to 1- generally within the range of 0.95-1.1 at the absolute extremes, but > more often around ~0.98- ~1.05. > > In order to compare these coefficients, I renormalize them to 1, so they can > represent the fractions of each component present. However, to test this I > took the new normalized coefficients and summed up the standards with their > respective weights to create this normalized "fit", and found that it is > worse than the initial one. Is this something I should be concerned about > when reporting the qualitative trends in how the composition changes? And if > so, is there a better way to do the fits in a more normalized way? > > Many thanks, > Patricia > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Normalization of LCF coefficients when fitting experimental spectra with theoretical spectra
Hi Patricia, When you say "worse than the initial one," what do you mean? If it's a "worse" match than nonsensical fit results, but makes some physical and chemical sense, I'd personally argue it's a much better fit ;) What you are doing seems reasonable to me, but I would further recommend keeping your fit component selection as simple as possible. I'm a big proponent of two-component fits, maybe three if there's a really good reason. I feel like a lot of people do multicomponent (3-4 fitting spectra, maybe even more) LCF with the argument that the inclusion of additional components improves the fit statistics...But to me that gives a false sense of certainty that the technique doesn't really allow (at least for the systems I work with). For reporting qualitative trends, it seems like you're on the right track. Perhaps unless it's a qualitative trend of a minor component that might not even be there at all and you're basing your entire argument on it definitely being there, which uhh. Seems to happen a lot. Cheers, Mike > On Mar 11, 2021, at 1:42 AM, Patricia Poths > wrote: > > > Hi, > > I am a theoretical chemistry PhD student working on fitting experimental > spectra with computed spectra in order to get a better understanding of the > composition. In the LCF process with athena, I have found that when I allow > "sum coefficients to 1", I get an unphysical negative coefficient of the last > standard- after reading through the mailing list I understood why, and so no > longer use that. The sum of my coefficients during the fitting now is close > to 1- generally within the range of 0.95-1.1 at the absolute extremes, but > more often around ~0.98- ~1.05. > > In order to compare these coefficients, I renormalize them to 1, so they can > represent the fractions of each component present. However, to test this I > took the new normalized coefficients and summed up the standards with their > respective weights to create this normalized "fit", and found that it is > worse than the initial one. Is this something I should be concerned about > when reporting the qualitative trends in how the composition changes? And if > so, is there a better way to do the fits in a more normalized way? > > Many thanks, > Patricia > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] Normalization of LCF coefficients when fitting experimental spectra with theoretical spectra
Hi, I am a theoretical chemistry PhD student working on fitting experimental spectra with computed spectra in order to get a better understanding of the composition. In the LCF process with athena, I have found that when I allow "sum coefficients to 1", I get an unphysical negative coefficient of the last standard- after reading through the mailing list I understood why, and so no longer use that. The sum of my coefficients during the fitting now is close to 1- generally within the range of 0.95-1.1 at the absolute extremes, but more often around ~0.98- ~1.05. In order to compare these coefficients, I renormalize them to 1, so they can represent the fractions of each component present. However, to test this I took the new normalized coefficients and summed up the standards with their respective weights to create this normalized "fit", and found that it is worse than the initial one. Is this something I should be concerned about when reporting the qualitative trends in how the composition changes? And if so, is there a better way to do the fits in a more normalized way? Many thanks, Patricia ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Ifeffit Digest, Vol 217, Issue 6
Dear Valerie Sorry! I don't know where I got the idea that it was Fe, I was probably working on Fe data at the time of writing. Having looked back I can see Mo. "I am using Larch XAS Viewer for the first time to analyze some Mo XANES data. It is fairly straightforward, however I am running into problems with energy calibration, which leads to problems with Linear Combination Fitting." For Mo I also have some standards, maybe these would be helpful for you. These are all calibrated with the first derivative of the Mo foil and so are consistent with each other. Although measured on a different monochromator, the likely would serve well to compare the edge position to make sure the calibration is done consistently for the standards you have from the canadian light source to give some idea of if things are reliable. Si(111): Mo MoO2 MoO3 Fe2Mo3O12 Mo2C NiMoO4 Adam __ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.cl...@psi.ch From: Ifeffit on behalf of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: Tuesday, March 9, 2021 7:00:01 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 6 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Re. Larch Energy Calibration (Mangold, Stefan (IPS)) 2. Re: Larch Energy calibration (Matt Newville) -- Message: 1 Date: Tue, 9 Mar 2021 11:20:38 + From: "Mangold, Stefan (IPS)" To: "Schoepfer, Valerie" Cc: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Re. Larch Energy Calibration Message-ID: <45116d6c-9314-4822-8e1b-7fb929333...@kit.edu> Content-Type: text/plain; charset="utf-8" Dear Valerie, The reason why I'm currently not using Larch for my data-evaluation chain is, that I didn?t found some features (like energy calibration; not as I use it; like Calibration of references, absorption and fluorescence spectra in one group) in Larch, which I need for my data evaluation process. They might be there, but I didn?t found them. for the XANES data evaluation your energy region might be a bit to short to fit a good background to the data. Anyway you have to fine-tune the parameters to reach a good background fit in the XANES region. While the automatic process in Athena produces quite good results for a lot of absorption edges, one has to be careful not add artefacts to the data in the XANES. Best regards Stefan > Am 08.03.2021 um 14:17 schrieb Schoepfer, Valerie > : > > Hi Chris and Adam, > > I'm actually looking at Mo, so the energy range is from about 19800 through > 20200 eV on a Si(220) monochromator. (But thank you for your Fe offer!) > The standards seem to be all from the Canadian Light Source, but going as far > back as 2013... > I'm not looking to make the LCF perfect at this point, but it does seem like > the deeper I go, the less confident I am that I have the correct standards. > > I'm doing alright in Athena with respect to the process, its just that I > can't get Larch to align properly. I'll probably just use Athena for data > prep, Larch just seemed nice to learn. > But then in Athena I run into trouble with incorrect standards. One thing > after another, you know? > > Thanks- > Valerie > > -Original Message- > From: Ifeffit On Behalf Of > ifeffit-requ...@millenia.cars.aps.anl.gov > Sent: Thursday, March 4, 2021 12:00 PM > To: ifeffit@millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 217, Issue 3 > > CAUTION: External to USask. Verify sender and use caution with links and > attachments. Forward suspicious emails to phish...@usask.ca > > > Send Ifeffit mailing list submissions to >ifeffit@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-requ...@millenia.cars.aps.anl.gov > > You can reach the person managing the list at >ifeffit-ow...@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: Larch energy calibration (Matt Newville) > > > -- > > Message: 1 >
