Extending what Scott said, I find it useful to make the coefficients abs(fracoxide) and abs(1-abs(fracoxide)) to avoid false minima with negative S0^2. mam On 9/4/2021 1:21 PM, Scott Calvin wrote:

Hi Zihao,

Do it by folding the molar ratio in to the amp parameter for each CIF. Of course S02 is part of that parameter, too.

So the amp for PtO2 might be parameterized as S02 * fracoxide and the amp for Pt3Fe as S02 * (1-fracoxide)

You could either assume the S02 is the same for the two phases (as I implicitly did by writing it with only one S02 variable), or you could use a standard for each (from a sample prepared and measured in a similar way) to fix the S02 for each phase.

Best, Scott Calvin Lehman College of the City University of New York

...

On Sep 4, 2021, at 4:02 PM, Zihao Yan wrote:

Dear Ifeffit members:

I have a sample which is a mixture of PtFe and PtO2. In order to do the EXAFS fitting, I imported 2 CIF files on Artemis and generated the following 3 paths: From PtO2: Pt-O @ 2.07 nm From Pt3Fe: Pt-Pt @ 2.736 nm, Pt-Fe @ 2.736 nm Then, I used these 3 bonds to do the fitting as in the online tutorial (which used 1 CIF file). The fitting result is good in terms of R^2 but it is not scientifically correct.

I think I didn't set up a parameter which determines the ratio between CIF(PtO2) and CIF(Pt3Fe). I mean there should be a parameter that regulates how much each CIF contributes to the fitting or the molar ratio between PtO2 and Pt3Fe in my system.

Could someone please give me some suggestions on how to do EXAFS fitting with 2 CIF files? Is there anywhere I can set up the molar ratio between PtO2 and Pt3Fe?

Yours sincerely, Zihao Yan _______________________________________________ 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

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Dear Scott, Matthew and Peng: Thank you so much for your answers! I have a couple of follow up questions: 1) for the CIF(Pt3Fe), there are 2 paths (Pt-Pt and Pt-Fe). Do the 2 paths share the same amplitude as: S02 * (1-fracoxide) ? I attached screenshots of my settings. Could you please take a look? 2) Is there any way to set up constraints on Artemis? For example, I want to set 0 wrote:

Just a quick question. For Zihao' sample, the 1st peak for Pt-O from PtO2 is at 2.07 A and the 2nd peak for Pt-Pt or Pt-Fe from Pt3-Fe is at 2.736 A. If these peaks are at different positions, could we use the molar ratio method to distinguish the contribution from each reference? My understanding is that if two paths contribute to the same peak, then the molar ratio method can be applied. I am not sure if my understanding is right or not.

Best Regards,

Peng Liu

China University of Geosciences

On Sun, Sep 5, 2021 at 5:00 AM Matthew Marcus wrote:

...

Extending what Scott said, I find it useful to make the coefficients abs(fracoxide) and abs(1-abs(fracoxide)) to avoid false minima with negative S0^2. mam

...

Hi Zihao,

Do it by folding the molar ratio in to the amp parameter for each CIF. Of course S02 is part of that parameter, too.

So the amp for PtO2 might be parameterized as S02 * fracoxide and the amp for Pt3Fe as S02 * (1-fracoxide)

You could either assume the S02 is the same for the two phases (as I implicitly did by writing it with only one S02 variable), or you could use a standard for each (from a sample prepared and measured in a similar way) to fix the S02 for each phase.

Best, Scott Calvin Lehman College of the City University of New York

...

On Sep 4, 2021, at 4:02 PM, Zihao Yan wrote:

Dear Ifeffit members:

I have a sample which is a mixture of PtFe and PtO2. In order to do

On 9/4/2021 1:21 PM, Scott Calvin wrote: the EXAFS fitting, I imported 2 CIF files on Artemis and generated the following 3 paths:

...

...

From PtO2: Pt-O @ 2.07 nm From Pt3Fe: Pt-Pt @ 2.736 nm, Pt-Fe @ 2.736 nm Then, I used these 3 bonds to do the fitting as in the online tutorial (which used 1 CIF file). The fitting result is good in terms of R^2 but it is not scientifically correct.

I think I didn't set up a parameter which determines the ratio between CIF(PtO2) and CIF(Pt3Fe). I mean there should be a parameter that regulates how much each CIF contributes to the fitting or the molar ratio between PtO2 and Pt3Fe in my system.

Could someone please give me some suggestions on how to do EXAFS fitting with 2 CIF files? Is there anywhere I can set up the molar ratio between PtO2 and Pt3Fe?

Yours sincerely, Zihao Yan _______________________________________________ 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

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-- Best Regards,

Peng Liu _______________________________________________ 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

Hi Kelly: Thank you so much for your help! I followed your advice and I attached the best 2 fittings I could get. I still cannot eliminate all the error messages. One of the error messages is "sigma2 for "[PtO2] O1.1 " is suspiciously large". Could you please help me take a look at my fitting? Is there any way to fix the errors or are they good to go? Thank you again for your time! SIncerely, Zihao Yan On Tue, Sep 7, 2021 at 11:02 AM Kelly, Shelly D. wrote:

Hi Zihao:

Here is an artemis project file showing how I’d set this up. I put Pt foil data in it, since I don’t have your data.

Kind regards,

Shelly

*From:* Ifeffit *On Behalf Of *Zihao Yan *Sent:* Sunday, September 5, 2021 9:35 PM *To:* XAFS Analysis using Ifeffit *Subject:* Re: [Ifeffit] EXAFS Fitting with 2 CIF files

Dear Scott, Matthew and Peng:

Thank you so much for your answers!

I have a couple of follow up questions:

1) for the CIF(Pt3Fe), there are 2 paths (Pt-Pt and Pt-Fe). Do the 2 paths share the same amplitude as: S02 * (1-fracoxide) ?

I attached screenshots of my settings. Could you please take a look?

2) Is there any way to set up constraints on Artemis? For example, I want to set 0

Thank you again for your help!

Sincerely,

Zihao Yan

On Sun, Sep 5, 2021 at 4:08 AM Peng Liu wrote:

Just a quick question. For Zihao' sample, the 1st peak for Pt-O from PtO2 is at 2.07 A and the 2nd peak for Pt-Pt or Pt-Fe from Pt3-Fe is at 2.736 A.

If these peaks are at different positions, could we use the molar ratio method to distinguish the contribution from each reference?

My understanding is that if two paths contribute to the same peak, then the molar ratio method can be applied.

I am not sure if my understanding is right or not.

Best Regards,

Peng Liu

China University of Geosciences

On Sun, Sep 5, 2021 at 5:00 AM Matthew Marcus wrote:

Extending what Scott said, I find it useful to make the coefficients abs(fracoxide) and abs(1-abs(fracoxide)) to avoid false minima with negative S0^2. mam

On 9/4/2021 1:21 PM, Scott Calvin wrote:

...

Hi Zihao,

Do it by folding the molar ratio in to the amp parameter for each CIF. Of course S02 is part of that parameter, too.

So the amp for PtO2 might be parameterized as S02 * fracoxide and the amp for Pt3Fe as S02 * (1-fracoxide)

You could either assume the S02 is the same for the two phases (as I implicitly did by writing it with only one S02 variable), or you could use a standard for each (from a sample prepared and measured in a similar way) to fix the S02 for each phase.

Best, Scott Calvin Lehman College of the City University of New York

...

On Sep 4, 2021, at 4:02 PM, Zihao Yan wrote:

Dear Ifeffit members:

I have a sample which is a mixture of PtFe and PtO2. In order to do the EXAFS fitting, I imported 2 CIF files on Artemis and generated the following 3 paths: From PtO2: Pt-O @ 2.07 nm From Pt3Fe: Pt-Pt @ 2.736 nm, Pt-Fe @ 2.736 nm Then, I used these 3 bonds to do the fitting as in the online tutorial (which used 1 CIF file). The fitting result is good in terms of R^2 but it is not scientifically correct.

I think I didn't set up a parameter which determines the ratio between CIF(PtO2) and CIF(Pt3Fe). I mean there should be a parameter that regulates how much each CIF contributes to the fitting or the molar ratio between PtO2 and Pt3Fe in my system.

Could someone please give me some suggestions on how to do EXAFS fitting with 2 CIF files? Is there anywhere I can set up the molar ratio between PtO2 and Pt3Fe?

Yours sincerely, Zihao Yan _______________________________________________ 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

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--

Best Regards,

Peng Liu

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