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Ke

Ke Yuan

15 Oct 2014 15 Oct '14

3:27 p.m.

Hello Sin Yuen, Thanks for forwarding me that study materials on E0. I use Athena to find the highest peak on the fist derivative of the spectra and pick that value as E0. I think I did not put E0 above this value. I will try to put it on the high energy side to see what will happen. Tks! Ke

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Pushkar

15 Oct 15 Oct

9:39 p.m.

Dear Ke Is there a reason you use first derivative?? I thought if you take second derivative on Athena and then click find zero and then calibrate that value is the correct way. I am learning XAFS myself for the first time and I am novice too. So may be I make no sense but just want to confirm if I am not doing anything wrong. What's your stake in this?? Pushkar Pushkar Shejwalkar Post-doctoral researcher, JSPS fellow, Catalysis Research Center Hokkaido University, Sapporo Japan-0010020

On १६ ऑक्टो, २०१४, at १२:२७ म.पू., Ke Yuan wrote:

Hello Sin Yuen,

Thanks for forwarding me that study materials on E0.

I use Athena to find the highest peak on the fist derivative of the spectra and pick that value as E0. I think I did not put E0 above this value. I will try to put it on the high energy side to see what will happen.

Tks! Ke

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Carlo Segre

9:55 p.m.

Either way is fine but I would suggest taht you not use the calibrate function, just read off the zero crossing and put it into the E0 location. Calibrate actually shifts the data and that is not necessarily what you want to do, particularly if you are comparing spectra.. Carlo On Thu, 16 Oct 2014, Pushkar wrote:

Dear Ke Is there a reason you use first derivative?? I thought if you take second derivative on Athena and then click find zero and then calibrate that value is the correct way. I am learning XAFS myself for the first time and I am novice too. So may be I make no sense but just want to confirm if I am not doing anything wrong. What's your stake in this?? Pushkar

Pushkar Shejwalkar Post-doctoral researcher, JSPS fellow, Catalysis Research Center Hokkaido University, Sapporo Japan-0010020

...
On १६ ऑक्टो, २०१४, at १२:२७ म.पू., Ke Yuan wrote:

Hello Sin Yuen,

Thanks for forwarding me that study materials on E0.

I use Athena to find the highest peak on the fist derivative of the spectra and pick that value as E0. I think I did not put E0 above this value. I will try to put it on the high energy side to see what will happen.

Tks! Ke

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org

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pushkar shejwalkar

10:17 p.m.

Thanks Carlo for that input. I will keep it in mind. Actually I also have this Eo>10 problem and I was following this dicussion closely. Thanks Ke for raising the problem. I think my problem lies with the 'Not so good modelling of data' as my compounds are Fe(II) based and the local structure of which is not known. These are new compounds. Although, I want to make sure that the basic steps such as E calibration and background removal is done correctly. I am still facing problem with the background removal. How would you know that the RBKG value if set to 1.2 or 1.4 etc is good and the Background removal is ok to use from Athena and take it over to Artemis? are there any set of parameters we should check, that if ok we can consider the BKG removal is good? Thank you everyone in advance for your anticipated help. Pushkar On Thu, Oct 16, 2014 at 6:55 AM, Carlo Segre wrote:

Either way is fine but I would suggest taht you not use the calibrate function, just read off the zero crossing and put it into the E0 location. Calibrate actually shifts the data and that is not necessarily what you want to do, particularly if you are comparing spectra..

Carlo

On Thu, 16 Oct 2014, Pushkar wrote:

Dear Ke

...
Is there a reason you use first derivative?? I thought if you take second derivative on Athena and then click find zero and then calibrate that value is the correct way. I am learning XAFS myself for the first time and I am novice too. So may be I make no sense but just want to confirm if I am not doing anything wrong. What's your stake in this?? Pushkar

Pushkar Shejwalkar Post-doctoral researcher, JSPS fellow, Catalysis Research Center Hokkaido University, Sapporo Japan-0010020

On १६ ऑक्टो, २०१४, at १२:२७ म.पू., Ke Yuan wrote:

...
Hello Sin Yuen,

Thanks for forwarding me that study materials on E0.

I use Athena to find the highest peak on the fist derivative of the spectra and pick that value as E0. I think I did not put E0 above this value. I will try to put it on the high energy side to see what will happen.

Tks! Ke

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,JSPS Fellow Hokkaido University, Sapporo, Japan

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Carlo Segre

11:18 p.m.

Hi Pushkar: There are several ways to work out the best background subtraction besides just increasing Rbkg. Making Rbkg as large as 1.2 or 1.4 is dangerous if you have an Fe-O distance or something equally short. Usually it is unwise to make Rbkg more than 1/2 of the distance to the nearest neighbor. I have sometimes been able to get the same results by cutting down the spline range to a value smaller than the highest value of k that you have in your data set. At the same time, it is usually necessary to cut your Forward FT range down. Another, but less effective parameter to change is the k-weight for background subtraction. Usually 2 is a good value but sometimes either 1 or 3 works better (this has only happened rarely for me). If nothing else works, I sometimes just leave the datqa the way it is and I live with the intensity at low R. The only way to really understand whether you have done it right is to take your model and inspect the results to determine if it makes physical sense. Then you use the same model with data which has been treated a different way to see how consistent your results are. Carlo On Thu, 16 Oct 2014, pushkar shejwalkar wrote:

Thanks Carlo for that input. I will keep it in mind. Actually I also have this Eo>10 problem and I was following this dicussion closely. Thanks Ke for raising the problem. I think my problem lies with the 'Not so good modelling of data' as my compounds are Fe(II) based and the local structure of which is not known. These are new compounds. Although, I want to make sure that the basic steps such as E calibration and background removal is done correctly. I am still facing problem with the background removal. How would you know that the RBKG value if set to 1.2 or 1.4 etc is good and the Background removal is ok to use from Athena and take it over to Artemis? are there any set of parameters we should check, that if ok we can consider the BKG removal is good? Thank you everyone in advance for your anticipated help. Pushkar

On Thu, Oct 16, 2014 at 6:55 AM, Carlo Segre wrote:

...
Either way is fine but I would suggest taht you not use the calibrate function, just read off the zero crossing and put it into the E0 location. Calibrate actually shifts the data and that is not necessarily what you want to do, particularly if you are comparing spectra..

Carlo

On Thu, 16 Oct 2014, Pushkar wrote:

Dear Ke

...
Is there a reason you use first derivative?? I thought if you take second derivative on Athena and then click find zero and then calibrate that value is the correct way. I am learning XAFS myself for the first time and I am novice too. So may be I make no sense but just want to confirm if I am not doing anything wrong. What's your stake in this?? Pushkar

Pushkar Shejwalkar Post-doctoral researcher, JSPS fellow, Catalysis Research Center Hokkaido University, Sapporo Japan-0010020

On १६ ऑक्टो, २०१४, at १२:२७ म.पू., Ke Yuan wrote:

...
Hello Sin Yuen,

Thanks for forwarding me that study materials on E0.

I use Athena to find the highest peak on the fist derivative of the spectra and pick that value as E0. I think I did not put E0 above this value. I will try to put it on the high energy side to see what will happen.

Tks! Ke

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org

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Sin Yuen Chang

16 Oct 16 Oct

6:28 a.m.

Dear Pushkar/Ke, I normally use different e0 values in Athena based on what I want to do: 1. e0 for energy scale calibration A generally accepted method is to use derivatives to match the energy scales, as described in the previous threads. I apply this to a known standard and shift the energy scale of the other spectrum that I want to calibrate by the same extent. 2. e0 in EXAFS modelling After I know that the energy scale I have is correct, then in EXAFS modelling, e0 is now the point where your EXAFS backscattering starts. That's why we are trying to avoid white lines here. It took me some time to figure out that e0 could mean several different things. There is a rich history in IFEFFIT discussion on e0, examples: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-June/011841.html http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-June/011836.html http://cars9.uchicago.edu/pipermail/ifeffit/2004-June/005614.html Best wishes, Sin Yuen -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Carlo Segre Sent: 15 October 2014 22:56 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Ke Either way is fine but I would suggest taht you not use the calibrate function, just read off the zero crossing and put it into the E0 location. Calibrate actually shifts the data and that is not necessarily what you want to do, particularly if you are comparing spectra.. Carlo On Thu, 16 Oct 2014, Pushkar wrote:

Dear Ke Is there a reason you use first derivative?? I thought if you take second derivative on Athena and then click find zero and then calibrate that value is the correct way. I am learning XAFS myself for the first time and I am novice too. So may be I make no sense but just want to confirm if I am not doing anything wrong. What's your stake in this?? Pushkar

Pushkar Shejwalkar Post-doctoral researcher, JSPS fellow, Catalysis Research Center Hokkaido University, Sapporo Japan-0010020

...
On १६ ऑक्टो, २०१४, at १२:२७ म.पू., Ke Yuan wrote:

Hello Sin Yuen,

Thanks for forwarding me that study materials on E0.

I use Athena to find the highest peak on the fist derivative of the spectra and pick that value as E0. I think I did not put E0 above this value. I will try to put it on the high energy side to see what will happen.

Tks! Ke

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org

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Carlo Segre
Ke Yuan
Pushkar
pushkar shejwalkar
Sin Yuen Chang