problem with Athena's E0 !
Hi all, I am using Athena (version: 08.058) to study the changes in the XANES profiles as a function of temperature of an organometallic compound containing Fe. I have a problem with the E0 value suggested by Athena : I noticed that it is not taking the same maximum in the first derivative. I am sending 2 examples of xanes taken at RT ( E0 guessed is 1722.8 eV ) and 10 K (1727.3 eV !), can any one help me please to solve this problem ? should I force athena to take the first maximum at 1722 eV ? I tough that my spectra have been properly calibrated: I first calibrated the iron foil -reference channel (E0=1712 eV) of a sample xanes and then I aligned the rest of the reference channels to that one. I though this was enough to calibrate my data. can you please tell me if my data processing is correct? I need to be sure about the E0 value in order to know the correct shift of the different xanes features as a function of temperature. Also, with a wrong E0 the normalization is not correct...did I miss an important step? I am having hard time with these basic questions...before using linear combination analysis and peak fitting analysis. Of course I have already looked in the IFFEFIT archive, but I did not find such problem. I only found a question about a wrong E0 because taken before the edge which is not my case. Thanks so much for your time, Bahia
Hi Bahia I have opened your file and I see that everything is ok Fe:K edge, reference at 7112 eV and your samples s11 at 7122.8 s32 at 7127 as a maxi of 1st derivative (for s32 is the highest maximum, but I would take 7121.97 as E0) it seams that Fe in your samples is not metallic one... darek
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Arezki, Bahia Sent: Wednesday, July 01, 2009 1:37 PM To: Bruce Ravel; XAFS Analysis using Ifeffit Subject: [Ifeffit] problem with Athena's E0 ! Importance: High
Hi all,
I am using Athena (version: 08.058) to study the changes in the XANES profiles as a function of temperature of an organometallic compound containing Fe. I have a problem with the E0 value suggested by Athena : I noticed that it is not taking the same maximum in the first derivative. I am sending 2 examples of xanes taken at RT ( E0 guessed is 1722.8 eV ) and 10 K (1727.3 eV !), can any one help me please to solve this problem ? should I force athena to take the first maximum at 1722 eV ? I tough that my spectra have been properly calibrated: I first calibrated the iron foil -reference channel (E0=1712 eV) of a sample xanes and then I aligned the rest of the reference channels to that one. I though this was enough to calibrate my data. can you please tell me if my data processing is correct?
I need to be sure about the E0 value in order to know the correct shift of the different xanes features as a function of temperature. Also, with a wrong E0 the normalization is not correct...did I miss an important step?
I am having hard time with these basic questions...before using linear combination analysis and peak fitting analysis. Of course I have already looked in the IFFEFIT archive, but I did not find such problem. I only found a question about a wrong E0 because taken before the edge which is not my case.
Thanks so much for your time,
Bahia
Hi Bruce and Darek, Bruce, thanks for the link, I am the only one here using xanes and athena , I learnt a lot from the Athena user's guide and the data I attached in my e-mail have been processed using the calibration and alignment dialogs and the procedure suggested. So, I was sure that this was enough to set correctly E0. It seems that ATHENA gives a spurious value for E0 (1728 eV for S36 xanes) due to a shoulder in the rising part of the white line which is quite intense at RT (s11) and decreases during the cooling of the sample. So, for s36 xanes at 10 K, ATHENA is simply taking the highest maximum in the 1st derivative which is this time higher in energy than the first one . Darek, thanks a lot for looking in my data and for your comments. Yes, the samples contain Fe2+ ions. cheers, Bahia ----------------------------------------------------------------- ________________________________________ De : ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] de la part de Zajac, Dariusz A. [dariusz.zajac@desy.de] Date d'envoi : mercredi 1 juillet 2009 13:54 À : XAFS Analysis using Ifeffit Objet : Re: [Ifeffit] problem with Athena's E0 ! Hi Bahia I have opened your file and I see that everything is ok Fe:K edge, reference at 7112 eV and your samples s11 at 7122.8 s32 at 7127 as a maxi of 1st derivative (for s32 is the highest maximum, but I would take 7121.97 as E0) it seams that Fe in your samples is not metallic one... darek
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Arezki, Bahia Sent: Wednesday, July 01, 2009 1:37 PM To: Bruce Ravel; XAFS Analysis using Ifeffit Subject: [Ifeffit] problem with Athena's E0 ! Importance: High
Hi all,
I am using Athena (version: 08.058) to study the changes in the XANES profiles as a function of temperature of an organometallic compound containing Fe. I have a problem with the E0 value suggested by Athena : I noticed that it is not taking the same maximum in the first derivative. I am sending 2 examples of xanes taken at RT ( E0 guessed is 1722.8 eV ) and 10 K (1727.3 eV !), can any one help me please to solve this problem ? should I force athena to take the first maximum at 1722 eV ? I tough that my spectra have been properly calibrated: I first calibrated the iron foil -reference channel (E0=1712 eV) of a sample xanes and then I aligned the rest of the reference channels to that one. I though this was enough to calibrate my data. can you please tell me if my data processing is correct?
I need to be sure about the E0 value in order to know the correct shift of the different xanes features as a function of temperature. Also, with a wrong E0 the normalization is not correct...did I miss an important step?
I am having hard time with these basic questions...before using linear combination analysis and peak fitting analysis. Of course I have already looked in the IFFEFIT archive, but I did not find such problem. I only found a question about a wrong E0 because taken before the edge which is not my case.
Thanks so much for your time,
Bahia
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
On Wednesday 01 July 2009 10:08:25 am Arezki, Bahia wrote:
It seems that ATHENA gives a spurious value for E0 (1728 eV for S36 xanes) due to a shoulder in the rising part of the white line which is quite intense at RT (s11) and decreases during the cooling of the sample. So, for s36 xanes at 10 K, ATHENA is simply taking the highest maximum in the 1st derivative which is this time higher in energy than the first one .
I have to object to this characterization. Athena has not done anything "spurious". In fact, in your case, it seems to have behaved exactly as documented. As Jeremy said, it is the responsibility of *you, the user* to correctly process your data. Athena is merely a computer program -- it can offer nothing more than default values and some simple algorithms. Sadly, science is not so simple that it can be done without the attention of a human. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Bruce, I think I was misunderstood, I have nothing against the capabilities of Athena, which I have chosen to use for my xanes processing/analysis and I am happy about that. In fact I only referred to the explanation in the Athena user's guide by telling that my case could be one of those few situations mentioned in the guide where one has to re-consider to the default value [ the human attention :-) ](see the text bellow) . "....There are a few situations where the default algorithm will fail. Very noisy data can result in a spurious identification of «e0». Materials which have two inflections in the edge, such as zero-valent zirconium, might have the wrong inflection chosen. Materials with huge edge peaks, such as K2CrO4 , will have a point in the leading edge of the peak chosen rather than a point in the main edge......" I know that Athena is simply a software and the user is responsible for its use.. As a user, I only needed your help and wanted to know if my data processing was correct. I need to be sure about that in order to do a correct analysis/ interpretation of my results. Once again, sorry for this misunderstanding (I realize just now that I did not chose the right objet name for my e-mail ) and thanks a lot for your help, Bahia ----------------------------------------------------------------- ________________________________________ De : ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] de la part de Bruce Ravel [bravel@bnl.gov] Date d'envoi : mercredi 1 juillet 2009 16:42 À : XAFS Analysis using Ifeffit Objet : Re: [Ifeffit] RE : problem with Athena's E0 ! On Wednesday 01 July 2009 10:08:25 am Arezki, Bahia wrote:
It seems that ATHENA gives a spurious value for E0 (1728 eV for S36 xanes) due to a shoulder in the rising part of the white line which is quite intense at RT (s11) and decreases during the cooling of the sample. So, for s36 xanes at 10 K, ATHENA is simply taking the highest maximum in the 1st derivative which is this time higher in energy than the first one .
I have to object to this characterization. Athena has not done anything "spurious". In fact, in your case, it seems to have behaved exactly as documented. As Jeremy said, it is the responsibility of *you, the user* to correctly process your data. Athena is merely a computer program -- it can offer nothing more than default values and some simple algorithms. Sadly, science is not so simple that it can be done without the attention of a human. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Athena attempts to find a reasonable Eo to make it faster for you to look at your data. After that, it is your responsibility to tell Athena what Eo value to use, and not the other way around. Some tools are provided to make it easier to choose consistent values, particularly in the data-calibrate tab. Also be aware that several selections in the settings-preferences tab affect Athena's initial guess for Eo. Jeremy Kropf
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Arezki, Bahia Sent: Wednesday, July 01, 2009 6:37 AM To: Bruce Ravel; XAFS Analysis using Ifeffit Subject: [Ifeffit] problem with Athena's E0 ! Importance: High
Hi all,
I am using Athena (version: 08.058) to study the changes in the XANES profiles as a function of temperature of an organometallic compound containing Fe. I have a problem with the E0 value suggested by Athena : I noticed that it is not taking the same maximum in the first derivative. I am sending 2 examples of xanes taken at RT ( E0 guessed is 1722.8 eV ) and 10 K (1727.3 eV !), can any one help me please to solve this problem ? should I force athena to take the first maximum at 1722 eV ? I tough that my spectra have been properly calibrated: I first calibrated the iron foil -reference channel (E0=1712 eV) of a sample xanes and then I aligned the rest of the reference channels to that one. I though this was enough to calibrate my data. can you please tell me if my data processing is correct?
I need to be sure about the E0 value in order to know the correct shift of the different xanes features as a function of temperature. Also, with a wrong E0 the normalization is not correct...did I miss an important step?
I am having hard time with these basic questions...before using linear combination analysis and peak fitting analysis. Of course I have already looked in the IFFEFIT archive, but I did not find such problem. I only found a question about a wrong E0 because taken before the edge which is not my case.
Thanks so much for your time,
Bahia
Jeremy, Thanks for your fast reply ! Actually I have used the data-calibrate tab to calibrate the reference channels. I will check the settings-preferences. thanks, Bahia ----------------------------------------------------------------- Dr. Bahia Arezki + UNIVERSITÄT SIEGEN FB7- Festkörperphysik Emmy-Noether-Campus, 57072 Siegen ( +49 2 71/ 740-3713 Ê +49 2 71/ 740-3763 Room ENC- B012 . bahia.arezki@uni-siegen.de web-site: www.fkp-siegen.de ----------------------------------------------------------------- ________________________________________ De : ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] de la part de Kropf, Arthur Jeremy [kropf@anl.gov] Date d'envoi : mercredi 1 juillet 2009 14:07 À : XAFS Analysis using Ifeffit Objet : Re: [Ifeffit] problem with Athena's E0 ! Athena attempts to find a reasonable Eo to make it faster for you to look at your data. After that, it is your responsibility to tell Athena what Eo value to use, and not the other way around. Some tools are provided to make it easier to choose consistent values, particularly in the data-calibrate tab. Also be aware that several selections in the settings-preferences tab affect Athena's initial guess for Eo. Jeremy Kropf
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Arezki, Bahia Sent: Wednesday, July 01, 2009 6:37 AM To: Bruce Ravel; XAFS Analysis using Ifeffit Subject: [Ifeffit] problem with Athena's E0 ! Importance: High
Hi all,
I am using Athena (version: 08.058) to study the changes in the XANES profiles as a function of temperature of an organometallic compound containing Fe. I have a problem with the E0 value suggested by Athena : I noticed that it is not taking the same maximum in the first derivative. I am sending 2 examples of xanes taken at RT ( E0 guessed is 1722.8 eV ) and 10 K (1727.3 eV !), can any one help me please to solve this problem ? should I force athena to take the first maximum at 1722 eV ? I tough that my spectra have been properly calibrated: I first calibrated the iron foil -reference channel (E0=1712 eV) of a sample xanes and then I aligned the rest of the reference channels to that one. I though this was enough to calibrate my data. can you please tell me if my data processing is correct?
I need to be sure about the E0 value in order to know the correct shift of the different xanes features as a function of temperature. Also, with a wrong E0 the normalization is not correct...did I miss an important step?
I am having hard time with these basic questions...before using linear combination analysis and peak fitting analysis. Of course I have already looked in the IFFEFIT archive, but I did not find such problem. I only found a question about a wrong E0 because taken before the edge which is not my case.
Thanks so much for your time,
Bahia
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
From the Athena User's Guide:
http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/params/e0.html B On Wednesday 01 July 2009 07:36:47 am you wrote:
Hi all,
I am using Athena (version: 08.058) to study the changes in the XANES profiles as a function of temperature of an organometallic compound containing Fe. I have a problem with the E0 value suggested by Athena : I noticed that it is not taking the same maximum in the first derivative. I am sending 2 examples of xanes taken at RT ( E0 guessed is 1722.8 eV ) and 10 K (1727.3 eV !), can any one help me please to solve this problem ? should I force athena to take the first maximum at 1722 eV ? I tough that my spectra have been properly calibrated: I first calibrated the iron foil -reference channel (E0=1712 eV) of a sample xanes and then I aligned the rest of the reference channels to that one. I though this was enough to calibrate my data. can you please tell me if my data processing is correct?
I need to be sure about the E0 value in order to know the correct shift of the different xanes features as a function of temperature. Also, with a wrong E0 the normalization is not correct...did I miss an important step?
I am having hard time with these basic questions...before using linear combination analysis and peak fitting analysis. Of course I have already looked in the IFFEFIT archive, but I did not find such problem. I only found a question about a wrong E0 because taken before the edge which is not my case.
Thanks so much for your time,
Bahia
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
participants (4)
-
Arezki, Bahia -
Bruce Ravel -
Kropf, Arthur Jeremy -
Zajac, Dariusz A.