RE: [Ifeffit] delR and delE
Ritika, delr and Eo are correlated. So you can (1) force delr to the same for two paths with different Eo-values, or (2) use two different delr-values with one Eo-value. Most prefer the second choice over the second choice. Also, Eo is important at low k-values. If you move your k-range that you use in the FT of your data you might find a different Eo value, or that only one Eo is needed with a shorter k-range than with a longer k-range. I do not think that you model is "okay" with three Eo values. How much does EO differ? Usually Eo is the last button I turn on when I try to make a model fit the data. Large Ezero values (> 10 eV) are common if you have a poor model. So use only one Eo at the beginning. Often I just set it to zero, and then when the model gets close, try to add one or two more to really get it right on. I would try only one Eo first. Let delr vary for all the paths and change the k-range. See how small the k-range needs to be before you can fit the data with only one E0 value. 1.9 Angstroms is a short distance. It would seem more reasonable to me that you might need two Eo values. One for this short shell and then one more for all the other shells. Give these things a try and tell us how it goes. Shelly
-----Original Message----- From: ritika.uppal@yale.edu [mailto:ritika.uppal@yale.edu] Sent: Wednesday, October 13, 2004 2:50 PM To: Segre, Carlo U.; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] delR and delE
I have 3 different values of Eo for the fit. 2 for the first shell and the 3rd for the rest of the paths. Actually the bond distance of the 6 oxygens in the first shell differs. 3 of them have a bond length of around 1.9 A and the other 3 around 2.2 A. So using one value of Eo does not fit the second peak very well.
Ritika
Quoting "Carlo U. Segre"
: delR is just the deviation from the distance you used in
the feff.inp
file to generate the paths. It can be positive or negative depending on
whether these atoms are closer or further away from the central atom.
By delE, do you mean Eo? When you say two values, do you mean different values for two different shells? Carlo
On Wed, 13 Oct 2004, ritika.uppal@yale.edu wrote:
Hi guys, I have a few questions about the fitting parameters. the delR for my fit has a negative value. Is that wrong or its possible to have a negative value?? and also for the first shell, I have 2 values of del E. Does that mean that the model I am using is not a good one??
Thanks for all your help Ritika _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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Shelly, thanks for the suggestions. I'll try these.
Ritika
Quoting "Kelly, Shelly D."
Ritika,
delr and Eo are correlated. So you can (1) force delr to the same for two paths with different Eo-values, or (2) use two different delr-values with one Eo-value. Most prefer the second choice over the second choice.
Also, Eo is important at low k-values. If you move your k-range that you use in the FT of your data you might find a different Eo value, or that only one Eo is needed with a shorter k-range than with a longer k-range.
I do not think that you model is "okay" with three Eo values. How much does EO differ? Usually Eo is the last button I turn on when I try to make a model fit the data. Large Ezero values (> 10 eV) are common if you have a poor model. So use only one Eo at the beginning. Often I just set it to zero, and then when the model gets close, try to add one or two more to really get it right on.
I would try only one Eo first. Let delr vary for all the paths and change the k-range. See how small the k-range needs to be before you can fit the data with only one E0 value.
1.9 Angstroms is a short distance. It would seem more reasonable to me that you might need two Eo values. One for this short shell and then one more for all the other shells.
Give these things a try and tell us how it goes.
Shelly
-----Original Message----- From: ritika.uppal@yale.edu [mailto:ritika.uppal@yale.edu] Sent: Wednesday, October 13, 2004 2:50 PM To: Segre, Carlo U.; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] delR and delE
I have 3 different values of Eo for the fit. 2 for the first shell and the 3rd for the rest of the paths. Actually the bond distance of the 6 oxygens in the first shell differs. 3 of them have a bond length of
around 1.9 A and the other 3 around 2.2 A. So using one value of Eo
does not fit the second peak very well.
Ritika
Quoting "Carlo U. Segre"
: delR is just the deviation from the distance you used in
the feff.inp
file to generate the paths. It can be positive or negative depending on
whether these atoms are closer or further away from the central atom.
By delE, do you mean Eo? When you say two values, do you mean different values for two different shells? Carlo
On Wed, 13 Oct 2004, ritika.uppal@yale.edu wrote:
Hi guys, I have a few questions about the fitting parameters. the delR for my fit has a negative value. Is that wrong or its possible to have a negative value?? and also for the first shell, I have 2 values of del E. Does that mean that the model I am using is not a good one??
Thanks for all your help Ritika _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre _______________________________________________ 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
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi guys, I have another question. I have started from the beginning so that I could follow all of Shelly's suggestions. I also looked up your start guide for artemis fitting in which it says u can click the "fit background" button if u see low R peaks. And then in the end it says to click the "use previous background" button. but I can't seem to find it. Could anyone direct me?? Thanks Ritika
On Thursday 14 October 2004 2:02 pm, ritika.uppal@yale.edu wrote:
I have another question. I have started from the beginning so that I could follow all of Shelly's suggestions. I also looked up your start guide for artemis fitting in which it says u can click the "fit background" button if u see low R peaks. And then in the end it says to click the "use previous background" button. but I can't seem to find it. Could anyone direct me??
That page is rather out of date. The procedure for dealing with the fitted background changed somewhat. Here's the current situation: 1. Co-refine the background by selecting the fit background button. 2. Play around with the value of Rmin to get a good background co-refinement without undue correlations with the fitting parameters. These correlations are reported in the log file. I would say that this procedure helps remove some of the mystery as the "correct" value for Rbkg -- the cutoff in Fourier space between background and data. If the correlations are quite high, that value is probably too high since you may be damaging the data by allowing the spline too much freedom. 3. In the Data menu is an option that says 'Save background subtracted as chi(k)'. This will write a file containing the data with the fitted spline subtracted out to the project space. You will then be offered an opportunity to replace the data with the background subtracted data. 4. Choosing to import the background subtracted data will change the data and unselect the "fit background" button. 5. You can now continue along with your data analysis, using the newly background-subtracted data. 6. If you ever want to return to the non-background-subtracted data, select "Project data -> Import project data" from the File menu. This will open the file selection dialog in the folder where the project's data is stored. You will see the original data along with the background-subtracted data and any other data you might have (at some point) imported into your project. HTH, B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Thanks, Bruce
Ritika
Quoting Bruce Ravel
On Thursday 14 October 2004 2:02 pm, ritika.uppal@yale.edu wrote:
I have another question. I have started from the beginning so that I could follow all of Shelly's suggestions. I also looked up your start guide for artemis fitting in which it says u can click the "fit background" button if u see low R peaks. And then in the end it says to click the "use previous background" button. but I can't seem to find it. Could anyone direct me??
That page is rather out of date. The procedure for dealing with the fitted background changed somewhat. Here's the current situation:
1. Co-refine the background by selecting the fit background button. 2. Play around with the value of Rmin to get a good background co-refinement without undue correlations with the fitting parameters. These correlations are reported in the log file. I would say that this procedure helps remove some of the mystery as the "correct" value for Rbkg -- the cutoff in Fourier space between background and data. If the correlations are quite high, that value is probably too high since you may be damaging the data by allowing the spline too much freedom. 3. In the Data menu is an option that says 'Save background subtracted as chi(k)'. This will write a file containing the data with the fitted spline subtracted out to the project space. You will then be offered an opportunity to replace the data with the background subtracted data. 4. Choosing to import the background subtracted data will change the data and unselect the "fit background" button. 5. You can now continue along with your data analysis, using the newly background-subtracted data. 6. If you ever want to return to the non-background-subtracted data, select "Project data -> Import project data" from the File menu. This will open the file selection dialog in the folder where the project's data is stored. You will see the original data along with the background-subtracted data and any other data you might have (at some point) imported into your project.
HTH, B
-- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642
NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
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participants (3)
-
Bruce Ravel
-
Kelly, Shelly D.
-
ritika.uppal@yale.edu