Sorry that I did not explain that clearly. Matt Newville's interpretation is correct. Ellen

On Jul 20, 2015, at 19:41, Matt Newville wrote:

I think Ellen wants to first do a linear combination fit with chi(k) data and then look at what that combination of spectral components would look like for the XANES region. It seems like a fine idea to me.

Off the top of my head I don't know the easiest way to do this. I don't think there is a single button for that, but I've been known to miss hidden features in Athena for years.

--Matt

...

On Jul 20, 2015 8:16 PM, "Scott Calvin" wrote: Hi Ellen,

Either I’m not understanding what you’re trying to do, or what you’re trying to do doesn’t make sense.

XANES is generally plotted as mu(E) or norm(E). To get from norm(E) to chi(k), two things must be done: a smooth background must be subtracted from norm(E), and E has to be converted to k. The conversion from E to k is reversible, but the background subtraction is not, since chi(k) is meant to be background independent. You therefore cannot, in principle, plot chi(k) data as norm(E).

—Scott Calvin Sarah Lawrence College

...

On Jul 20, 2015, at 7:48 PM, Ellen Daugherty wrote:

Hello,

I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: "chi data cannot be plotted in energy." Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue.

Thank you!

Ellen

-- Ph.D. Candidate Research Assistant, Borch Lab Department of Chemistry Colorado State University http://borch.agsci.colostate.edu/group-members/ellen-daugherty/ _______________________________________________ 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

Leslie had a good suggestion. That would, I think, be close to what you want. There is not a button to automate exactly what you want -- not even one that I've been hiding from Matt all these years. Another way of doing what you want would be to jot down the best fit values for the weights, then use the data summation tool (http://bruceravel.github.io/demeter/aug/process/sum.html) to make that sum of norm(E) spectra. These is no automated interaction between these tools, so you'll have to do the tedious work of setting things up in the summation tool. Another idea would be to jot down the best fit value, then mark the data group and the groups used as the fitting standards, then select "Save marked groups as ... norm(E)" from the File menu. Import that file into Excel or whatever and use the weights you jotted down. Again, there is no automation to do this. That said, "plot this result in norm(E) for a fit in chi(k)" is a good and useful idea. I'll put it on my to do list. B On 07/20/2015 10:09 PM, Ellen Daugherty wrote:

Sorry that I did not explain that clearly. Matt Newville's interpretation is correct.

Ellen

On Jul 20, 2015, at 19:41, Matt Newville mailto:newville@cars.uchicago.edu> wrote:

...

I think Ellen wants to first do a linear combination fit with chi(k) data and then look at what that combination of spectral components would look like for the XANES region. It seems like a fine idea to me.

Off the top of my head I don't know the easiest way to do this. I don't think there is a single button for that, but I've been known to miss hidden features in Athena for years.

--Matt

On Jul 20, 2015 8:16 PM, "Scott Calvin" mailto:scalvin@sarahlawrence.edu> wrote:

Hi Ellen,

Either I’m not understanding what you’re trying to do, or what you’re trying to do doesn’t make sense.

XANES is generally plotted as mu(E) or norm(E). To get from norm(E) to chi(k), two things must be done: a smooth background must be subtracted from norm(E), and E has to be converted to k. The conversion from E to k is reversible, but the background subtraction is not, since chi(k) is meant to be background independent. You therefore cannot, in principle, plot chi(k) data as norm(E).

—Scott Calvin Sarah Lawrence College

...

On Jul 20, 2015, at 7:48 PM, Ellen Daugherty mailto:ellen.daugherty@colostate.edu> wrote:

Hello,

I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: "chi data cannot be plotted in energy." Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue.

Thank you!

Ellen

-- Ph.D. Candidate Research Assistant, Borch Lab http://borch.agsci.colostate.edu/ Department of Chemistry Colorado State University http://borch.agsci.colostate.edu/group-members/ellen-daugherty/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto: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

-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

Thank you, all, for your responses. I think Leslie's suggestion will do the trick for now. I did not realize that changing the fitting space post-fitting would allow me to plot the fit differently. Thanks again! Ellen On Tue, Jul 21, 2015 at 7:01 AM, Bruce Ravel wrote:

On 07/21/2015 08:52 AM, Bruce Ravel wrote:

...

That said, "plot this result in norm(E) for a fit in chi(k)" is a good and useful idea. I'll put it on my to do list.

So is "plot in chi(k) for this fit in norm(E)", for that matter.

B

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973

Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit