Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 13

Hi Bruce, Thank you very much for the effort. jiahui -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 12 December 2012 22:17 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 118, Issue 13 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: How to do with diffraction peak (Bruce Ravel) 2. Re: How to do with diffraction peak (Anatoly I Frenkel) 3. Re: Ifeffit Digest, Vol 118, Issue 6 (Bruce Ravel) 4. Re: How to do with diffraction peak (Dr. Dariusz A. Zaj?c) 5. Re: How to do with diffraction peak (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 12 Dec 2012 13:03:46 -0500 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <8927581.5aRJTKJtsK@lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" On Wednesday, December 12, 2012 09:49:45 AM Matthew Marcus wrote:

Here's one last trick that I used to use when I used a plastic scintillator at NSLS and didn't have a spinner. WARNING - this is painful! I used to tape a piece of Polaroid film to the face of the detector, run through a scan, develop the film, see where the white spots were, and put Pb tape on the detector at those spots. Told you it was painful!

These days, I suspect the painful part is *finding* polaroid film! :) 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ------------------------------ Message: 2 Date: Wed, 12 Dec 2012 18:04:00 +0000 From: Anatoly I Frenkel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <545F89325F51764C902D37B42C9F4D531363A77F@YUWEXCPM12.yuad.uds.yu.edu> Content-Type: text/plain; charset="iso-8859-7" (For masochists only): I still have Matthew's plastic scintillator in my cabinet at the NSLS, so if anyone is willing to try this trick with the original hardware, let me know. Anatoly ________________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Matthew Marcus [mamarcus@lbl.gov] Sent: Wednesday, December 12, 2012 12:49 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] How to do with diffraction peak Here's one last trick that I used to use when I used a plastic scintillator at NSLS and didn't have a spinner. WARNING - this is painful! I used to tape a piece of Polaroid film to the face of the detector, run through a scan, develop the film, see where the white spots were, and put Pb tape on the detector at those spots. Told you it was painful! Aside from that, I think Bruce is right - you're screwed with 1-channel data, especially if the Bragg peaks are broad and/or come in the XANES region. If you have to take data without a spinner or multi-element detector, the trial-and-error method of changing the sample orientation often works to shift the Bragg peaks away from sensitive parts of the spectrum to where you don't mind too much losing some points. I have never tried fitting peak shapes to the Bragg peaks (say, a Lorentzian or pseudo-Voight plus a smooth polynomial; don't subtract the polynomial). I suspect that the peak shapes aren't 'nice' enough for that to work reliably. The shapes of the tails, for instance, would be influenced by the angular divergence of the beam onto the sample and into the monochromator and any strain. mam On 12/12/2012 7:28 AM, Bruce Ravel wrote:

On Tuesday, December 11, 2012 04:08:03 PM Zhaomo Tian wrote:

...

I got XAFS data for Ag with CO adsorption( using Ag K edge), Ag is thin film~300nm deposited on Si/SiO2 substrate. But in the original ?(E) spectra, from 25894-26044eV, four obvious diffraction peaks appear( I attached the file), and I guess they will influence the quality of fitting. Is there anyone who knows how to deal with these diffraction peak? Will it be corrected by smoothing or changing some origin data points in the original file? I want the modification that will not destroy data analysis later.

You have received some decent advice on how to post-process your data to minimize the effect of the diffraction peak. I think it bears mentioning that not all prblems are best solved after the fact in software. Some problems should be addressed as the data are measured or even beforehand.

I see from the data file you sent that you were at beamline 10C at Pohang. It is hard to tell for certain from the data file or from the website, but it seems as though you were using a PIPS detector to measure your fluorescence XAFS.

This is an experimental setup can be a difficult one to combine with a sample that diffracts. The sort of PIPS commonly used at an XAS beamline tends to be of a very large surface area. That means that the likelihood of some diffraction peak from the sample hitting the detector during the measurement is pretty high. In fact, it happened 4 times for you. That means you have a lot of data points to deglitch, were you to follow Kicaj's advice. Because you used a PIPS rather than a multi-element detector, you don't have the option of following any of Matthew's (excellent) advice.

I hate to say it, but I think you are screwed. The best you can do is deglitch as best you can. Because you will be removing so many points from the data, you will introduce substantial systematic error into the data set that remains. I don't really see what you can do about that at this late date.

So, what might you do the next time you visit the synchrotron to obtain better data? In fact, there are number of things that you can consider at the stages of sample preparation or of data collection.

1. You don't say a lot about the sample or its substrate. Perhaps you have a reason that the substrate *must* be crystalline. Perhaps not. Putting your film on an amorphous substrate would obviate the problem of diffraction from the substrate. That may be your best bet.

2. The large size of the PIPS detector is a contributing factor to the problem. Simply using a detector with a smaller surface area reduces (but certainly does not eliminate!) the likelihood of diffraction peaks hiiting it. Moving the detector farther away from the sample would serve the same purpose. Of course, doing so would also serve to reduce your count rate, thus reducing the quality of your data. There is a cost to everything!

3. Use the 13 element Ge detector instead of the PIPS. Then you can simply eliminate channels hit by Bragg peaks or do the post-processing trick Matthew described.

4. At my beamline, we have users almost every cycle who measure stuff on crystalline substrates. Our favorite trick is to mount the sample on a spinner (e.g. http://dx.doi.org/10.1063/1.1147815) At my beamline, we actually attach the sample the sort of small DC fan that is used to cool electronics. Inexpensive, simple, and effective! By keeping the sample constantly in motion, the energy at which the Bragg condition is met is constantly changing. This serves to reduce the effect of the Bragg peak by a few orders of magnitude by spreading it out in energy. Usually, it can be made smaller than chi(k), resulting in analyzable data.

The bottom line is that you have the sort of problem that I think needs to be solved up front rather than after the fact.

I know that's not helpful right now, but hopefully it will be the next time you go to the beamline.

Cheers, B

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ Message: 3 Date: Wed, 12 Dec 2012 13:53:23 -0500 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6 Message-ID: <2296463.dEQb5rDBsc@lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" Jiahui, Thanks again for the bug report. Your CIF file exposed a rather subtle bug in the code that parses CIF files. It will be fixed in the next release -- hopefully before the end of the month. Cheers, B On Monday, December 10, 2012 11:16:14 PM jiahui wrote:

Hi Bruce,

I am a windows user. The two log file(Artemis and Atoms) and one of the CIF files I used are attached to this email. Please let me know if you need more information,

Hi Dan,

I use Mercury to open the CIF file then save as another CIF file as you suggested. The new CIF file can be read by (D)Artemis with an warning message basically says there're some problem with this file and some possible ways to solve the problem(s).

I actually went to download an old version of IFEFFIT: Ifeffit 1.2.11. This version can read the CIF files. I ran atoms and FIFF on it. Then save the file. It could be opened by (D)Artemis without problem.

Thank you very much for your help and solutions,

Jiahui

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 10 December 2012 18:00 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 118, Issue 6

Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov

To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request@millenia.cars.aps.anl.gov

You can reach the person managing the list at ifeffit-owner@millenia.cars.aps.anl.gov

When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..."

Today's Topics:

1. Help: Artemis closes without error message when open .cif file (jiahui) 2. Re: Help: Artemis closes without error message when open .cif file (Bruce Ravel) 3. Re: Help: Artemis closes without error message when open.cif file (Daniel Whittaker)

----------------------------------------------------------------------

Message: 1 Date: Mon, 10 Dec 2012 15:42:27 -0000 From: "jiahui" To: Subject: [Ifeffit] Help: Artemis closes without error message when open .cif file Message-ID: <50c602e5.424cb40a.0dd5.42e3@mx.google.com> Content-Type: text/plain; charset="us-ascii"

Dear list,

I am having this problem when I try to open the crystal structure file in .cif format. I've tried many times already--each time when I try to open the crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will close by themselves without any error message. What can I do to solve this problem and carry on with my work? I am using Demeter 0.9.13 version.

Thank you very much for your help,

[jiahui]

------------------------------

Message: 2 Date: Mon, 10 Dec 2012 10:48:21 -0500 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Help: Artemis closes without error message when open .cif file Message-ID: <61620056.C2dlAnbQpv@lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii"

Jiahui,

It would be helpful to me to see an example of a CIF file that triggers this problem. If you are running on Windows, then I would also like to see the contents of the %APPDATA%\demeter\dartemis.log file. See

http://bruceravel.github.com/demeter/pods/bugs.pod.html

If you are a linux user, I would need to see the messages sent to the terminal, which requires running the program from the terminal rather from some launcher widget.

As I have said many times before on this mailing list, CIF support is rather weak at this time. I am using a CIF parsing tool written by someone else and it has its problems. That said, as people report these problems, I am able to build more smarts into Demeter so that it at least deals gracefully with a CIF file it doesn't understand.

Cheers, B

On Monday, December 10, 2012 03:42:27 PM jiahui wrote:

...

Dear list,

I am having this problem when I try to open the crystal structure file in .cif format. I've tried many times already--each time when I try to open the crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will close by themselves without any error message. What can I do to solve this problem and carry on with my work? I am using Demeter 0.9.13 version.

Thank you very much for your help,

[jiahui]

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

Dear list,

I am having this problem when I try to open the crystal structure file in .cif format. I've tried many times already--each time when I try to open the crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will close by themselves without any error message. What can I do to solve this problem and carry on with my work? I am using Demeter 0.9.13 version.

Thank you very much for your help,

[jiahui]

_______________________________________________ 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 Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ------------------------------ Message: 4 Date: Wed, 12 Dec 2012 23:09:29 +0100 From: "Dr. Dariusz A. Zaj?c" To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <50C90099.902@ifj.edu.pl> Content-Type: text/plain; charset=UTF-8; format=flowed W dniu 12-12-12 18:49, Matthew Marcus pisze:

I have never tried fitting peak shapes to the Bragg peaks (say, a Lorentzian or pseudo-Voight plus a smooth polynomial; don't subtract the polynomial). I have never tried too, simply I took care of data during experiment, as is mentioned in posts before. And I suppose it would be very painful, more than Pb tape... Anyway - good ideal with this Pb tape.

coming back to the problem with Bragg peaks, does anyone knows if it is possible to analyse EXAFS with more than 1 interest regions? like 2 or more FT windows - before, between and after Bragg peaks, or is possible to introduce one own FT window function in Athena? regards kicaj ------------------------------ Message: 5 Date: Wed, 12 Dec 2012 17:16:35 -0500 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <1733074.77ouYmhRdV@lachesis.bnl.gov> Content-Type: text/plain; charset="utf-8" On Wednesday, December 12, 2012 11:09:29 PM Dr. Dariusz A. Zaj?c wrote:

coming back to the problem with Bragg peaks, does anyone knows if it is possible to analyse EXAFS with more than 1 interest regions? like 2 or more FT windows - before, between and after Bragg peaks, or is possible to introduce one own FT window function in Athena?

Interesting question. Some days I really love this mailing list. A similar question came up recently on the mailing list, although I think here you are asking whether regions can be chosen in k-space. (The previous discussion was about regions in R space.) I am commenting off the top of my head here, so I may be neglecting something. But I think what you are suggesting to have a windowing function that goes up, then down, then up again, then down again. I think the problem with that is that it would introduce low frequency components into the transformed data. Granted, the transform of the theory would have the same effect, but I worry about how that kind of windowing function would be correlated with the parameters of the fit. As Scott suggested in the earlier conversation, another option is to do a multiple data set fit where the data is imported twice. For one instance of the data, the FT window is set over the first range. For the other instance, the window is set over the second range. Again, I worry about how the choice of windows may be correlated with the parameters of the fit, given the limited information content used in each part of the MDS fit. I don't plan on exploring this myself. But if someone wanted to do so and attempt to convince me that it should be implemented in the software, I am -- as always -- willing to listen. Cheers, 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 118, Issue 13 ****************************************