Re: [Ifeffit] Self absorption Correction

[Richard Mayes]

Farzana,

I'm copying the IFEFFIT mail list, they may have the information buried in
the archives somewhere.

That link points to Grant Bunker's webpage containing his XAFS tutorials
and it will not open for me at the moment either. However, there are
several very good books that have come out lately on XAFS that explain self
absorption quite well.  If you're not interested in getting a copy of the
books, there is a discussion thread from when I was a newbie to
overabsorption that is found on the XAFS.org tutorials page.  I suggest
going through it as several contributed substantial knowledge in that
thread (http://www.xafs.org/Experiment/OverAbsorption).

Cheers,
-Rich

On Mon, May 4, 2015 at 7:47 PM, Farzana Nasreen 
wrote:

> Dear Rich,
>
> http://cars9.uchicago.edu/pipermail/ifeffit/2009-February/008631.html
>
> I was looking at this above link to find out similar information that Jen
> had. Unfortunately, I couldn't open the link in the reply that you gave to
> her.
> Do you know where I can download this paper by
>
> *http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf 
> *
>
> I am working on some PFY-XAS data on some uranium compounds.
>
> Thanks
>
> Farzana
>
>
>
>
>
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Re: [Ifeffit] plots from athena

[Richard Mayes]

I thought PGPlot was the graphics part of the IFEFFIT suite, I could have
been wrong.  I was referring to the window where the plots are shown when
Athena and/or Artemis is used.

If I'm understanding you correctly, I think it can be done by simply
clicking the checkbox beside the file if in Athena and then clicking the
appropriate button to show the fits (if in Artemis, if I remember correctly,
you highlight the appropriate files and click the appropriate button to show
the plots).


HTH,
-Rich

On Mon, May 31, 2010 at 6:50 PM, Saugata Datta wrote:

>
> Hello, if you can help me with this question:
>
> I am trying to plot directly from athena via powerpoint for a
> publication/manuscript quality plot., I read a message posted that " "If you
> want to adjust things like fonts and line sizes on the plot for publication,
> then you have the option to save the plot as a metafile from the PGPlot
> window and import it into PowerPoint.  Then convert the metafile into a
> drawing object with the "ungroup" feature.  From this point you can change
> fonts, line shapes, colors, etc. to get the plot how you want it to look for
> publication.  You can then re-save that slide as a picture (gif, tiff,
> metafile, etc) to be imported into the manuscript.  This can get time
> intensive, but it's an alternative if all you want to do is adjust fonts and
> line colors/sizes. One caveat though, don't change the data!  You can easily
> and unknowingly change the data if you're not careful (performing an action
> on one part of the drawing object without realizing another is highlighted
> for example) so always compare the final product to the original to make
> sure it's the same"...
>
> But I cannot find where the PGPlot window is., if you can kindly help.
>
>
> Say I want to plot six standards plotted /stacked one on top of the other
> in one figure, with correct seuqnce of legend? Can I do this without
> exporting to excel???
>
>
> Thanks again...
> Saugata
>
>
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Re: [Ifeffit] Exporting derivative data

[Richard Mayes]

Paul,

If you're just wanting to adjust things like fonts and line sizes on the
plot for publication, then you have the option to save the plot as a
metafile from the PGPlot window and import it into PowerPoint.  Then convert
the metafile into a drawing object with the "ungroup" feature.  From this
point you can change fonts, line shapes, colors, etc. to get the plot how
you want it to look for publication.  You can then re-save that slide as a
picture (gif, tiff, metafile, etc) to be imported into the manuscript.  This
can get time intensive, but it's an alternative if all you want to do is
adjust fonts and line colors/sizes.

One caveat though, don't change the data!  You can easily and unknowingly
change the data if you're not careful (performing an action on one part of
the drawing object without realizing another is highlighted for example) so
always compare the final product to the original to make sure it's the same.

-Rich

On Sun, May 30, 2010 at 6:47 AM, Paul Bingham
wrote:

> Hi, I wonder if you can help:
>
> I'm using Athena to process some XANES data and wish to export the
> derivative
> data so that I can use a package such as Excel to prepare the data for
> publication. However, the derivative data that is presented visually in the
> graphics window is a much cleaner, smoother data set than the one I get
> when I
> export it in either deriv Mu(E) or deriv Norm(E). I tried the smoothing
> option
> in Data-Smooth mu(E) with 3 iterations and again with 10 iterations on the
> interpolative smoothing. Both gave far noisier data than the data shown in
> the
> Graphics window.
>
> Please can you tell me how to get exported derivative data that will be
> (more or
> less) the same as that shown in the graphics window? Basically I' hoping
> for
> WYSIWYG if that's possible? Any thoughts or suggestions would be very
> welcome
> and thanks for your time.
>
> --
> Dr. Paul Bingham
> Postdoctoral Research Associate
> Immobilisation Science Laboratory
> Dept. of Engineering Materials
> University of Sheffield
> Mappin Street
> Sheffield
> S1 3JD
> UK
>
> Email: p.a.bing...@sheffield.ac.uk
> Direct Line: (0114) 2225473
>
>
>
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Re: [Ifeffit] consultation

[Richard Mayes]

Mingliang,

For more information on self-absorption, read the links found here:
http://www.xafs.org/Experiment/OverAbsorption

This includes a link to a discussion on the mail list about self-absorption
and how to understand it.

-Richard

2010/1/29 Welter, Edmund 

> Dear Mingliang,
>
> Thanks for your explain. But I am still puzzled. Following your
>> instruction, I performed *Self-Absorption *for the samples, choosing
>> *XANES(Fluo) *from *algorithm*, but I did not know the real meaning of
>>  *Formula*. Does it mean the species formula which I wish to detect? Or the
>> whole composition of the sample?
>>
> The composition of the whole sample. You do not need to know the species,
> you "only" need to know thew elemental composition of your sample. A hairy
> task if you don't digest your sample completely and put it into an ICP-MS or
> anything like that. I don't know which precision is necessary to yield
> usable results. Maybe someone else tested or calculated it.
> In principle the matrix produces just a smooth background absorption and
> knowing the composition it is easy to calculate the amount of this
> absorption using tabulated scattering factors. But it should also be
> possible to determine this background experimentally, for instance
> extrapolating the background before the edge. But for this you would need a
> blank spectrum to "calibrate" the mued value.
> If you follow the link to the "document section" in Athena a very
> instructive webpage will open and among other things you will find citations
> of the original papers underlying the four different algorithms used for the
> self absorption correction.
>
>
> I used natural mineral to interact with selenite, then I wish to check the
>> speciation of the selenium reaction product. For my case, should I fill the
>> blank with Se or FeSe or both of them (because currently I do not know the
>> exactly containing speciation)?
>>
> As said before, the "chemical Formula" of the entire sample. "Chemical
> formula" here does not mean you have any kind of chemical bond, it just
> means molar ratio.
>
> For the angles, normally are they 45? Becuase I measured the samples in
>> fluorescence mode, and didnot measure the angles between sample, incoming
>> beam and detector. I tried to input *Se *in the *Formula* entry, and select
>> 45 for the angles, then I got a corrected spectra which was higher than the
>> original one.
>>
>
> 45 degrees is the usually used geometry. However, the program asks for the
> geometry which you used not for the usually used geometry! If it was 45
> degrees than its fine. Obviously the algorithm does what it is supposed to
> do, it amplifies the oscillations. But this does not mean that the result is
> correct! It will only be "correct" if the input parameters were correct.
>
> But when I using this spectra for LCF analysis, I still could not got
>> overlapping line for the fitted spectra with the sample spectra...
>>
> Using pure Se in the self absorption correction is definitely wrong, it
> overestimates the effect dramatically. Actually the effect more or less
> disappears for diluted samples. But even if the spectra were properly
> corrected I can not see any reason why the used set of reference spectra
>  MUST fit the spectrum of your sample. There are many possible reasons for
> this, the most likely is that you are missing one or more important
> reference spectrum (Or you are not using enough references/free parameters
> in your fit...;-)
>
> Best regards,
> Edmund Welter
>
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Re: [Ifeffit] (no subject)

[Richard Mayes]

Here's the Penner-Hahn webpage, there is Zn info here, plus contact info and
publication lists:  http://www.umich.edu/~jphgroup/

-Richard






2010/1/19 JeongEunSuk 

>  Thank Anatoly.
> Do you know J.penner-Hahn's e-mail or exact reference name?
> I cant find his paper in search site.
>
> --
> Date: Tue, 19 Jan 2010 20:06:59 -0500
> From: fren...@bnl.gov
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] (no subject)
>
>  There was a paper by J. Penner-Hahn et al. studying ZnCl2 by EXAFS and
> using it to demonstrate the quadrupole (1s-3d) transition by analyzing
> angular dependence of pre-edge features of Zn K-edge. You may contact him
> directly for exact reference.
>
> Anatoly
>
>  --
> *From:* ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of JeongEunSuk
> *Sent:* Tue 1/19/2010 8:01 PM
> *To:* ifeffit@millenia.cars.aps.anl.gov
> *Subject:* [Ifeffit] (no subject)
>
> Hi all
> I have a question for XANES of Zinc compounds.
> It is known that the pre-edge for Zinc k-edge generally doesnt exist
> because 3d state of Zinc atom is occupied.
> However, I got it from ZnMgO with wurtzite structure. 4 oxygen in first
> shell and 12 zinc in second shell are located around Absorbing atom, Zinc in
> wurtzite structure.
> And then I know that some Mg atoms are replaced on zinc site from EXAFS.
> I wonder the reason for the appearence of pre-edge. Is it structural
> problem? or substituted Mg?
> If anybody know reference papers for pre-edge of zinc K-edge, Please answer
> me.
>
>
> --
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Re: [Ifeffit] Reply

[Richard Mayes]

Mingliang,

When I opened the same file from your picture in Sixpack, I get the same
error about the filename characters, but when I click ok to acknowledge the
error, I get the import dialogue and it appears that I would be able to
import the data anyway (and I did not get the error in background function
information that looks like a Python error and suggests things are
missing).

As for the Grnd.exe problem, it sounds like something is getting moved
around or not being copied to your computer during the installation, and
unfortunately I can't help you with that other than to suggest a reinstall.


wish I could be more help, but this is as far as I can go
-Richard

2009/11/12 康明亮 

> Dear Richard,
> Acctually, I opened one of the decompression files from the attached "data
> process.rar" with Sixpack, then I encountered the problem that  *WARNING!
> Filename contain characters not compatible with IFEFFIT.*
> Here, I have snapped each step and attached in the enclosure. Hope I have
> answer these questions.
> Thank you!
> Best regards
> Mingliang
>
>
> 在2009-11-12，"Richard Mayes"  写道：
>
> Are you trying to open the "data process.rar" file (the very same file you
> sent to Matt) with Sixpack?  Athena or Sixpack can not do that, you must
> unpack the file to access the individual files it contains.
>
> To solve the "*Cann't execute Grnd.exe to open the graphics window"*
> problem, follow the suggestions from Matt posted below (which is the initial
> response you recieved from your very first post - read the last sentence
> very closely, that is the question you have yet to answer; without these
> answers no one can help you):
>
> Some suggestions:
>-  Try clicking on "runner.exe" in the Ifeffit bin folder.  A
> simple selection box should pop up and you should be able to choose
> Athena, Artemis, etc.
>-  Trying clicking on GrWnd.exe in the Ifeffit bin folder.  A
> window should pop up.
>-  The installation was not complete, or got moved somehow.
> Reinstalling might help.
> If the solution isn't obvious from those, let us know what happened
> for each of these steps.
>
> 2009/11/11 康明亮 
>
>> Dear Richard,
>> Thanks for your reply.
>> To be honest, I don't know what question she/he has asked. As I have said
>> , I have followed the procedure which she/he suggested. But, I still can't
>> import the raw data for processing. I double clicked* runner.exe*,
>> selected *Sixpack*, entered to the *Samview* interface, clicked *Add file
>> *, and selected a file from the attached, it prompted* WARNING! Filename
>> contain characters not compatible with IFEFFIT.* The* *other function
>> like *Background Removal *is the same case. That's the problem I
>> encountered. As I selected Athena, it prompted: *Cann't execute Grnd.exe
>> to open the graphics window. *I have re-installed the programme, but it
>> still won't work. Since you have said there's nothing wrong with the data,
>> * *I really don't know how to solve this problem.
>> Best regards
>> Mingliang
>>
>>
>> Sorry for the trouble. It's a little hard to tell what's gone wrong,
>> but here are some hints:  The icon to run athena (and others) simply
>> runs the program "runner.exe" in the Ifeffit "bin" folder (usually
>> C:\Program Files\Ifeffit\bin).   This program sets the path and other
>> environmental variables so that GrWnd.exe can be run.
>> Some suggestions:
>>-  Try clicking on "runner.exe" in the Ifeffit bin folder.  A
>> simple selection box should pop up and you should be able to choose
>> Athena, Artemis, etc.
>>-  Trying clicking on GrWnd.exe in the Ifeffit bin folder.  A
>> window should pop up.
>>-  The installation was not complete, or got moved somehow.
>> Reinstalling might help.
>> If the solution isn't obvious from those, let us know what happened
>> for each of these steps.
>>
>>
>>
>> 在2009-11-12，"Richard Mayes"  写道：
>>
>> Mingliang,
>>
>> There's nothing wrong with the data (I opened one of the files), so at
>> this point I suggest you reinstall IFEFFIT, or answer Matt's questions in
>> the hope of understanding and solving your problem (without the re-install).
>>
>> -Richard
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Nov 11, 2009 at 8:22 PM, Matt Newville <
>> newvi...@cars.uchicago.edu> wrote:
>>
>>> > I am not mean you need to help me to process them, I just don't know
>>> why
>>> > these da

Re: [Ifeffit] Reply

[Richard Mayes]

Are you trying to open the "data process.rar" file (the very same file you
sent to Matt) with Sixpack?  Athena or Sixpack can not do that, you must
unpack the file to access the individual files it contains.

To solve the "*Cann't execute Grnd.exe to open the graphics window"*
problem, follow the suggestions from Matt posted below (which is the initial
response you recieved from your very first post - read the last sentence
very closely, that is the question you have yet to answer; without these
answers no one can help you):

Some suggestions:
   -  Try clicking on "runner.exe" in the Ifeffit bin folder.  A
simple selection box should pop up and you should be able to choose
Athena, Artemis, etc.
   -  Trying clicking on GrWnd.exe in the Ifeffit bin folder.  A
window should pop up.
   -  The installation was not complete, or got moved somehow.
Reinstalling might help.
If the solution isn't obvious from those, let us know what happened
for each of these steps.

2009/11/11 康明亮 

> Dear Richard,
> Thanks for your reply.
> To be honest, I don't know what question she/he has asked. As I have said ,
> I have followed the procedure which she/he suggested. But, I still can't
> import the raw data for processing. I double clicked* runner.exe*,
> selected *Sixpack*, entered to the *Samview* interface, clicked *Add file*,
> and selected a file from the attached, it prompted* WARNING! Filename
> contain characters not compatible with IFEFFIT.* The* *other function like
> *Background Removal *is the same case. That's the problem I encountered.
> As I selected Athena, it prompted: *Cann't execute Grnd.exe to open the
> graphics window. *I have re-installed the programme, but it still won't
> work. Since you have said there's nothing wrong with the data,* *I really
> don't know how to solve this problem.
> Best regards
> Mingliang
>
>
> Sorry for the trouble. It's a little hard to tell what's gone wrong,
> but here are some hints:  The icon to run athena (and others) simply
> runs the program "runner.exe" in the Ifeffit "bin" folder (usually
> C:\Program Files\Ifeffit\bin).   This program sets the path and other
> environmental variables so that GrWnd.exe can be run.
> Some suggestions:
>-  Try clicking on "runner.exe" in the Ifeffit bin folder.  A
> simple selection box should pop up and you should be able to choose
> Athena, Artemis, etc.
>-  Trying clicking on GrWnd.exe in the Ifeffit bin folder.  A
> window should pop up.
>-  The installation was not complete, or got moved somehow.
> Reinstalling might help.
> If the solution isn't obvious from those, let us know what happened
> for each of these steps.
>
>
>
> 在2009-11-12，"Richard Mayes"  写道：
>
> Mingliang,
>
> There's nothing wrong with the data (I opened one of the files), so at this
> point I suggest you reinstall IFEFFIT, or answer Matt's questions in the
> hope of understanding and solving your problem (without the re-install).
>
> -Richard
>
>
>
>
>
>
>
> On Wed, Nov 11, 2009 at 8:22 PM, Matt Newville  > wrote:
>
>> > I am not mean you need to help me to process them, I just don't know why
>> > these data can't open in Sixpack or other programm. Is there any problem
>> > with the raw data? Wish to obtain guidance from you.
>>
>> I have not looked at the data you sent.  Did you expect I would?  You
>> have not answered to my original questions.At this point, I want
>> you to tell me why do you keep posting questions to this list when you
>> have not answered the questions in my original reply?
>>
>> Explain this, then answer the original questions, and then we may be
>> able to start helping you.  We will not analyze your data,  and we
>> cannot help you unless you help us understand what does and does not
>> work.
>>
>> --Matt
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>>
>
>
>
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Re: [Ifeffit] Reply

[Richard Mayes]

Mingliang,

There's nothing wrong with the data (I opened one of the files), so at this
point I suggest you reinstall IFEFFIT, or answer Matt's questions in the
hope of understanding and solving your problem (without the re-install).

-Richard







On Wed, Nov 11, 2009 at 8:22 PM, Matt Newville
wrote:

> > I am not mean you need to help me to process them, I just don't know why
> > these data can't open in Sixpack or other programm. Is there any problem
> > with the raw data? Wish to obtain guidance from you.
>
> I have not looked at the data you sent.  Did you expect I would?  You
> have not answered to my original questions.At this point, I want
> you to tell me why do you keep posting questions to this list when you
> have not answered the questions in my original reply?
>
> Explain this, then answer the original questions, and then we may be
> able to start helping you.  We will not analyze your data,  and we
> cannot help you unless you help us understand what does and does not
> work.
>
> --Matt
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Re: [Ifeffit] Plotting Athena mu(E) with pre / post edge lines

[Richard Mayes]

Joseph,

See the FAQ here (scroll down to "How do I make publication quality
plots..."):

http://cars9.uchicago.edu/ifeffit/FAQ/HoraeQuestions#head-2536b76fd9a517c8cff6b367d89e9fd03cbf5999

-Rich

On Tue, Oct 27, 2009 at 6:33 PM, Joseph Washington wrote:

> Hello all,
> How do I export absorption data showing the pre edge, post edge, and
> background function to a text file so I can plot this in origin or excel?
>
> Joseph
> --
> Joseph Washington
> Research Assistant
> Department of Physics
> North Carolina State University
> 431 Riddick Hall
> Raleigh, NC 27695-8202
> email: jswas...@ncsu.edu
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Re: [Ifeffit] Rbkg value

[Richard Mayes]

Chris,

If you look at Shelly Kelly's tutorial on xafs.org, she suggests Rbkg be
"about half the R value for the first peak."  This setting worked well in my
case with vanadyl-silicates where my first feature was around 1.6 A. Her
tutorial also discusses setting Rbkg and what to look for when doing so.

-Richard

On Fri, Oct 23, 2009 at 3:51 PM, Chris Patridge wrote:

>  Hello everyone,
>
>
>
> In removing background, most literature suggests Rbkg value of 1.0 because
> below this represents mostly noise and low freq components not part of the
> scattering effect.  In using Feff and viewing the individual paths
> calculated a number of them have paths near 1.5 A, therefore meaning that
> they have some contributions very close to 1.0 A and below in R space due to
> phase shift.  Has anyone modeled materials which contain these rather short
> Reff and how did you decide what was scattering and noise?
>
>
>
> Thank you all,
>
>
>
>
>
>
>
> Chris Patridge
>
> UB Graduate Student
>
> Department of Chemistry
>
> Cell: 315-529-0501
>
>
>
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Re: [Ifeffit] 8 coordination crystal

[Richard Mayes]

Mohamed,

Are you trying to use the simple first shell analysis or is this from the
feff calculation?  (an example project file to look at would be helpful)

You can find tutorials at
http://www.xafs.org/Tutorialsthat will
guide you through both Athena and Artemis.

-Richard

On Tue, Sep 15, 2009 at 3:24 PM, mohamed sobhy wrote:

>  Dear
> I am trying to simulate CeO2 crystal lattice but I found that in Artemis
> documentations the following
>
> *Currently the following coordination geomatries are available:*
> ** 4-coordinate crystal*
> ** 6-coordinate crystal*
> ** octahedral molecule*
> ** tetrahedral molecule*
> ** square-planar molecule*
> **
> CeO2 has coordination no of 8, so what is the meaning of that
>
> Also is there any manual or working examples for Artemis
>
> Thnaks
>
> Mohamed
>
>
>
>
>
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Re: [Ifeffit] Vanadium pre edge peak contributes to K-space?

[Richard Mayes]

Chris,

You'll answer this question when you post a project file; but since you
mention the pre-edge feature, have you reset the Eo to approx. halfway up
the absorption edge instead of on the pre-edge feature itself?

-Richard

On Tue, Aug 25, 2009 at 11:10 AM, Carlo Segre  wrote:

>
> Hi Chris:
>
> If you could attach an Athena project file, it would help us to answer
> your question.
>
> Carlo
>
> On Tue, 25 Aug 2009, Chris Patridge wrote:
>
> > Hello all,
> >
> > After calibration, alignment and merging V K edge data, there seems to
> > be a large peak in R space below 1 A.  From most examples and readings,
> > this would seem to be noise since atoms do not reside that close to each
> > other.  Adding a background addresses this noise but then the number of
> > variables becomes too large and meaningless to the first shell R space
> > range.  I believe the problem lies with the large pre edge feature seen
> > with high valence state Vanadium compounds.  Any suggestions on how to
> > work through this and make realistic EXAFS analysis on these compounds.
> >
> > Thanks everyone,
> >
> >
>
> --
> Carlo U. Segre -- Professor of Physics
> Associate Dean for Graduate Admissions, Graduate College
> Illinois Institute of Technology
> Voice: 312.567.3498Fax: 312.567.3494
> se...@iit.edu   http://www.iit.edu/~segre   se...@debian.org
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Re: [Ifeffit] Pellet sample preparation

[Richard Mayes]

Dominik,

Boron nitride has been used as a diluent.

You might check Polymer Source (www.polymersource.com) for the polyethylene
you're looking for, however they seem to be quite expensive.  ChemPlex (
www.chemplex.com) also has binders and specializes in products for XRF
analysis.

HTH,
-Richard

On Wed, Aug 19, 2009 at 2:27 PM, Dominik Samuelis wrote:

> Dear list,
>
> for many years, I have used  "Merck Uvasol Polyethylene for
> spectroscopy" PE powder as a diluent and binder for pressing
> self-supporting pellets especially of air-sensitive substances. When I
> today wanted to order a new bottle, I had to learn that it's not
> available anymore (actually, since 2002... :-)).
>
> Does anyone of you know about any other supplier of spectroscopy-grade
> polyethylene powder? And more general, which binder/diluent do you use
> for preparing pellets of sensitive substances ?
>
> Best regards,
> Dominik
>
>
> --
> Dr. Dominik Samuelis
> d.samue...@fkf.mpg.de
> Max-Planck-Institut für Festkörperforschung
> Max Planck Institute for Solid State Research
> Heisenbergstr. 1
> 70569 Stuttgart
> Germany
> Phone +49-711-689-1769
> Fax   +49-711-689-1722
> Web   http://www.fkf.mpg.de/maier/
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Re: [Ifeffit] Kapton in glove box

[Richard Mayes]

Todd,

Are you working with oxygen sensitive or moisture sensitive samples (or
both)?  If it's just moisture sensitive, then you can use regular 2-sided
tape from your local office supply and polypropylene film to seal samples in
polycarbonate or aluminum holders (or even pellets if you're lucky enough to
be able to press pellets that hold their shape).  Chemplex Industries is
where I have gotten the polypropylene films I have used (and Kapton as well
- www.findtape.com also has a good selection of Kapton tape).

I used this method with many samples that involved heavily chlorided
titanium on silica and had few problems if they're used within 5-7 days
after packing in a glove box (the samples with problems resulted from
improperly sealed samples).  You can get jars (baby food jars work very well
to ship individual samples) to store the samples for shipping and if you
pack the jars in the glove box, you will have the box atmosphere in the
jars, for a little while anyway.

A note on oxygen sensitivity (and to an extent moisture sensitivity):  you
probably already know this, but I'll say it anyway...if cardboard is present
in the role of Kapton tape, you may have oxygen/water diffusion from the
cardboard for a few days after you take it into the box.  Our rule of thumb
was to pull vacuum on anything involving cardboard for at least 48 hrs
before taking it into the box.  All that to say, take your supplies into the
box a few days ahead of time to allow your box catalyst to take care of any
residual oxygen/water that make their way in.

HTH,
-Richard

On Wed, Aug 5, 2009 at 7:27 PM, Scott Calvin  wrote:

> Hi Todd,
> I've taken the liberty of posting your question to the Ifeffit mailing
> list. You're likely to get more accurate and quicker answers to these kinds
> of questions there.
>
> (For the rest of you: Todd is asking about the technique of preparing
> air-sensitive samples in a glove box, putting them on Kapton tape, sealing
> them in plastic bags, and transporting them to the beamline, shooting right
> through the bags.)
>
> I'll take my shots, though:
>
> It's hard for me to imagine adsorbed oxygen on the Kapton being more
> significant than the other sources of stray oxygen that can be present in a
> glove box. After all, the Kapton's in there too. And I don't think it's
> going to be more significant than the oxygen that diffuses through the
> plastic bags during transport.
>
> The thinner the Kapton tape, the better, as that will minimize the
> absorption due to the tape. It used to be hard to find 1 mil Kapton tape
> with adhesive, but now it's easy. Hephaestus will give you the absorption of
> Kapton, so you can judge how big an effect it will be at the energies at
> which you'll work.
>
> --Scott Calvin
> Sarah Lawrence College
>
> On Aug 4, 2009, at 2:39 PM, Monson, Todd wrote:
>
> Scott,
>
> Thanks.  Is it pretty reasonable to assume that the kapton tape that you
> put your samples on doesn’t have any adsorbed oxygen that could affect your
> samples?  Do you do anything to clean the kapton?  Where are some good
> places to buy the kapton (and do you need to purchase rather thin kapton
> tape for doing XAFS)?
>
> Thanks again,
>
> Todd
>
> *From:* Scott Calvin
> *Sent:* August 04, 2009 11:34 AM
> *To:* Monson, Todd
> *Cc:* Scott Calvin
> *Subject:* Re: mossbauer
>
> Hi Todd,
>
> Regular zip-loc bags work just fine. For heat sealers I've used everything
> from a heat sealer manufactured for the purpose to a little propane
> torch--even a cigarette lighter should work. Putting one sealed bag inside
> another, if the energy you're working at allows it, seems to work quite
> well.
>
> --Scott
>
>
> On Aug 4, 2009, at 1:15 PM, Monson, Todd wrote:
>
>
> Scott,
>
> I had another question – what kind of plastic bags and heat sealers do you
> use for sealing up your air-sensitive XAFS samples?  And where could I buy
> them?
>
> Thanks,
>
> Todd
>
>
>
>
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Re: [Ifeffit] Sorry

[Richard Mayes]

Chris,

In cases where intense pre-edge features are observed, such as the one you
attached, you should manually set the Eo and not accept the Athena
defaults.  I usually start with half-way up the absorption edge (you can
look at the derivative and move the Eo value to the maximum in the
derivative; however, make sure you don't move it back to the pre-edge).

More detailed information on setting Eo and background removal can be found
here:

http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/index.html

Also, www.xafs.org is an excellent resource for more information.

-Richard


On Wed, Jul 22, 2009 at 6:23 PM, Chris Patridge wrote:

> I forgot to post a bitmap of the spectra of the previous message.  Thank
> you all.
>
> --
> Christopher J. Patridge
> Graduate Student
> SUNY Buffalo - Dept of Chemistry
> 716-645-6800 x 2110
> 315-529-0501
>
>
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Re: [Ifeffit] residual saving

[Richard Mayes]

Guvenc,

There are 2 ways that I know of:  the first is "save residual" under the
File menu.  You may have to save the chi(k) and the residuals separately (I
have never done this so I'm not sure on the exact procedure) and then
overlay the plots in some graphing software similar to Excel.

The second is to save the picture showing the fit and the residuals as a
metafile and import the image into PowerPoint and modify the image (line
size, line colors, etc) using the drawing options (the procedure for this is
found here:
http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions?highlight=(Horae)|(faq)#head-2536b76fd9a517c8cff6b367d89e9fd03cbf5999
).

-Richard



On Tue, Apr 14, 2009 at 5:55 PM, Guvenc Akgul  wrote:

> dear all,
>
> I need save residual as k^3*Chi(k) but I could not save it because it is
> saving only as Chi(k).how can do for this?
>
> thanks in advance
>
> guvenc
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Re: [Ifeffit] Transferability of S02

[Richard Mayes]

Scott,

This paper may help:  B. Lengeler and P. Eisenberger,  Physical Review B,
22(8), 1980, 3551-3562.


-Rich




2009/3/21 Scott Calvin 

> Hi all,
>
> One of the most universally accepted facts used in EXAFS analysis is that
> the amplitude reduction factor S02 is chemically transferable.
>
> I've been trying to find a good reference for this--either a key study
> establishing it, or a review article asserting it. I know there has been
> plenty of good work in recent years trying to make theoretical calculations
> of S02, and that they are gradually becoming more accurate. But these recent
> advances can't be the reason we treat S02 as transferable, because we've
> been doing it for decades.
>
> How was this established? It seems devilishly difficult to do
> experimentally with good accuracy, because S02 will correlate to some extent
> with other parameters.  Those correlations can be broken to some extent by
> using *k* dependence, but it seems the uncertainties would still be
> somewhat high. On the other hand, were there compelling theoretical reasons
> back in the 80's for believing transferability to hold?
>
> Currently, how good do we think the assumption of transferability really
> is? Good to 5% for any compound at that edge? Good to 1% for compounds with
> similar local environments at that edge? Better than that? (I'm asking about
> the EXAFS region; say, more than two inverse angstroms above the edge.)
>
> I eagerly await your collective wisdom, knowledge, and humorous anecdotes.
>
> --Scott Calvin
> Sarah Lawrence College
>
> P.S. I resent this to change the subject line to something more
> appropriate; this may be a thread that people will want to find in searches
> later. Sorry for the double post!
>
>
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>
-

Richard Mayes
Graduate Research Assistant
Craig Barnes Group
450 Buehler Hall
Dept. of Chemistry
Univ. of Tennessee
Knoxville, TN 37996
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Re: [Ifeffit] (no subject)

[Richard Mayes]

Anther question that I have how can I get to the past discussions in the
> forum- is there any database for questions and answers that I can learn on
> the analysis of EXAFS data?
>


The archive is found here:
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/

It can be searched using the Advanced search feature of Google and restrict
the domain to the above address.

-Rich
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Re: [Ifeffit] Self absorption Correction

[Richard Mayes]

Jens,

Since no one has answered yet, I'll chime in.  First let me direct you to a
discussion of self-absorption and other sample-related distortions:
http://www.xafs.org/Experiment/OverAbsorption  (this is a link from the
tutorials page of www.xafs.org).

As for your questions:

I think that you should use the non-normalized XANES data to perform the SA
correction.

for the angle-in and angle-out meanings, see Grant Bunker's paper on
self-absorption here:
http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf

Now, how do you determine if you have self-absorption effects?  I have to
defer here to those with more experience.  What you suggest sounds
appropriate, but I'm not sure how you could determine this without studying
multiple concentrations of your absorber and watch the signals, i.e. does a
10% increase in absorber concentration translate to a 10% increase in
fluorescence yield (similar to what Matthew Marcus and Alain Manceau
describe in their paper, from the over-absorption link above).

HTH,
-Rich

On Fri, Jan 30, 2009 at 11:49 AM, Jens Kruse wrote:

> Hi there,
>
> I have measured a pure reference compound with high absorber
> concentration in fluorescence mode (P K-edge XANES).  I tried to use the
> Self absorption correction  included in Athena but I don't really
> understand the results.
> Fist: Do I have to use the edge step normalized spectrum or the spectrum
> without normalization ? I tried both and the results  of course a quite
> different. I would rather use the not normalized spectrum.
> Second: the value "Angel in"  is this the angle between the incident
> beam and the sample surface" and "Angle out"  the angle between the
> sample surface and the detector position?
> Third: More general- How can I identify a spectrum suffering self
> absorption? Just comparing the relative peak intensities of total
> electron yield signal with the fluorescence yield signal ?
>
> thanks a lot for your comments,
> cheers,
>  Jens
>
> --
> Jens Kruse
> Institute for Land Use
> Faculty for Agricultural and Environmental Sciences
> Rostock University
> Justus-von-Liebig-Weg 6
> 18059 Rostock GERMANY
> Phone: +49(0)381-498 3190
>
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Re: [Ifeffit] Trouble with fitting with Artemis

[Richard Mayes]

Juraci,

Can you please attach a project file so we can look at it and try to find
the problem.  My first guess would be the parameters are not defined in the
"guess,def,set" page like they are in the path list but without seeing the
project file, it's hard to be specific.

-Rich

On Wed, Jan 28, 2009 at 1:34 PM, Juraci A. Sampaio wrote:

>  Hi there!
>
> I'm getting the following message when I try to fit my data:
> WARNING.  The following variables had no effect on the fit:
> !!  >> amp
> !!  >> enot
> !!  >> delr
> !!  >> ss
>
> The data that I am trying to fit is the Cu metal example that come with the
> iffefit package. I am running Artemis on a Mac, OSX 10.4.11.
> I could run the fitting on a mac OSX 10.5 and it worked fine. I reinstall
> the IXAFS package but it didn't work.
>
> I am wondering what could be wrong with my machine/software?
>
> Thanks a lot.
>
>
> Juraci Sampaio
>
>
> --
> Notícias direto do New York Times, gols do Lance, videocassetadas e muitos
> outros vídeos no MSN Videos! Confira já! 
>
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Re: [Ifeffit] small-screen version of Athena document

[Richard Mayes]

XAFS on a Blackberry or iPhone...then you can market it as a brainteaser
game and make a little extra money.

-Rich

On Mon, Jan 26, 2009 at 1:35 PM, Frenkel, Anatoly  wrote:

> Bruce and Matt:
>
> When Athena and Artemis are completely moved to BlackBerry and iPhone,
> there will be a number of really nice options out there. For example,
> ringtones for a really bad fit should be made very unpleasant, and even more
> so, when Delta E0 is out of bounds, or r-factor is greater than 0.02..
>
> Anatoly
>
> -Original Message-
> From: ifeffit-boun...@millenia.cars.aps.anl.gov
> [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov]on Behalf Of Ravel,
> Bruce
> Sent: Monday, January 26, 2009 10:02 AM
> To: XAFS Analysis Using Ifeffit
> Subject: [Ifeffit] small-screen version of Athena document
>
>
>
> Hi,
>
> There is now a version of the Athena User's Guide which is intended
> for small-screen device (like my the new toy I got this weekend).
> Here is the URL:
>
>  
> http://cars9.uchicago.edu/~ravel/software/doc/Athena/mobile/
>
> This is very similar to the normal html version of the User's Guide,
> except for a few changes in layout to make it work better on a small
> screen.
>
> The mobile version is not perfect yet, but it is much more legible
> than the normal version.  I have tested it mostly in Explorer on
> Windows Mobile 6.  (I have also tested it under Opera for mobile
> devices, but I am not happy with how either version gets displayed
> there.)
>
> Hopefully this will be helpful for someone.
>
> Regards,
> B
>
> --
>
>  Bruce Ravel   bra...@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/
>
>
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Re: [Ifeffit] Co doped ZnO

[Richard Mayes]

Guvenc,

You may want to start here (look at # 14):  <
http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling?highlight=(doped)#head-b273ecfd19542ec82ea031bbcc57ff8861fc11f9
>


HTH,
-Richard



On Thu, Nov 13, 2008 at 8:27 PM, Guvenc Akgul (gakgul)
<[EMAIL PROTECTED]>wrote:

> dear all,
>
> I have 10%Co doped ZnO EXAFS data and I would like to figure out :Co-Co
> distance in the 10%Co doped ZnO.what will i do for this?if you can help to
> me about this i will be very glad.
>
> thanks all
>
> guvenc
>
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Re: [Ifeffit] feff8

[Richard Mayes]

Information on FEFF is found here:
http://leonardo.phys.washington.edu/feff/welcome.html

-Rich



On Fri, Oct 24, 2008 at 2:42 PM, Guvenc Akgul (gakgul)
<[EMAIL PROTECTED]>wrote:

> Hi all,
>
> I  want to calculate L2and L3 absorption edges for Fe  as theoretical.
> Where can I find feff8 software programme??
>
> thanks
>
> guven
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Re: [Ifeffit] Reference spectra for KCl

[Richard Mayes]

Andrei,

What you are looking for may be located here:

http://ixs.iit.edu/database/data/Farrel_Lytle_data/RAW/periodic-table.html

If not, a publication database is also available (
http://www.xafs.org/Databases) that might guide you to someone who has the
data.

HTH,

Richard

On Fri, Oct 3, 2008 at 5:52 AM, <[EMAIL PROTECTED]> wrote:

> Hi everybody,
>
> I would greatly appreciate if someone could provide me with K K-edge
> spectra for KCl and K2CO3. Cl K-edge in KCl would be useful too.
>
> Thanks in advance,
> Andrei Shiryaev
>
> Institute of crystallography,
> Moscow, Russia
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Re: [Ifeffit] plot linetypes option in athena windows version

[Richard Mayes]

Malte,

Scott's right!  See question # 10 and 11 here:

http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions

-Richard


> Hi Malte,
>
> Don't do this for a thesis! Athena was never intended to produce
> publication-quality graphs. Export the data and read it into whatever
> graphing program your institution normally uses. Even Excel (or its
> open-source equivalents) gives you more control than Athena.
>
> --Scott Calvin
> Sarah Lawrence College
>
> On Sep 22, 2008, at 7:58 AM, Malte Schulz wrote:
>
>> Hi there,
>>
>> I would like to export graphics from Athena to use them in my b&w
>> printed thesis. Therefore it would be really useful to have Athena
>> cycle through linetypes instead of colors. I found the "linetypes"
>> option in the "plot" section of the preferences menu. However it
>> doesn't seem to have any effect. I am using Athena v. 0.8.056 for
>> windows.
>>
>> Malte
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-- 
Richard Mayes

Barnes Group
450/452 Buehler Hall
Department of Chemistry
University of Tennessee
Knoxville, TN 37996

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Re: [Ifeffit] reference spectra for Cu(OH)2

[Richard Mayes]

Darek,

Have you checked the Farrell Lytle Database?

http://ixs.iit.edu/database/data/Farrel_Lytle_data/index.html

You might also look in the other databases available at
www.xafs.org/Databases

I'm not sure if copper(II) hydroxide is available, but it's a good place
to start looking.

Rich


> Hi all,
> as now we have a time for XAS spectra requests, I would like to ask you
> also for one. I need spectra of Cu(OH)_{2}. If someone could help I
> would preciate. Thanks in advance
> darek
>
> 
> dr. Zajac Dariusz A.   Deutsches Elektronen-Synchrotron -Hasylab
> phone:  +49-40-8998-2932Notkestr. 85
> fax:+49-40-8998-2787   22607 Hamburg
> e-mail: [EMAIL PROTECTED]Germany
> 
>
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> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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Re: [Ifeffit] quotation of figures

[Richard Mayes]

>
> I also dislike the phrase "Debye-Waller factor" for the exafs disorder
> term.  In crystallography, the Debye-Waller factor refers to disorder
> of atoms about their lattice positions.  In exafs, the disorder is
> about the path length of the N-body configuration -- clearly not the
> same thing.  I am, apparently, in the minority on this topic --
> "Debye-Waller factor" is in wide use in the exafs literature.  But, as
> everyone here knows, I often like to stand up on my soapbox and yell
> into the crowd. ;-)
>

Bruce,

While you're on your soapbox, if we drop "Debye-Waller factor" to describe
the EXAFS disorder term, would you suggest using only "disorder" or do you
have a better phrase to use?

Rich

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Re: [Ifeffit] iron L edges

[Richard Mayes]

Bruce,

At first glance, check...

Spectroscopic studies of the reaction of water with metal oxide 
surfaces. Kendelewicz, T.; Liu, P.; Brown, G. E., Jr.; Nelson, E. 
J.; McCarthy, M. I.; Chambers, S. A.   Mineralogical Magazine 
(1998),  62A(Pt. 2),  763-764.

It's supposed to have the Fe L-edge spectra.  I'm still looking for the 
paper to find out for sure.

-Richard

Bruce Ravel wrote:
> Hi everyone,
> 
> I have just spent a fruitless half hour with google scholar trying to
> find a paper that publishes Fe L2,3 edge spectra (not K -- I have
> those!) of the FeOOH species goethite and lepidocrocite.  Can anyone
> point me in the right direction?  Thanks a million!
> 
> B
> 
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Re: [Ifeffit] Sulphur spectra database?

[Richard Mayes]

Jenny,

Don't know how much help this will be, but check here:

<http://www.xafs.org/Databases>

HTH,
Richard


> Hi,
>
> I wonder if I have to run many pure sulphur compounds (the standards) by
> myself for fitting my sample's spectrum. Is there a spectrum database for
> sulphur compounds, e.g.,  thiophene, sulphide, sulphate, disulphide, etc.,
> so I can import the spectra to Athena to do the fitting?
>
> Thank you.
>
> Jenny
>
>
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Re: [Ifeffit] Rutile Rbkq remove question.

[Richard Mayes]

Pei,

The following page will help:

http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/rbkg.html

I think what you are seeing is just effects of removing data that
contributes to the mu(E) spectrum.

As for why the feature (low-R junk) increases as Rbkg is adjusted from 1.0
to 1.21 but disappears at 1.22, I'm not sure but my guess is that this is
an artifact of removing some of the data that contributes to the feature,
and by 1.22 you have removed enough that the feature disappears (hopefully
someone will correct me if I'm wrong).  I would be weary of using an Rbkg
of 1.22 though (as I think you see why in the plots - Question 3).

Cheers,
Richard


> To Dear authors:
>We have a Rbkg question about Rutile, and in order to
>   demonstrate these questions more clearly, we make it
>   up on attach .ppt file, and thanks for your great helping
>   before.
>
>   Pei
>
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Re: [Ifeffit] sorting files in Athena

[Richard Mayes]

Check out the section on marking groups in the Athena manual to see if
that meets your needs.  This may not be the answer you're looking for, but
it's a way to sort data by selecting data sets that have a common
expression that matches your search parameters.  The command is under Mark
then mark regex I think.

The Athena manual is found here

http://cars9.uchicago.edu/iffwiki/Documentation

Richard




> Hi,
> I can not find one small thing - sorting files in Athena - it makes me
> crazy ;)
> I work with QEXAFS data  - usualy few tens of files or even more. Files
> are named in such way: "file_name"rXX.fio where XX is next file number
> (1, 2, 3, ... ,10, 11, 12, ... , 20, 21, etc.).
> I use Iffefit under Win XP, and every time when I open (import) more
> files I have them in such order: 1, 11, 12, 13, ... , 19, 2, 20, 21, 22,
> ... , 29, 3, 30, 31 ... etc.
> So, my question is if there is some "hidden" way to sort automatically
> files during importing or in the menue. Do you know something about? Is
> the sorting lexigraphical (from Windows)?
>
> another problem which apears, is the limitation of the memmory...
>
> thanks for answer and greetings
> kicaj
> 
> Zajac Dariusz A.Deutsches Elektronen-Synchrotron
> -Hasylab
> phone:  +49-40-8998-2932Notkestr. 85
> fax:+49-40-8998-2787   22607 Hamburg
> e-mail:  Germany
> 
>
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Department of Chemistry
University of Tennessee
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Re: [Ifeffit] saving a window function in Athena/Artemis

[Richard Mayes]

Renske,


To search the IFEFFIT mail list archives, use the advanced search feature
of Google, .  Under the advanced search page of Google,
look for the line that starts with "Domain" and set it to "only" return
results from <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/>.  then
you can type your key words in the lines at the top of the page and search
the archives.

As an aside, this morning I had trouble accessing the IFEFFIT webpages
while getting error messages that said the APS firewall was denying my
access.  If this happens, try hitting the back button in the browser then
the link again.  This seemed to work for me.

Richard

>
> Hi!
>
> Could anyone tell me whether it is possible to save a specific window
> function together with the data in either Athena or Artemis?
>
> Another general question: how can I easily search for specific key words
> in the archive folders of the mailing list (without going through them
> individually)?
>
> Thanks & happy new year to you all!
>
> Renske
>
>
>
> Renske M. van der Veen
> PhD student Chergui Group EPFL
> Paul Scherrer Institut
> Swiss Light Source WSLA/210
> 5232 Villigen PSI
> Switzerland
>
> Phone: +41 56 310 5362
> Fax: +41 56 310 3171
> E-mail: [EMAIL PROTECTED]
> Web: http://lsu.epfl.ch
> http://femto.web.psi.ch
>
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Department of Chemistry
University of Tennessee
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Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?

[Richard Mayes]

Kefan,

As someone who was in your place 2 years ago, one thing Bruce mentioned
was reading the papers of people you find on the mail list, however he
didn't specifically mention searching the mail list.  When I had
questions, the answers were often already discussed on the mail-list.  If
you're not a member of the mail-list, I highly recommend you join.  As I
currently struggle writing a how-to manual that's supposed to shorten the
XAFS learning curve for our group, I find myself searching the mail-list
archives often to see how different people approach different issues.

Good luck on your quest!
-Richard


>
>> Hi Bruce
>
>> I have spent 1 month to learn the Athena by using your "ATHENA User's
>> Guide"
>> updated at Aug. 31,2007. I am very satisfied with it and thank you very
>> much. Now I am learning the ARTEMIS. However, till now I can not find a
>> suitable guide for a beginner. The PPT wrote by Shelly is not suitable
>> for
>> me. And the "artemisdoc.pod" is also puzzled me. Is there a Artemis
>> User's
>> Guide like the Athena?
>
>> Thanks
>
>> Kefan
>
>> --
>> Kefan Wang
>> School of Physics and Electronics
>> Henan University, 475004
>> E-mail: [EMAIL PROTECTED]; [EMAIL PROTECTED]
>
>
> Hi Kefan,
>
> I suspect that my answer to this question will be of broad interest,
> so I am taking the liberty of CCing the Ifeffit mailing list.
>
> Thank you for the very kind words regaridng Athena.  I am pleased that
> you found the Athena User's Guide so helpful.  Sadly, I have not yet
> written a document of comparable extent for Artemis.  I certainly
> understand that there is a need for comparable user guide, but finding
> the time and energy to write one has not yet happened.  Writing the
> Athena User's Guide was fairly exhausting and I need to take a break
> before embarking on a similarly large document for Artemis.
>
> I have to defend Shelly's various presentations.  I think they have a
> lot of good information in them.  I think that using them along with
> other resources can give you enough of an overview of Artemis to get
> started.  I strongly recommend that you work through Scott Calvin's
> ZnO example, which can be foun at
>http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib
> ZnO is somewhat of an idealized example -- many of us work on
> problems that are pretty far removed from a simple crystal like ZnO.
> However, Scott's example is quite thorough.  Working through it while
> carefully following his comments in the project journals will
> introduce many of Artemis' features.
>
> As for the pod file -- those are the files that get displayed when you
> click on one of the documentation buttons from within Artemis.  I
> acknowledge that they are thin on details and somewhat out of date.
>
> The last bit of advice I can give you is to read the papers written by
> the names you see on the Ifeffit mailing list.  The folks who offer
> answers to question on the list are also some of the best
> practitioners of EXAFS analysis using Feff.  Although it might seem
> funny to read papers by Anatoly Frenkel or Paul Fons if you are
> studying environmental science (or Shelly Kelly's if you are a
> materials scientist), I strongly recommend doing so anyway.  Their
> science might be pretty far away from what you do, but the EXAFS
> analysis strategies are quite instructive and are certainly
> transferable.
>
> I know that is not the answer you were hoping for, but it may be
> helpful nonetheless.
>
> Regards,
> B
>
> --
>  Bruce Ravel  --- [EMAIL PROTECTED]
>
>  National Institute of Standards and Technology
>  Synchrotron Methods Group at Brookhaven National Laboratory
>  Building 535A
>  Upton NY, 11973
>
>  My homepage:http://cars9.uchicago.edu/~ravel
>  EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>
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Department of Chemistry
University of Tennessee
Knoxville, TN 37996

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Re: [Ifeffit] SA and issue with importing into Artemis

[Richard Mayes]

DO'OH!

Thanks Anatoly!  I must be blind.  I totally missed that.

-Richard


> Richard,
>
> I tried with Athena v50 and Artemis v007 and it worked (the data were
> ported correctly). I do not think it is version dependent.
>
> The data that you save in Athena are ported to Artemis with 0
> k-weighting, so you have to manually set your k-weighting in artemis if
> you want to match the same k-weighting that you liked in athena. As you
> know, there is k-weighting for FT and k-weigthting for plotting data in
> k-space, which have nothing to do with each other.
>
> Note that the vertical axis in the bottom figure of your PDF file has
> unit of A^-3 which means it was indeed k2-weighting in FT in Artemis.
> You just have to make it k3 weighting in FT and it will give you the
> same plot as the top figure (and the unit will be A^-4).
>
> Anatoly
>
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Richard
> Mayes
> Sent: Friday, November 09, 2007 12:13 PM
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] SA and issue with importing into Artemis
>
>
>
> Oops!  Forgot the attachments.  Sorry about that.
>
> I should also add, the file I'm trying to import into Artemis is
> "k_3.191_13.860".
>
> -Richard
>
>
>> Everyone, thanks for the info on self absorption!  I'm currently
> working
>> on writing a short summary for our group based on the information
> everyone
>> shared.
>>
>> Bruce, I'm having an issue importing a k3-weighted project into
> Artemis
>> from Athena.  (I looked on the mail list and your webpage for a bug
> report
>> and couldn't find one, my apologies if I missed it.)
>>
>> The problem:  I'm trying to import a k3-weighted spectrum into
> Artemis,
>> but it appears to be importing the k2-weighted spectrum instead.  I
> don't
>> know if this is related or a change between versions of Artemis, but
> the
>> k-weight used in Athena isn't being carried over into Artemis as the
> fit
>> k-weight as well.  Attached is the Athena and Artemis projects showing
>> this and a pdf with pics of the 2 spectra I'm seeing (in case this is
> an
>> issue only on my computer).  I tried changing the group name and
> deleting
>> all the groups in Athena except the one I wanted and this still
> occurs.
>>
>> Any ideas on how to get around this?
>>
>> FYI:  I'm running Athena (0.8.054) and Artemis (0.8.011) on a laptop
> (1.7
>> GHz Pentium M processor & 2 GB RAM) with Windows XP Pro.
>>
>> Thanks!!
>> -Richard
>>
>> --
>> Richard Mayes
>>
>> Barnes Group
>> 450/452 Buehler Hall
>> Department of Chemistry
>> University of Tennessee
>> Knoxville, TN 37996
>>
>
>
> --
> Richard Mayes
>
> Barnes Group
> 450/452 Buehler Hall
> Department of Chemistry
> University of Tennessee
> Knoxville, TN 37996
>
>
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Department of Chemistry
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[Ifeffit] SA and issue with importing into Artemis

[Richard Mayes]

Everyone, thanks for the info on self absorption!  I'm currently working
on writing a short summary for our group based on the information everyone
shared.

Bruce, I'm having an issue importing a k3-weighted project into Artemis
from Athena.  (I looked on the mail list and your webpage for a bug report
and couldn't find one, my apologies if I missed it.)

The problem:  I'm trying to import a k3-weighted spectrum into Artemis,
but it appears to be importing the k2-weighted spectrum instead.  I don't
know if this is related or a change between versions of Artemis, but the
k-weight used in Athena isn't being carried over into Artemis as the fit
k-weight as well.  Attached is the Athena and Artemis projects showing
this and a pdf with pics of the 2 spectra I'm seeing (in case this is an
issue only on my computer).  I tried changing the group name and deleting
all the groups in Athena except the one I wanted and this still occurs.

Any ideas on how to get around this?

FYI:  I'm running Athena (0.8.054) and Artemis (0.8.011) on a laptop (1.7
GHz Pentium M processor & 2 GB RAM) with Windows XP Pro.

Thanks!!
-Richard

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Department of Chemistry
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[Ifeffit] Self absorption questions

[Richard Mayes]

Greetings all!

I'm trying to explain self absorption for our group's guide to EXAFS and I
need some help understanding some of the finer details of self absorption.
 In the realm of fluorescence EXAFS, am I correct in that at a given
energy there is a certain penetration depth of the X-rays that is expected
(in a thick, dilute sample), but in a thick, concentrated sample, the
penetration depth is actually less than the expected depth in thick,
dilute samples (causing the decrease in the amplitude of the oscillation
peak in Bruce's "wiggle up" of the XAFS oscillation)?  Then, in the
"wiggle down" of the XAFS oscillation, the penetration depth is actually
more than what would be expected so the depth of the oscillation valley
decreases.  As a result, for thick concentrated samples like a metal foil,
in the "wiggle up," the fluorescence accounts for fewer than expected
absorbing atoms and in the "wiggle down" the fluorescence accounts for
more than expected absorbing atoms.

Next, in our amorphous silicates (doped with Ti, V, Cr, W, or Sn), is the
self absorption effect greater in the lower Z elements (like titanium)
than in the higher Z elements (like tin)?  Does the high background due to
the silicon at the lower energies (4.9 keV) in relation to the higher
energies (29.2 keV) have an effect or is it just an underlying,
independent issue that is more pronounced with the lower Z elements when
self absorption occurs?

Thanks!

-Richard

-- 
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University of Tennessee
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Re: [Ifeffit] Iron(III) carboxylate structures

[Richard Mayes]

Scott,

Maybe these refs will help.

Rich Mayes


New trends in the chemistry of iron(III) citrate complexes: correlations
between X-ray structures and solution species probed by electrospray mass
spectrometry and kinetics of iron uptake from citrate by iron chelators.  
  Gautier-Luneau, Isabelle; Merle, Claire; Phanon, Delphine; Lebrun,
Colette; Biaso, Frederic; Serratrice, Guy; Pierre, Jean-Louis.   
Chemistry--A European Journal  (2005),  11(7),  2207-2219.

Synthesis, crystal structure and magnetic property of a binuclear
iron(III) citrate complex. Hao, Xiang; Wei, Yongge; Zhang, Shiwei.   
Transition Metal Chemistry (Dordrecht, Netherlands)  (2001),  26(4-5), 
384-387.

Salicylaldoxime (H2salox) in iron(III) carboxylate chemistry: Synthesis,
X-ray crystal structure, spectroscopic characterization and magnetic
behavior of trinuclear oxo-centered complexes. Raptopoulou, Catherine
P.; Sanakis, Yiannis; Boudalis, Athanassios K.; Psycharis, Vassilis. 
Polyhedron  (2005),  24(5),  711-721.




> Hi all,
>
> Anyone out there have a structure (or a reference to a structure) for
> a carboylate salt of iron(III), e.g. iron(III) acetate or iron(III)
> citrate? The closest I've found is a really short Nature article from
> 1965, but I'd like something more quantitative. I'm particularly
> interested in the Fe-Fe coordination and distance.
>
> --Scott Calvin
> Sarah Lawrence College
>
> P.S. The mailing list's spam filter has decided that when I send
> messages from home I am actually engaged in something shady and is
> blocking me. This is the last day I know I'll be at SLC for a while,
> so I'm likely to have a hard time responding via the list until this
> gets straightened out. It's just the Ifeffit list, though--I can
> still send to people inside the ANL firewall with no problems.
>
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Re: [Ifeffit] Low amp results

[Richard Mayes]

Joji,

An "amp" of 0.3 is low.  Check out <http://xafs.org/Tutorials> and
<http://www.nsls.bnl.gov/newsroom/events/workshops/2006/exafs/agenda.asp>
for .pdf files that will explain the use of GDS parameters.  These
tutorials are an excellent way to get started.

Rich


> I analyzed EXAFS spectra of trace of Fe in lithium tantalate crystals. At
> first, I created the feff.inp file of LiTaO3. Then I changed central Li
> atom
> to Fe atom and added Fe atom at the Ta site. So that, the fitted results
> is
> good except amp(amp results is 0.3). I think that the model structure is
> good, but I can not understand why amp is too low. How do you think about
> this results? And, I tried to fitting treatment using GDS parameters. But,
> I
> do not know that the general method how to use the GDS parameters. Please
> tell me the general way of GDS manipulation. My PC runs under Win XP, and
> My
> Artemis runs under feff8 conditions. Thank you.
> Joji Kuniya
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Department of Chemistry
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Re: [Ifeffit] An Ifeffit question.

[Richard Mayes]

There's another way to get better looking plots out of Athena and Artemis
(for those of us who can't completely give up microsoft just yet),
although it's probably a little more time intensive than the options Bruce
mentioned...in the pgplot menu, save the image as a metafile, then import
the metafile into Powerpoint and convert it into a drawing object with the
drawing toolbar (click on the image, then click "ungroup").  That gives
you the options of broadening the lines, changing the colors, enlarging
the numbers, etc.  The drawing object can then be saved as a jpeg and
imported into various other programs.

Rich Mayes

GRA
Barnes Group
450/452 Buehler Hall
Dept. of Chemistry
Univ. of Tennessee
Knoxville, TN 37996


> On Friday 18 May 2007, Christian Lange wrote:
>> I am using "your" Athena and so on-software package for the evaluation
>> of my XAS-measurements. So far everything is working fine, but i have
>> one problem. The plots of this "graphics window" are a bit inconvenient
>> if it comes to a publication, because I cannot change line styles,
>> colors and so on. Or at least I don't know how to do this.
>>
>> That's why I want to ask you, whether it is possible to get the data for
>> the fourier transform plots in some sort of ASCII-format to import it in
>> Origin. Maybe with some file jiggling at the DOS prompt level?
>
>
> Hi Christian,
>
> This is a good question for the Ifeffit mailing list, so I am taking
> the liberty of CCing my answer there.
>
> This should be answered in the FAQ -- it certainly is frequently asked
> in my email!
>
> I completely agree that the plots made by pgplot are not pretty enough
> for publication and I suspect that Matt would not argue either.  We
> use pgplot because it works well within the context of Ifeffit,
> because it is free and redistributable, and because it works
> equivalently on Windows, Unix, and the Mac.  Matt and I both prefer to
> spend our limited time making good XAS software -- neither of us
> really felt particularly inclined to make and maintain publication
> quality plotting software.  There are, after all, plenty of excellent
> packages out there for making beautiful plots.
>
> The trick, then, is the link between Athena and your favorite plotting
> package. In the File menu, there are a number of option for exporting
> data into plain-text, column-data files.  These can then be imported
> easily into your favorite plotting program.  The File menu options
> from "Save mu(E)" through "Save chi(q)" will save the current data
> group (i.e. the one highlighted in the groups list and the one whose
> parameters are currently on display in the main window).  The mu(E)
> file, for instance, contains columns for energy data, background, I0,
> pre-edge line, and post-edge polynomial.  You can import these columns
> into your favorite plotting program and have your way with them.  The
> chi(R) file, as another example, has columns of R, real part,
> imaginary part, magnitude, phase, and back-transform window in R.
>
> Below those options is a submenu labeled "Save marked groups as
> data".  The idea there is to save column data file where each column
> contains the data from a marked group (i.e. the ones with the little
> purple button in the groups list clicked).  There are options for
> saving data in this way in each of the plotting spaces.
>
> Finally, it is possible to have some control over how the plots are
> made.  In the Settings menu, select "Edit preferences".  Then open up
> the Plot branch by clicking on its little plus sign.  The options c0
> through c9 and the linetypes option might be of interest to your.
> Nothing among the preferences will magically make pgplot prettier, but
> it may help you visualize your data.
>
> HTH,
> B
>
> P.S. You can join the Ifeffit mailing list at
>
>http://cars9.uchicago.edu/mailman/listinfo/ifeffit/
>
> It tends to be high quality conversation (except the parts written by
> me, of course) and high signal-to-noise.
>
> --
>  Bruce Ravel  --
> [EMAIL PROTECTED]
>
>  Molecular Environmental Science Group, Building 203, Room E-165
>  MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007
>
>  Argonne National Laboratory phone and voice mail: (1) 630 252
> 5033
>  Argonne IL 60439, USAfax: (1) 630 252
> 9793
>
>  My homepage:http://cars9.uchicago.edu/~ravel
>  EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>
>
>
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Re: [Ifeffit] large Eo's and neg. D-W factors

[Richard Mayes]

Scott,

I think I understand now.  By restraining the negative Debye-Waller 
factor, I may have been treating the symptom instead of the cause.  I'll 
go back and check my model.

Also, should I be worried if my Debye-Waller factors get small 
(0.0005-0.001) if I optimize my model in FEFF to a point that my delr's 
are on the order of 0.005-0.01 Angstroms?  This has been a concern of 
ours since we started doing EXAFS, especially since all of our 
measurements are at room temp.  We haven't seen this as much with our 
vanadium on silica samples, but it seems to be true with all of our 
titanosilicate samples

Rich

Scott Calvin wrote:
> Hi Rich,
> 
> Oh--I think I should have been more specific. It sounds like you're 
> restraining the sigma2's. In my experience, that is not as effective 
> in the cases of switching paths as restraining the delr's. After all, 
> the sigma2's are just a symptom; the delr's are the direct measure of 
> switching.
> 
> As for Anatoly's observation, I'd qualify it. If it's a matter of 
> trying to pound a square peg into a round hole, then yeah, that's 
> dubious. I often have found, though, that I get lousy fit after lousy 
> fit for a long time. Then I make some key change to how I'm 
> =physically= modelling the system...allowing vacancies, or putting in 
> a minority phase, or changing the morphology, or allowing for local 
> distortion, or whatever, and suddenly the fits get much much better. 
> I often have pretty high confidence in the results when that happens. 
> It suggests that in that system I can't get a good fit with the wrong 
> model just by tinkering. In the other extreme, if I have the kind of 
> combination of data and model that seems to give a "good" fit no 
> matter what I do, but from one fit to the next the parameters jump 
> all over the place, then I have low confidence in the results. In 
> other words, I want systems that generate lousy fits unless I get the 
> structure right. :)
> 
> --Scott Calvin
> Sarah Lawrence College
> 
> At 08:55 AM 5/2/2007, you wrote:
>> Scott,
>>
>> Thanks for the clues!  The restraints seem to be working to get the DW
>> factors positive.  I'm still battling Ifeffit reversing the paths, but
>> things are getting slowly better.
>>
>> Rich
>>
>>> Hi Rich,
>>>
>>> I know you posted this a while ago, so you may have gotten other
>>> answers, but I don't see them in my overflowing inbox. :)
>>>
>>> Years ago, I did some work with V2O3, and it was a very stubborn
>>> system to get a good fit on. Other people I knew who were working on
>>> the system have also had some trouble. This and other evidence led to
>>> some people publishing speculations on local distortions that get
>>> averaged out in XRD but show up in EXAFS. I also recall people
>>> talking about similar difficulties with other vanadium oxide systems.
>>> (Sorry; I don't have those references handy anymore, but searches
>>> should locate them).
>>>
>>> As far as the second issue you mention, with Ifeffit reversing the
>>> position of two atoms of the same species, it does happen some times.
>>> Why not? A V-O path is basically a V-O path to FEFF; it doesn't know
>>> that one's a single bond and one's a double bond. But since moving a
>>> path by more than about 0.1 Angstrom in Ifeffit starts to reduce the
>>> accuracy of the FEFF calculation, it's something you do want to try
>>> to prevent. One way to do that is with restraints; it shouldn't take
>>> much incentive for Ifeffit to refrain from switching the paths.
>>>
>>> --Scott Calvin
>>> Sarah Lawrence College
>>>
>>>
>>> At 05:02 PM 4/18/2007, you wrote:
 Greetings!

 I have inherited a vanadium EXAFS data set (due to a group member
 graduating - lucky dog!) that is giving me major fits.  I am getting
 consistent numbers with all my fits which visually look fantastic,
 that is until I look at the numbers...one Debye-Waller factor is
 negative (a V-O path) and the Eo's are large, the V-Cl path is on
 the order of -20 eV, the V=O path is on the order of 17 eV, and the
 V-O path falling at -11 eV.  ARe there any "tricks" outside of
 restraints or constraints that I can attempt to get more realistic
 values?  (I understand that a large Eo can be realistic, but a
 negative Debye-Waller factor doesn't make sense.)  I can restrain
 the V-O Debye-Waller factor and get a positive value, but then the
 V=O D-W factor is negative.  If I restrain both D-W factors, the fit
 falls apart, suggesting something else is wrong that I just can't find.

 Another issue I'm having involves something in Artemis that's
 confusing me.  Sometimes after a fit, the Artemis Pallet shows the
 V=O feature as the one at 1.8 Angstroms and the V-O feature at 1.6
 Angstroms, completely reversed to the FEFF model.  I have seen this
 when I separated the chlorides as well (I attempted to model the Cl
 at different distances as reported by Deguns, et. al. (attach

Re: [Ifeffit] large Eo's and neg. D-W factors

[Richard Mayes]

Scott,

Thanks for the clues!  The restraints seem to be working to get the DW
factors positive.  I'm still battling Ifeffit reversing the paths, but
things are getting slowly better.

Rich

> Hi Rich,
>
> I know you posted this a while ago, so you may have gotten other
> answers, but I don't see them in my overflowing inbox. :)
>
> Years ago, I did some work with V2O3, and it was a very stubborn
> system to get a good fit on. Other people I knew who were working on
> the system have also had some trouble. This and other evidence led to
> some people publishing speculations on local distortions that get
> averaged out in XRD but show up in EXAFS. I also recall people
> talking about similar difficulties with other vanadium oxide systems.
> (Sorry; I don't have those references handy anymore, but searches
> should locate them).
>
> As far as the second issue you mention, with Ifeffit reversing the
> position of two atoms of the same species, it does happen some times.
> Why not? A V-O path is basically a V-O path to FEFF; it doesn't know
> that one's a single bond and one's a double bond. But since moving a
> path by more than about 0.1 Angstrom in Ifeffit starts to reduce the
> accuracy of the FEFF calculation, it's something you do want to try
> to prevent. One way to do that is with restraints; it shouldn't take
> much incentive for Ifeffit to refrain from switching the paths.
>
> --Scott Calvin
> Sarah Lawrence College
>
>
> At 05:02 PM 4/18/2007, you wrote:
>>Greetings!
>>
>>I have inherited a vanadium EXAFS data set (due to a group member
>>graduating - lucky dog!) that is giving me major fits.  I am getting
>>consistent numbers with all my fits which visually look fantastic,
>>that is until I look at the numbers...one Debye-Waller factor is
>>negative (a V-O path) and the Eo's are large, the V-Cl path is on
>>the order of -20 eV, the V=O path is on the order of 17 eV, and the
>>V-O path falling at -11 eV.  ARe there any "tricks" outside of
>>restraints or constraints that I can attempt to get more realistic
>>values?  (I understand that a large Eo can be realistic, but a
>>negative Debye-Waller factor doesn't make sense.)  I can restrain
>>the V-O Debye-Waller factor and get a positive value, but then the
>>V=O D-W factor is negative.  If I restrain both D-W factors, the fit
>>falls apart, suggesting something else is wrong that I just can't find.
>>
>>Another issue I'm having involves something in Artemis that's
>>confusing me.  Sometimes after a fit, the Artemis Pallet shows the
>>V=O feature as the one at 1.8 Angstroms and the V-O feature at 1.6
>>Angstroms, completely reversed to the FEFF model.  I have seen this
>>when I separated the chlorides as well (I attempted to model the Cl
>>at different distances as reported by Deguns, et. al. (attached) due
>>to the immediate environment around the V in our sample being
>>similar to the one they report in scheme 1-(I), p5008).  Attached is
>>a text file that shows an Artemis Pallet output illustrating what
>>I'm trying to describe for the V=O and V-O paths.  The Artemis
>>project that generated the output is also attached.
>
>
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Re: [Ifeffit] Athena and Artemis reference

[Richard Mayes]

Mihail,

Go to  ; the cititation is listed under the
"Hephaestus, Athena, Artemis" link.  The Ifeffit citation is also listed
under its link.

Cheers,
Rich



> Dear Bruce,
> What reference we can give in our papers for using Athena and Artemis
> packages, which you guys have been provided so generously to the user
> community?
> Thanks,
> Mihail
>
> -
> Dr Mihail Ionescu
> Senior Research Scientist
> Ion Beam Accelerator Applications
> Australian Nuclear Science and Technology Organisation ANSTO
> Bld. 53, New Illawarra Rd, Lucas Heights, NSW 2234
> Australia
>
> PMB1, Menai, NSW 2234
> Ph: +612 9717 3301
> Fax: +612 9717 3257
> -
>
>
>
>
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Re: [Ifeffit] Help with MoOx fitting

[Richard Mayes]

T.D.Tilley's molecular precursors may be a good model of the local 
environment around the molybdenum (Chem. Mater. 2005, 17(7), 1818-1828). 
  I don't remember if he gives a crystal structure for his 
Moly-silicates, but it's a starting place.  If you can find the crystal 
structure for a moly-silicate, you should be able to build a decent 
model using a blank Atoms template.

HTH,

-Richard Mayes


g d wrote:
> Hi all,
> Is there anyone having experience with MoOx fitting? The sample I have is 
> MoOx supported on structured silica (most possibly with tetrahedral 
> coordination, because it's R space and EXAFS is very like that of 
> (NH4)2MoO4). The only standard atom.inp files I have are MoO3.inp and 
> MoO2.inp. I didn't get good fitting with these two. Is it better that I use 
> the standard file that corresponding to tetrahedron? If so, could any one 
> share the atom.inp file with me? Thank you so much!
> 
> Gd
> 
> _
> The average US Credit Score is 675. The cost to see yours: $0 by Experian. 
> http://www.freecreditreport.com/pm/default.aspx?sc=660600&bcd=EMAILFOOTERAVERAGE
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Re: [Ifeffit] viewing individual Fourier components with Athena

[Richard Mayes]

Bruce,

There was a miscommunication dealing with what I was told to do.  Sorry 
for the confusion.

Rich

Bruce Ravel wrote:
> On Tuesday 20 March 2007 16:36, Richard Mayes wrote:
>> Basically, I have been asked to plot what Artemis gives for the theory
>> when an individual path is plotted, except I'm supposed to do it for the
>> raw data...that is, plot the individual paths that sum to the observed
>> chi(k).
>>
>> However, looking at the picture from some old rhodium dimer EXAFS given
>> to me by the good guy that signs my checks ;-) (a pic I'm supposed to
>> use as a guide), I'm "chasing a rabbit."  Problem solved (it's a "use
>> the theory, Homer" moment, i.e. DO'OH!).
> 
> Richard,
> 
> I'm confused in the same way that Scott is.  There is no way to
> deconstruct your chi(k) data into path components a priori.  The only
> way that we have understanding data in a path-by-path manner is to
> compute some theory and plot each of the paths from the theory.  Even
> better is to do a fit and plot each of the paths after the fitted
> parameters have been evaluated.
> 
> It occurs to me that you may be thinking of Fourier filtering the
> peaks.  That is done in Athena by placing an R window around some
> region of your chi(R) spectrum then pressing the "kq" button.  A word
> of caution -- plotting a Fourier filtered spectrum is NOT the same
> thing as plotting a path.  In certain situations, a path from Feff and
> the Fourier filter of a region of chi(R) might be very similar.
> Indeed, they might be sufficiently similar that the filtered spectrum
> can be interpretted as the contribution from a path. 
> 
> More often, however, that is a very flawed assumption.  In any
> situation where two or more paths conbtribute to a peak in chi(R) (and
> excellent example would be the first peak in iron metal, which
> contains contributions from the first two coordination shells and
> which cannot be separated by Fourier filtering) it would be quite
> incorrect to call the filtered specutm a "path contribution". 
> 
> HTH,
> B
> 
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Re: [Ifeffit] viewing individual Fourier components with Athena

[Richard Mayes]

Scott,

Basically, I have been asked to plot what Artemis gives for the theory 
when an individual path is plotted, except I'm supposed to do it for the 
raw data...that is, plot the individual paths that sum to the observed 
chi(k).

However, looking at the picture from some old rhodium dimer EXAFS given 
to me by the good guy that signs my checks ;-) (a pic I'm supposed to 
use as a guide), I'm "chasing a rabbit."  Problem solved (it's a "use 
the theory, Homer" moment, i.e. DO'OH!).

Thanks for the help!

Richard




Scott Calvin wrote:
> Hi Richard,
> 
> I'm not sure what you're asking for. Do you mean you'd like to see 
> individual paths? If so, the answer is no. Athena only processes the 
> data; individual paths require a model (if we could get them straight 
> out of data, things would be much simpler!). Modeling is done via 
> Artemis, not Athena. But I may have misunderstood your question.
> 
> --Scott Calvin
> Sarah Lawrence College
> 
> At 04:53 PM 3/20/2007, you wrote:
>> Hello all.
>>
>> Is it possible to view the individual Fourier components of a Fourier
>> transformed EXAFS spectrum in Athena?  If so, can someone please direct
>> me toward the documentation that explains how I can do this.
> 
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[Ifeffit] viewing individual Fourier components with Athena

[Richard Mayes]

Hello all.

Is it possible to view the individual Fourier components of a Fourier 
transformed EXAFS spectrum in Athena?  If so, can someone please direct 
me toward the documentation that explains how I can do this.



Thanks!
-Richard Mayes



Barnes Group
450/452 Buehler Hall
Dept. of Chemistry
Univ. of Tennessee
Knoxville, TN 27996
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Re: [Ifeffit] CN and bond distances in Artemis

[Richard Mayes]

Juan,

There are 2 ways to apply the self-absorption correction in Athena.  The 
first way is to pick thicknesses starting with a couple microns and 
going thicker and thicker until the correction has no effect.  I like 
this method because it gives an idea of the effects that thickness and 
concentration can have on the fluorescence.  The other way is to simply 
use a thickness that will be in the infinite thickness domain to begin 
with.  Either way, you get the information needed.


To do the self-absorption correction in Athena go to Data then 
self-absorption, pick your algorithm (I suggest reading the Athena 
document section to see which you should use), plug in the formula for 
the sample and then either plot the information depth or plot data and 
correction.


Rich

Juan Antonio Maciá Agulló wrote:


Ok, how can I apply an "infinite" sample correction? The other samples are
measured also in fluorescence mode, then is it better to measure Ptfoil in the
same conditions (fluorescence)?

Thanks a lot

Best regards,
JA

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Re: [Ifeffit] Artemis import error

[Richard Mayes]

Bruce,

I am now able to import my data from the Athena project file into 
Artemis.  I had quotes around my group name ("TiO4") and when I removed 
the quotes Artemis opened the file.  I didn't expect the " " around the 
group name to be a problem, but that is what it appears to be.


Thanks for the help!

Rich

Bruce Ravel wrote:

On Monday 23 October 2006 10:46, Richard Mayes wrote:

I'm having trouble importing an Athena project file into Artemis.  When
I try to import a particular set of data into Artemis as an Athena
project file, Artemis keeps giving the errors "Use of uninitialized
value in...at artemis line 11223." (where the ... is either hash element
or method).  I have attached a screenshot (.jpg) of the error message
and the offending data as an Athena project file.

I can open the rest of my data in Artemis with no problems, even from a
file with this data in it, but when I try to open this set of data, it
won't work.  Any ideas on what the problem is?


Hi Rich,

I am on travel right now and will return to beamtime when I get home on 
Wednesday.  So I won't be able to look into this properly until next week.  

I cannot replicate your problem on my linux computer, so you're going to have 
to wait until I can look on my windows computer back home before I can offer 
any useful feedback.


B


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[Ifeffit] Incorporating FEFF8 into IFEFFIT

[Richard Mayes]

Bruce,

I have just recieved a copy of FEFF8.  Is there a way to incorporate it 
into Artemis on the windows version of IFEFFIT?  In theory, we should be 
able to play a "shell game" with the names of the executable files and 
get FEFF8 to work while IFEFFIT thinks it's running FEFF6l (by changing 
the FEFF6l.exe file to something else, and rename the FEFF8 file to 
FEFF6l.exe) and then replace the DAT files to those for FEFF8.


Is this possible or is it just better to run FEFF8 independently and 
import the .inp files into Artemis?


Rich Mayes

Barnes Group
Dept. of Chemistry
Univ. of Tennessee
Knoxville, TN 37996
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