Re: [Ifeffit] Questions about fitting of EXAFS

[Fuxiang Zhang]

Thank you all for the answers.
The Kmax effect on the shape of magnitude of FTs of one of my samples may
come from the low signal/noise ratio.
I still not sure if there's any physical meaning of DeltaE0, Does it relate
to the shift of absorption edge?

Fuxiang

On Thu, Aug 4, 2016 at 1:35 PM, Scott Calvin 
wrote:

> I’ll add to Bruce’s comment that if the choice of kmax has a great effect
> on the parameters found by the fit, that’s an indication of a problem! Good
> fits should be stable to modest changes in kmax (e.g., an inverse angstrom
> or two one way or another). The statistics may suggest one kmax or another
> is somewhat better, but the fitted parameters should not be drifting
> outside of the ranges defined by their uncertainties. If they are, you have
> an unstable fit. In that case, there are several possibilities: perhaps you
> are including an artifact in your k-range (e.g. the beginning of another
> edge) or a lot of data dominated by noise. Or perhaps your model is having
> trouble distinguishing between two fitting minima, and is flipping back and
> forth between them (this is more likely if your fitting model is fairly
> complicated, with many free parameters). In any case, if you’re fit is
> highly sensitive to kmax you should investigate to try to determine why.
>
> —Scott Calvin
> Sarah Lawrence College
>
> > On Aug 4, 2016, at 11:07 AM, Bruce Ravel  wrote:
> >
> >>
> >> 2. The cutting range of Kmax (FT transform parameters) has great effect
> >> on FTs of EXAFS, how do I know to use the best value of Kmax;
> >
> > If you have measured data with signal well above the level of noise, why
> would you choose to use less data?
> >
> > Similarly, if, at some point in your data, the signal becomes dominated
> by noise -- either statistical or systematic -- why would you include it in
> the analysis?
>
>
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Re: [Ifeffit] Questions about fitting of EXAFS

[Scott Calvin]

I’ll add to Bruce’s comment that if the choice of kmax has a great effect on 
the parameters found by the fit, that’s an indication of a problem! Good fits 
should be stable to modest changes in kmax (e.g., an inverse angstrom or two 
one way or another). The statistics may suggest one kmax or another is somewhat 
better, but the fitted parameters should not be drifting outside of the ranges 
defined by their uncertainties. If they are, you have an unstable fit. In that 
case, there are several possibilities: perhaps you are including an artifact in 
your k-range (e.g. the beginning of another edge) or a lot of data dominated by 
noise. Or perhaps your model is having trouble distinguishing between two 
fitting minima, and is flipping back and forth between them (this is more 
likely if your fitting model is fairly complicated, with many free parameters). 
In any case, if you’re fit is highly sensitive to kmax you should investigate 
to try to determine why.

—Scott Calvin
Sarah Lawrence College

> On Aug 4, 2016, at 11:07 AM, Bruce Ravel  wrote:
> 
>> 
>> 2. The cutting range of Kmax (FT transform parameters) has great effect
>> on FTs of EXAFS, how do I know to use the best value of Kmax;
> 
> If you have measured data with signal well above the level of noise, why 
> would you choose to use less data?
> 
> Similarly, if, at some point in your data, the signal becomes dominated by 
> noise -- either statistical or systematic -- why would you include it in the 
> analysis?


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Re: [Ifeffit] Questions about fitting of EXAFS

[Bruce Ravel]

On 08/03/2016 05:36 PM, Fuxiang Zhang wrote:

Hi, Everyone,
I have several detailed questions about EXAFS processing and fitting
1. Are there any physical meaning for DeltaE0 in the paths, why it
should be less than 10eV


This paper is a good explanation of why Delta E0 should be reasonably sized:

https://doi.org/10.1107/S0909049598002970



2. The cutting range of Kmax (FT transform parameters) has great effect
on FTs of EXAFS, how do I know to use the best value of Kmax;


If you have measured data with signal well above the level of noise, why 
would you choose to use less data?


Similarly, if, at some point in your data, the signal becomes dominated 
by noise -- either statistical or systematic -- why would you include it 
in the analysis?




3. How to make refinement equation for multi-scattering paths?
Such as in NiFe alloys (simple fcc structure), the path [Ni-FM-3m] Fe1.1
Ni1.4 Fe1.1., I use 0.67*Efe+0.33*Eni for DeltaE0, and
0.67*ssFe1+0.33*ssNi4 for sigma2, is that right?
Many thanks


Have you been reading the messages posted on this mailing list?  If so, 
you have certainly noticed that I often answer questions like this one 
in terms of whether or not a fitting result is "defensible".  For example:


http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05551.html
http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04067.html
http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg00396.html

and many others.

Make use of the resources at

http://bruceravel.github.io/XAS-Education/
http://bruceravel.github.io/demeter/
http://xafs.org/Tutorials

and elsewhere.

Check out Scott's book,

https://www.crcpress.com/XAFS-for-Everyone/Calvin/p/book/9781439878637

or Grant's book

http://www.cambridge.org/us/academic/subjects/physics/condensed-matter-physics-nanoscience-and-mesoscopic-physics/introduction-xafs-practical-guide-x-ray-absorption-fine-structure-spectroscopy?format=HB


The library at your university may have either or both of those.

B

--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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[Ifeffit] Questions about fitting of EXAFS

[Fuxiang Zhang]

Hi, Everyone,
I have several detailed questions about EXAFS processing and fitting
1. Are there any physical meaning for DeltaE0 in the paths, why it should
be less than 10eV
2. The cutting range of Kmax (FT transform parameters) has great effect on
FTs of EXAFS, how do I know to use the best value of Kmax;
3. How to make refinement equation for multi-scattering paths?
Such as in NiFe alloys (simple fcc structure), the path [Ni-FM-3m] Fe1.1
Ni1.4 Fe1.1., I use 0.67*Efe+0.33*Eni for DeltaE0, and
0.67*ssFe1+0.33*ssNi4 for sigma2, is that right?
Many thanks

Fuxiang Zhang
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Re: [Ifeffit] Questions

[Bruce Ravel]

On 06/06/2016 11:50 AM, dien...@srs.gov wrote:

I am using Demeter Artemis version 9.18, however, I could not open the
Artemis file that was generated from Artemis Version 9.21 from my
collaborator, anyone can instruct or help? Thanks.


Since you did not provide any actual ... y'know ... information about 
the problem, there is nothing I can possibly do to help.


http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html

Robert's advice seems pretty good to me.

B

--
 Bruce Ravel   bra...@bnl.gov

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

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Questions

[Robert Gordon]

Has it occurred to you to upgrade your version (and your colleague too)? 
Current version is 0.9.24.


-R.

On 6/6/2016 8:50 AM, dien...@srs.gov wrote:

Hi, All

I am using Demeter Artemis version 9.18, however, I could not open the 
Artemis file that was generated from Artemis Version 9.21 from my 
collaborator, anyone can instruct or help? Thanks.


Dien Li, Ph.D.
Environmental Sciences and Biotechnology
Savannah River National Laboratory
Aiken, South Carolina, 29808
Tel: 803-725-7520


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[Ifeffit] Questions

[Dien . Li]

Hi, All

I am using Demeter Artemis version 9.18, however, I could not open the 
Artemis file that was generated from Artemis Version 9.21 from my 
collaborator, anyone can instruct or help? Thanks.

Dien Li, Ph.D.
Environmental Sciences and Biotechnology
Savannah River National Laboratory
Aiken, South Carolina, 29808
Tel: 803-725-7520
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Re: [Ifeffit] Questions to Bruce

[Godfrey, Ian]

>" How many scans did you try to import? ... There is a memory limit." (Robert)

>"Having said that, this is quite the file for Athena to work with: 100 element 
>Ge detector data with separate columns of FFn, SCA2.n, ICRn, and OCRn for each 
>element n. In my hands (Windows 8.1, 64 bit, Demeter Athena 0.9.24 using 
>Ifeffit backend), I get a Perl interpreter crash if I try to import >50 
>selected Ge FF columns into a single mu(E), and in any case can only select up 
>to 87 columns." (Erik)

There's a limit to how many datasets Athena can handle at any given time, see:

http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04818.html
http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04817.html

Ian

Ian Godfrey

PhD Student,
UCL/JAIST Programme

Industrial Doctorate Centre in Molecular Modelling and Materials Science,
Department of Chemistry,
University College London,

And

School of Materials Science,
Japan Advaned Institute of Science and Technology

i.godf...@ucl.ac.uk<mailto:i.godf...@ucl.ac.uk> 
i.godf...@jaist.ac.jp<mailto:i.godf...@jaist.ac.jp>

02076 794864

From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of 
Robert Gordon
Sent: 23 March 2016 22:57
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Questions to Bruce

Hi Dien,

To perhaps forestall a scolding from Bruce, let me point out the following 
advice on
error reporting:
https://bruceravel.github.io/demeter/pods/bugs.pod.html

RE:1. I am able to import multiple scans with reference data. My test was to 
try 3 scans and
associated reference data. I am using version 0.9.24. How many scans did you 
try to import?
Is there a problem with one of the scans you tried to import? There is a memory 
limit.
More information is needed to diagnose the problem you are having. It does not 
seem to
be a bug in the software. Look for the log file
that may contain information on why the program crashed. What does it say?
"Each of the GUI programs (Athena, Artemis, and Hephaestus) writes its output 
messages to a log file.
In win 7 to 10, This can be found in C:\Users\\AppData\Roaming\

RE: 2. It opens fine for me. Win10pro x64 system using version 0.9.24 with the 
SSRL plugin registry
entries selected. Did you activate the SSRLmicro plugin? If I deactivate it, I 
cannot read the file.

regards,
Robert
On 3/23/2016 2:51 PM, dien...@srs.gov<mailto:dien...@srs.gov> wrote:
HI, Bruce and Matt

I have two questions for you, please help me.

1. I collected U EXAFS data on APS 10-ID, while I input a single data file with 
reference data in Athena, it was OK, however, when I input multiple data files 
(scans) also with reference data, it was crushed. I could input multiple data 
files without reference data, which Matt helped me trouble shoot. The Demeter 
8.24 version is used on my computer, I believe. Matt suggested me to update to 
the current version. I do not know if other users have this problem.

2. I have a U EXAFS data file which was collected at SSRL, however, I could not 
input this data file using Athena, how to fix this? format? See the attachment. 
thanks you so much.




Dien Li, Ph.D.
Environmental Sciences and Biotechnology
Savannah River National Laboratory
Aiken, South Carolina, 29808
Tel: 803-725-7520




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Re: [Ifeffit] Questions to Bruce

[Robert Gordon]

Hi Dien,

To perhaps forestall a scolding from Bruce, let me point out the 
following advice on

error reporting:
https://bruceravel.github.io/demeter/pods/bugs.pod.html

RE:1. I am able to import multiple scans with reference data. My test 
was to try 3 scans and
associated reference data. I am using version 0.9.24. How many scans did 
you try to import?
Is there a problem with one of the scans you tried to import? There is a 
memory limit.
More information is needed to diagnose the problem you are having. It 
does not seem to

be a bug in the software. Look for the log file
that may contain information on why the program crashed. What does it say?
"Each of the GUI programs (Athena, Artemis, and Hephaestus) writes its 
output messages to a log file.

In win 7 to 10, This can be found in C:\Users\\AppData\Roaming\

RE: 2. It opens fine for me. Win10pro x64 system using version 0.9.24 
with the SSRL plugin registry
entries selected. Did you activate the SSRLmicro plugin? If I deactivate 
it, I cannot read the file.


regards,
Robert

On 3/23/2016 2:51 PM, dien...@srs.gov wrote:

HI, Bruce and Matt

I have two questions for you, please help me.

1. I collected U EXAFS data on APS 10-ID, while I input a single data 
file with reference data in Athena, it was OK, however, when I input 
multiple data files (scans) also with reference data, it was crushed. 
I could input multiple data files without reference data, which Matt 
helped me trouble shoot. The Demeter 8.24 version is used on my 
computer, I believe. Matt suggested me to update to the current 
version. I do not know if other users have this problem.


2. I have a U EXAFS data file which was collected at SSRL, however, I 
could not input this data file using Athena, how to fix this? format? 
See the attachment. thanks you so much.





Dien Li, Ph.D.
Environmental Sciences and Biotechnology
Savannah River National Laboratory
Aiken, South Carolina, 29808
Tel: 803-725-7520


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Re: [Ifeffit] Questions on Correlated Debye in FEFF6

[Bruce Ravel]

Doran,

You mentioned not finding what you were looking for in the code, so
most of my answers are in the form of links to the relevant bits of
code.


I have just recently begun learning about EXAFS and running EXAFS
simulations using FEFF6. I have a few very basic questions about the
underlying calculations for the correlated Debye model implemented in
FEFF6 (called by DEBYE keyword). For the questions below, I am
assuming I input a single crystallographic structure and want the
correlated Debye model to simulate the influence of a thermal
distribution on the EXAFS spectrum.  I would appreciate any insight you
can give me into the questions below. I would also welcome any and all
references for the original papers where that is appropriate.


This is the reference for the correlated Debye model used in Feff,
Ifeffit, and Larch:  http://dx.doi.org/10.1103/PhysRevB.20.4908


1. Are the Debye-Waller factors calculated for each path individually?
(It seems like they should be since the paths will have different levels
of influence from the thermal distribution of atomic positions)


Yes.  From the Ifeffit manual:
http://cars.uchicago.edu/~ifeffit/refman/node19.html

From the Larch manual:
http://cars.uchicago.edu/xraylarch/xafs/feffpaths.html#models-for-calculating 




2. Assuming the DW factors are calculated path-by-path, is the magnitude
of the DW  factor determined by assuming the total path length R is the
appropriate length to use for the correlation term in the Debye spectral
density? It seems like it would not be reasonable to treat all paths of
the same R as having the same Debye-Waller factor since a single
scattering path and multiple scattering paths are perturbed by a
different set of relative atomic motion that are likely to have
different correlations. I couldn’t locate a clear statement about how
this calculations is actually done within the code.


In Ifeffit:
https://github.com/newville/ifeffit/blob/master/src/lib/sigms.f

In Larch:
https://github.com/xraypy/xraylarch/blob/master/plugins/xafs/sigma2_models.py 



The CDM is calculated on a path-by-path basis.  R matters.



3. Is the C1 shift that results from the vibrational motion normal to
the bond axis along a path incorporated in the calculation? (Presumably
using \Delta C1 = sigma_perp^2/(2r)) And is this formula still
appropriate in multiple-scattering paths?


In Ifeffit:
https://github.com/newville/ifeffit/blob/master/src/lib/chipth.f#L103

In Larch:
https://github.com/xraypy/xraylarch/blob/master/plugins/xafs/feffdat.py#L377


4. Assuming the C1 shift is incorporated, does the correlated Debye
model assume that the perpendicular and parallel displacements have the
same spectral density?


I think the answer is yes, but I am not sure I understand the
question.

HTH,
B


--
 Bruce Ravel   bra...@bnl.gov

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

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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[Ifeffit] Questions on Correlated Debye in FEFF6

[Bennett, Doran (D)]

Hi Everyone,

I have just recently begun learning about EXAFS and running EXAFS simulations 
using FEFF6. I have a few very basic questions about the underlying 
calculations for the correlated Debye model implemented in FEFF6 (called by 
DEBYE keyword). For the questions below, I am assuming I input a single 
crystallographic structure and want the correlated Debye model to simulate the 
influence of a thermal distribution on the EXAFS spectrum.  I would appreciate 
any insight you can give me into the questions below. I would also welcome any 
and all references for the original papers where that is appropriate.

1. Are the Debye-Waller factors calculated for each path individually? (It 
seems like they should be since the paths will have different levels of 
influence from the thermal distribution of atomic positions)

2. Assuming the DW factors are calculated path-by-path, is the magnitude of the 
DW  factor determined by assuming the total path length R is the appropriate 
length to use for the correlation term in the Debye spectral density? It seems 
like it would not be reasonable to treat all paths of the same R as having the 
same Debye-Waller factor since a single scattering path and multiple scattering 
paths are perturbed by a different set of relative atomic motion that are 
likely to have different correlations. I couldn't locate a clear statement 
about how this calculations is actually done within the code.

3. Is the C1 shift that results from the vibrational motion normal to the bond 
axis along a path incorporated in the calculation? (Presumably using \Delta C1 
= sigma_perp^2/(2r)) And is this formula still appropriate in 
multiple-scattering paths?

4. Assuming the C1 shift is incorporated, does the correlated Debye model 
assume that the perpendicular and parallel displacements have the same spectral 
density?



Thank you for the assistance!

Doran



Doran I. G. Bennett
The Dow Chemical Company
Core RD, Inorganic Material and Heterogeneous Catalysis
Phone: (610)-244-7062
Alternate Phone: (630)-222-2906

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Re: [Ifeffit] Questions for Artemis fit

[Scott Calvin]

Hi Yanyun,

The shift observed in R-space is due to the effect of the potential of the 
absorbing and scattering atoms. 

You are asking a series of questions that, while thoughtful, are covered in 
basic tutorials and XAFS textbooks. I suggest you search for introductions to 
XAFS analysis, many of which are freely available and which come in many forms 
(videos, tutorial files, wikis, PowerPoints, chapters/books, etc.) and work 
through one or more of them.

Beginners are encouraged to use this list, but beginners and advanced users 
alike are also urged to see if the answer to their questions is readily and 
clearly available elsewhere first.

--Scott Calvin
Sarah Lawrence College

On Aug 20, 2014, at 1:11 AM, huyan...@physics.utoronto.ca wrote:

 Hi all,
 
 Does Feff take into account of the radius of the each atom when it  
 calculates atom-pair distance? I am wondering if the calculated  
 atom-pair distance (Reff) in each SS path has already excluded the  
 radius size of absorber and scatterer atoms? In the R-space spectra, I  
 always have a big peak at R smaller than any of the calculated path  
 distances, in other words, I feel there is no possible path  
 contributing to this peak.
 
 My goal is trying to understand where the filler atom is in a unit  
 cell, so if the above question is 'yes', the true position of the  
 filler atoms is very likely to be far away from the site I input in  
 the ATOM file ?
 
 Best regards,
 Yanyun
 
 
 Quoting Scott Calvin scal...@sarahlawrence.edu:
 
 Hi Yanyun,
 
 This topic has been dealt with multiple times on the mailing list.  
 Please search the archive:
 
 http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/
 
 For example, searching for sites will give you several discussions  
 of the topic.
 
 --Scott Calvin
 Sarah Lawrence College
 
 On Aug 19, 2014, at 2:49 PM, huyan...@physics.utoronto.ca  
 huyan...@physics.utoronto.ca wrote:
 
 Hi all,
 
 How would you deal with the case that the absorber atoms are occupying
 two different crystallography sites? Should I still use/guess the same
 'S02' for paths calculated from two sites?
 
 Best,
 Yanyun
 
 
 Quoting huyan...@physics.utoronto.ca:
 
 Hi Scott,
 
 Thank you for giving me detailed examples. I will go with your
 suggestion and try to reduce free parameters.
 
 Best,
 Yanyun
 Quoting Scott Calvin scal...@sarahlawrence.edu:
 
 Hi Yanyun,
 
 On Aug 19, 2014, at 12:05 PM, huyan...@physics.utoronto.ca wrote:
 
 But my question is, for each path there are a set of Path Parameters,
 does that mean we have to fit this set of path parameters independent
 from those used in other paths?  For instance, if I am going to
 include 30 paths in my fitting, do I need to guess about 150
 (30*5=150) parameters (except guess the same 'enot' for all paths)?
 
 No. One of the great principles of Ifeffit (and thus Artemis) is
 that the path parameters do not have to be the same as the fit
 parameters.
 
 As a simple example, it's good to start with the model that all
 paths have the same value for E0. So you can guess a single
 parameter and then use that parameter for the E0 for all paths.
 
 As another simple example, a cubic crystal might be modelled as
 having a uniform thermal (or Vegard's law) expansion. Then there
 could be a single guessed parameter indicating the fractional
 expansion (called, for example, alpha) while the delr for each path
 could then be entered as alpha*reff.
 
 Much more complicated constraint schemes are possible, but for fits
 with large number of paths, the number of guessed parameters is
 almost always much much lower than the number of path parameters.
 
 
 As shown on the fit Log file, the Correlation value between two fit
 parameters is the bigger the better, or the smaller the better?
 
 Not necessarily. Correlations are provided to help understand the
 relationship between guessed parameters, but there's nothing
 inherently wrong with a high correlation...the uncertainty
 associated with that relationship is already represented in the
 uncertainties reported with the fit. In other words, it is more
 direct to focus on getting the uncertainties to be lower, rather
 than the correlations.
 
 --Scott Calvin
 Sarah Lawrence College
 
 
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Re: [Ifeffit] Questions for Artemis fit

[huyanyun]

Hi Dr. Newville,

I had similar situation and questions as with choosing Path  
Parameters. My goal is to identify the occupancy sites for a doped  
element in my sample. We have a rough guess of two possible sites,  
part of the doped atoms are filling a void site of the unit cell, the  
other part is to substitute an existing atom sites.


I was being able to writing two ATOM files and run FEFF twice to  
calculate all possible PATH. But when I was going to define/guess the  
parameters ('N','amp', 'enot', 'delr','ss')for EACH path, I totally  
lost idea how to group all those paths, or how to guess all those five  
parameters for each path. Of course, I couldn't get a good fit as I  
don't know how to build the model and to refine parameters in this step.


Here I post my understanding of the five parameters: 'N', path  
degeneracy, or coordination number; 'amp', usually close to 1, but as  
I have doping elements, I am expecting small partial numbers in some  
of the 'amp' to adjust for partial occupancy; 'enot', I think it is  
just the energy shift of your spectra, and as I believe my spectra are  
well aligned, I will SET 'enot' to zero. 'delr' is the variation of  
the real atom-atom distances from the calculated ones (I think I need  
to group paths to refine 'delr' but I don't know what's the criteria  
to group paths). 'ss' is to consider about the disorder effect and  
typically I use the Debye model.  Let me know if I am wrong in any way.


Could you please give me some suggestion how did you get started? I am  
looking forward to hearing from you.


Best regards,
Yanyun

Quoting Matt Newville newvi...@cars.uchicago.edu:


On Mon, Aug 18, 2014 at 7:45 PM, 이국승 lks3...@postech.ac.kr wrote:


  Dr Newville,

Thank you for your reply.

My first question is that I did not find the atoms.inp file in the demeter
installer. If that is true, where can I get the atoms.inp file?


You might find what you're looking for at
http://cars9.uchicago.edu/~newville/adb/search.htmlMetallic Au (fcc) is
there.


Anyway, I did copy and paste the atoms.inp file of an old version of
Artemis from my colleague's PC. I followed the Artemis intruction video for
fitting Au foil data.



Hmm, it seems likely that you missed a step.


I filled the crystal lattice information, run atoms, and Feff calculation.


Did you import and define a Path after doing this calculation?  Did you
define Path Parameters and variables for this fit?


Finally I clicked the Fit button and I got the error message that I
attached. Now here is my second question. What can I do to successfully Fit
without errors? Do you have any idea from the error message?


It indicates that you have defined variables to refine in the fit ('amp',
'enot', and so forth) but not explained how those variables should alter
the EXAFS signal.   You'll probably want to use these in the Path
Parameters for the first shell Au-Au scattering.  But, you are doing the
analysis, so the most important thing is that you understand how the
variables you are asking to be refined actually effect the EXAFS signal.
These error messages are a feature of the program to remind you that you
need to understand the model you are using for the EXAFS signal.

So,  what do you intend 'amp', 'enot', 'delr', and 'ss' to do?If you
don't know, go back and review the tutorial information.  The goal is not
to get a fit, the goal is to understand what the fit results mean.

Another question (it might seem random, but it is not):  what is your
fitting range?

--Matt

PS: to be clear, these are not rhetorical questions.  If you feel the need
to respond, please actually think about and answer all questions above.




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Re: [Ifeffit] Questions for Artemis fit

[Matt Newville]

On Tue, Aug 19, 2014 at 9:55 AM, huyan...@physics.utoronto.ca wrote:

 Hi Dr. Newville,

 I had similar situation and questions as with choosing Path Parameters. My
 goal is to identify the occupancy sites for a doped element in my sample.
 We have a rough guess of two possible sites, part of the doped atoms are
 filling a void site of the unit cell, the other part is to substitute an
 existing atom sites.

 I was being able to writing two ATOM files and run FEFF twice to calculate
 all possible PATH. But when I was going to define/guess the parameters
 ('N','amp', 'enot', 'delr','ss')for EACH path, I totally lost idea how to
 group all those paths, or how to guess all those five parameters for each
 path. Of course, I couldn't get a good fit as I don't know how to build the
 model and to refine parameters in this step.

 Here I post my understanding of the five parameters: 'N', path degeneracy,
 or coordination number; 'amp', usually close to 1, but as I have doping
 elements, I am expecting small partial numbers in some of the 'amp' to
 adjust for partial occupancy; 'enot', I think it is just the energy shift
 of your spectra, and as I believe my spectra are well aligned, I will SET
 'enot' to zero. 'delr' is the variation of the real atom-atom distances
 from the calculated ones (I think I need to group paths to refine 'delr'
 but I don't know what's the criteria to group paths). 'ss' is to consider
 about the disorder effect and typically I use the Debye model.  Let me know
 if I am wrong in any way.

 Could you please give me some suggestion how did you get started? I am
 looking forward to hearing from you.


For each Path in a model, you need
a) a Feff.dat file -- this can be read from any Feff calculation, and
those can be generated from a crystal structure
b) a set of Path Parameters -- the physically meaningful quantities
N*S02, E0, deltaR, sigma2, etc from the EXAFS Equation.

Each of the Path Parameters is given as an equation in terms of the set of
Fit Parameters.  Often times, the equations are very simple.That is,
sigma2 for Path1 may simply be defined to be evaluated from 'ss'.  You
could make it 'ss*2', or something else.

There is also a set of Fit Parameters -- named quantities that may be
adjusted in the fit to make the sum of Paths best match your data.  These
can be set, in which case they are frozen -- not varied in the fit.In
Artemis, the Fit Parameters are shown in the Guess/Set/Def  page.   The
quantities like enot, delr, ss, etc are Fit Parameters.  You need to
fill out an expression for each Path Parameter you want changed in the fit
in terms of the set of Fit Parameters.

Artemis will help you by complaining if some of the Fit Parameters defined
are not used in any Path Parameters -- changing these values won't alter
the fit, so you should not have them defined as a variable Fit Parameter.

The system is designed to be very flexible.  But this means that before you
do a fit you need to understand what each of the Fit Parameters does to the
Path Parameters for the Paths you are using in the fit.   We could guess
that by enot, you mean the value for the Path Parameter 'E0', and that
you want to make sure that the E0 Path Parameter is given as enot for all
Paths.   But this would be only a guess.   You are setting up the model, so
you have to ask yourself why you have a variable 'enot', and what that
means for your model.

--Matt
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Re: [Ifeffit] Questions for Artemis fit

[huyanyun]

Hi Matt,

Thank you for your quick response. Your explanations of the Path  
Parameter and Fit Parameter are very clear. Basically we have to guess  
Fit parameters in GDS page and to know what a Fit Parameter does to  
your Path Parameters by using math expression.


But my question is, for each path there are a set of Path Parameters,  
does that mean we have to fit this set of path parameters independent  
from those used in other paths?  For instance, if I am going to  
include 30 paths in my fitting, do I need to guess about 150  
(30*5=150) parameters (except guess the same 'enot' for all paths)?


As shown on the fit Log file, the Correlation value between two fit  
parameters is the bigger the better, or the smaller the better?


Thanks,
Yanyun

Quoting Matt Newville newvi...@cars.uchicago.edu:


On Tue, Aug 19, 2014 at 9:55 AM, huyan...@physics.utoronto.ca wrote:


Hi Dr. Newville,

I had similar situation and questions as with choosing Path Parameters. My
goal is to identify the occupancy sites for a doped element in my sample.
We have a rough guess of two possible sites, part of the doped atoms are
filling a void site of the unit cell, the other part is to substitute an
existing atom sites.

I was being able to writing two ATOM files and run FEFF twice to calculate
all possible PATH. But when I was going to define/guess the parameters
('N','amp', 'enot', 'delr','ss')for EACH path, I totally lost idea how to
group all those paths, or how to guess all those five parameters for each
path. Of course, I couldn't get a good fit as I don't know how to build the
model and to refine parameters in this step.

Here I post my understanding of the five parameters: 'N', path degeneracy,
or coordination number; 'amp', usually close to 1, but as I have doping
elements, I am expecting small partial numbers in some of the 'amp' to
adjust for partial occupancy; 'enot', I think it is just the energy shift
of your spectra, and as I believe my spectra are well aligned, I will SET
'enot' to zero. 'delr' is the variation of the real atom-atom distances
from the calculated ones (I think I need to group paths to refine 'delr'
but I don't know what's the criteria to group paths). 'ss' is to consider
about the disorder effect and typically I use the Debye model.  Let me know
if I am wrong in any way.

Could you please give me some suggestion how did you get started? I am
looking forward to hearing from you.



For each Path in a model, you need
a) a Feff.dat file -- this can be read from any Feff calculation, and
those can be generated from a crystal structure
b) a set of Path Parameters -- the physically meaningful quantities
N*S02, E0, deltaR, sigma2, etc from the EXAFS Equation.

Each of the Path Parameters is given as an equation in terms of the set of
Fit Parameters.  Often times, the equations are very simple.That is,
sigma2 for Path1 may simply be defined to be evaluated from 'ss'.  You
could make it 'ss*2', or something else.

There is also a set of Fit Parameters -- named quantities that may be
adjusted in the fit to make the sum of Paths best match your data.  These
can be set, in which case they are frozen -- not varied in the fit.In
Artemis, the Fit Parameters are shown in the Guess/Set/Def  page.   The
quantities like enot, delr, ss, etc are Fit Parameters.  You need to
fill out an expression for each Path Parameter you want changed in the fit
in terms of the set of Fit Parameters.

Artemis will help you by complaining if some of the Fit Parameters defined
are not used in any Path Parameters -- changing these values won't alter
the fit, so you should not have them defined as a variable Fit Parameter.

The system is designed to be very flexible.  But this means that before you
do a fit you need to understand what each of the Fit Parameters does to the
Path Parameters for the Paths you are using in the fit.   We could guess
that by enot, you mean the value for the Path Parameter 'E0', and that
you want to make sure that the E0 Path Parameter is given as enot for all
Paths.   But this would be only a guess.   You are setting up the model, so
you have to ask yourself why you have a variable 'enot', and what that
means for your model.

--Matt




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Re: [Ifeffit] Questions for Artemis fit

[Bruce Ravel]

Yanyun, Kug-Seung,

Have you watched the videos that the folks at Diamond kindly host at

  http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html

The ones titled Introduction to Artemis and EXAFS fitting and More
Artemis and EXAFS fitting go a long way towards answering the
questions you both are asking.  Granted, you have to look at my ugly
face for a long time, which is pretty horrifying.  But I think you
might find them helpful.

B

--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Questions for Artemis fit

[huyanyun]

Hi all,

How would you deal with the case that the absorber atoms are occupying  
two different crystallography sites? Should I still use/guess the same  
'S02' for paths calculated from two sites?


Best,
Yanyun


Quoting huyan...@physics.utoronto.ca:


Hi Scott,

Thank you for giving me detailed examples. I will go with your  
suggestion and try to reduce free parameters.


Best,
Yanyun
Quoting Scott Calvin scal...@sarahlawrence.edu:


Hi Yanyun,

On Aug 19, 2014, at 12:05 PM, huyan...@physics.utoronto.ca wrote:


But my question is, for each path there are a set of Path Parameters,
does that mean we have to fit this set of path parameters independent
from those used in other paths?  For instance, if I am going to
include 30 paths in my fitting, do I need to guess about 150
(30*5=150) parameters (except guess the same 'enot' for all paths)?


No. One of the great principles of Ifeffit (and thus Artemis) is  
that the path parameters do not have to be the same as the fit  
parameters.


As a simple example, it's good to start with the model that all  
paths have the same value for E0. So you can guess a single  
parameter and then use that parameter for the E0 for all paths.


As another simple example, a cubic crystal might be modelled as  
having a uniform thermal (or Vegard's law) expansion. Then there  
could be a single guessed parameter indicating the fractional  
expansion (called, for example, alpha) while the delr for each path  
could then be entered as alpha*reff.


Much more complicated constraint schemes are possible, but for fits  
with large number of paths, the number of guessed parameters is  
almost always much much lower than the number of path parameters.




As shown on the fit Log file, the Correlation value between two fit
parameters is the bigger the better, or the smaller the better?


Not necessarily. Correlations are provided to help understand the  
relationship between guessed parameters, but there's nothing  
inherently wrong with a high correlation...the uncertainty  
associated with that relationship is already represented in the  
uncertainties reported with the fit. In other words, it is more  
direct to focus on getting the uncertainties to be lower, rather  
than the correlations.


--Scott Calvin
Sarah Lawrence College


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[Ifeffit] Questions for Artemis fit

[이국승]

 Dear,
I am a biginer in this area and I have two stupid questions.

I met a problem while I was trying to fit a Au foil data using Artemis following the process of'Artemis instruction videos' which (I guess) was made by Bruce.
I followed exactly the same procedure as the 'Artemis instruction video'. But, when I click the Fit button, a popup window appeared with some error messages. The image of the popup window is attached.

Before I met this problem, I could not load the 'atoms.inp' when I clicked the 'Import crystal data or a Feff calculation' button. The atoms.inp file does not exist in any place of my PC. I installed demeter again, and nothing different. Does demeter installer file not contain atoms.inp file?

Your kind instruction or explanation will be deeply appreciated.
Thank you.

Kug-Seung Lee



Fit error.PNG
Description: Binary data
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[Ifeffit] Questions for Artemis fit

[이국승]

 Dear,
I am a biginer in this area and I have two stupid questions.
I met a problem while I was trying to fit a Au foil data using Artemis following the process of'Artemis instruction videos' which (I guess) was made by Bruce.
I followed exactly the same procedure as the 'Artemis instruction video'. But, when I click the Fit button, a popup window appeared with some error messages. The image of the popup window is attached.

Before I met this problem, I could not load the 'atoms.inp' when I clicked the 'Import crystal data or a Feff calculation' button. The atoms.inp file does not exist in any place of my PC. I installed demeter again, and nothing different. So, I did copy and paste the atoms.inp file from one of the old version Artemis installed my colleague's PC. Does demeter installer file not contain atoms.inp file? 

Your kind instruction or explanation will be deeply appreciated.
Thank you.

Kug-Seung Lee





Fit_error.PNG
Description: Binary data
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Re: [Ifeffit] Questions for Artemis fit

[이국승]

 Dr Newville,
Thank you for your reply.
My first question is that I did not find the atoms.inp file in the demeter installer. If that is true, where can I get the atoms.inp file?

Anyway, I did copy and paste the atoms.inp file of an old version of Artemisfrom my colleague's PC. Ifollowed the Artemis intruction videofor fitting Au foil data. I filled the crystal lattice information, run atoms, and Feff calculation.Finally I clicked the Fit button and I got the error message that I attached. Now hereis mysecond question. What can I do to successfully Fit without errors? Do you have any idea from the error message?

Sincerely
Kug-Seung Lee



 원본 메일 내용 보낸 사람 : "Matt Newville"newvi...@cars.uchicago.edu받는 사람 : "XAFS Analysis using Ifeffit" ifeffit@millenia.cars.aps.anl.gov메일 제목 : Re: [Ifeffit] Questions for Artemis fit보낸 날짜 : Mon, 18 Aug 2014 07:14:05 -0500

Hi 

On Mon, Aug 18, 2014 at 3:01 AM, 이국승 lks3...@postech.ac.kr wrote:

Dear,I am a biginer in this area and I have two stupid questions.I met a problem while I was trying to fit a Au foil data using Artemis following the process of 'Artemis instruction videos' which (I guess) was made by Bruce.I followed exactly the same procedure as the 'Artemis instruction video'. But, when I click the Fit button, a popup window appeared with some error messages. The image of the popup window is attached.Before I met this problem, I could not load the 'atoms.inp' when I clicked the 'Import crystal data or a Feff calculation' button. The atoms.inp file does not exist in any place of my PC. I installed demeter again, and nothing different. So, I did copy and paste the atoms.inp file from one of the old version Artemis installed my colleague's PC. Does demeter installer file not contain atoms.inp file?
It does not. Was there a second question?

You definitely need to have a Feff calculation to do the fit, and an atoms.inp file is a reasonable way to start that.  You need to run the Feff calculation and select some paths from that calculation. 
Of course, it's hard for us to tell which steps in the video you did or did not "follow exactly". You need to run Feff, have a Path defined and selected as "use for this fit', and the parameters used for this Path need to all be defined. 
--Matt
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Re: [Ifeffit] Questions for Artemis fit

[Matt Newville]

On Mon, Aug 18, 2014 at 7:45 PM, 이국승 lks3...@postech.ac.kr wrote:

   Dr Newville,

 Thank you for your reply.

 My first question is that I did not find the atoms.inp file in the demeter
 installer. If that is true, where can I get the atoms.inp file?

You might find what you're looking for at
http://cars9.uchicago.edu/~newville/adb/search.htmlMetallic Au (fcc) is
there.

 Anyway, I did copy and paste the atoms.inp file of an old version of
 Artemis from my colleague's PC. I followed the Artemis intruction video for
 fitting Au foil data.


Hmm, it seems likely that you missed a step.

 I filled the crystal lattice information, run atoms, and Feff calculation.

Did you import and define a Path after doing this calculation?  Did you
define Path Parameters and variables for this fit?

 Finally I clicked the Fit button and I got the error message that I
 attached. Now here is my second question. What can I do to successfully Fit
 without errors? Do you have any idea from the error message?

It indicates that you have defined variables to refine in the fit ('amp',
'enot', and so forth) but not explained how those variables should alter
the EXAFS signal.   You'll probably want to use these in the Path
Parameters for the first shell Au-Au scattering.  But, you are doing the
analysis, so the most important thing is that you understand how the
variables you are asking to be refined actually effect the EXAFS signal.
These error messages are a feature of the program to remind you that you
need to understand the model you are using for the EXAFS signal.

So,  what do you intend 'amp', 'enot', 'delr', and 'ss' to do?If you
don't know, go back and review the tutorial information.  The goal is not
to get a fit, the goal is to understand what the fit results mean.

Another question (it might seem random, but it is not):  what is your
fitting range?

--Matt

PS: to be clear, these are not rhetorical questions.  If you feel the need
to respond, please actually think about and answer all questions above.
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[Ifeffit] questions about ifeffit

[Artillery]

Hi,
  
 I am a student from Shanghai. Now I am using IFEFFIT to do my thesis. Athena 
is useful to process the raw data and provides figures after background removal 
or E-k space transformation. I want to know whether I can obtain the processed 
data. For example, the data after the spectrum has been normalized. How can I 
get these data?
 I am looking forward to your reply.
  
 Best regards,
 Jingyuan___
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Re: [Ifeffit] questions about ifeffit

[Matt Newville]

Athena has pull down menus to export data to ASCII column files.
'nor' gives the normalized XAFS.  See

http://bruceravel.github.io/demeter/aug/output/index.html

On Mon, Mar 24, 2014 at 7:27 AM, Artillery katie_wu0...@qq.com wrote:
 Hi,

 I am a student from Shanghai. Now I am using IFEFFIT to do my thesis. Athena
 is useful to process the raw data and provides figures after background
 removal or E-k space transformation. I want to know whether I can obtain the
 processed data. For example, the data after the spectrum has been
 normalized. How can I get these data?
 I am looking forward to your reply.

 Best regards,
 Jingyuan

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-- 
--Matt
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Re: [Ifeffit] questions about ifeffit

[Alison Tebo]

Hi Jingyuan,

You can save any plot that you make under PlotSave last plot as...
You can also export your data to be graphed in whatever other program you
choose. Bruce specifically goes over this in the Athena document:
http://bruceravel.github.io/demeter/aug/output/column.html

Best,
Alison Tebo


On Mon, Mar 24, 2014 at 1:27 PM, Artillery katie_wu0...@qq.com wrote:

 Hi,

 I am a student from Shanghai. Now I am using IFEFFIT to do my thesis.
 Athena is useful to process the raw data and provides figures after
 background removal or E-k space transformation. I want to know whether I
 can obtain the processed data. For example, the data after the spectrum has
 been normalized. How can I get these data?
 I am looking forward to your reply.

 Best regards,
 Jingyuan

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[Ifeffit] questions related to ifeffit fitting

[davood dar]

Respected Sir,



I am new in the field of EXAFS. I have few questions regarding
to IFEFFIT i.e., fitting of theoretical models to the  experimental EXAFS
data.

1.What is the ideal value of R- factor for any fit.

2.  ** Can we use (fit) the theoretical model generated from square
pyramidal structure to EXAFS  data of  octahedral structure by assigning
degeneracy of 2 for the apical atom. OR using octalhedral for square planar
by not using apical path



Yours faithfully

Davood Ah. Dar

EXAFS research scholar

India
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[Ifeffit] questions regarding to ifeffit fitting

[davood dar]

Respected Sir,



I am new in the field of EXAFS. I have few questions regarding
to IFEFFIT i.e., fitting of theoretical models to the  experimental EXAFS
data.

1.   What is the ideal value of R- factor for any fit.

2.  *   * Can we use (fit) the theoretical model generated from square
pyramidal structure to EXAFS  data of  octahedral structure by assigning
degeneracy of 2 for the apical atom. OR using octalhedral for square planar
by not using apical path



Yours faithfully

Davood Ah. Dar

EXAFS research scholar

India
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[Ifeffit] questions about plotting old fits with demeter/artemis

[Georges Siddiqi]

Hi All,

I recently upgraded to the new version of demeter/athena/artemis, and while
it is very nice to use, I am thoroughly lost in some areas.

In the old version of Artemis, it is very easy to select old fits and plot
them compared to the experimental data/new fits.  I cannot figure out how
to do this in the new version.

The tutorial merely says The history plotting tool is not currently
working, making it difficult to write this bit of documentation!

Currently what I do is goto the history box of the main window, and goto
the plot tool tab, but I can only add the 9 first fits to the plotting
list.

Any suggestions?  am I missing something obvious? or is this (as the
tutorial implies) a functionality that hasnt been added yet?

thanks,
georges
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Re: [Ifeffit] questions about plotting old fits with demeter/artemis

[Bruce Ravel]

I answered a similar question two weeks ago:

http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012-October/010782.html

Between beamtime and hurricanes, I have not made progress since then.
As I said, improviing this is on my to-do list.

B


On Tuesday, November 13, 2012 11:24:08 AM Georges Siddiqi wrote:
 Hi All,
 
 I recently upgraded to the new version of demeter/athena/artemis, and while
 it is very nice to use, I am thoroughly lost in some areas.
 
 In the old version of Artemis, it is very easy to select old fits and plot
 them compared to the experimental data/new fits.  I cannot figure out how
 to do this in the new version.
 
 The tutorial merely says The history plotting tool is not currently
 working, making it difficult to write this bit of documentation!
 
 Currently what I do is goto the history box of the main window, and goto
 the plot tool tab, but I can only add the 9 first fits to the plotting
 list.
 
 Any suggestions?  am I missing something obvious? or is this (as the
 tutorial implies) a functionality that hasnt been added yet?
 
 thanks,
 georges


-- 

 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

 Homepage:http://xafs.org/BruceRavel
 Software:https://github.com/bruceravel
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Re: [Ifeffit] questions and storms

[So. Muru]

Dear Bruce,
we are waiting for your best answers,
apart from that, please take care of you and your family,
yes, the resent storm was a big considerably, so please take care,

with warm regards
S Murugesan
Kalpakkam
Tamilnadu, India.

~~
Dr S Murugesan
Tamil Nadu
India

Email : muru...@gmail.com
~~

On Thu, Nov 1, 2012 at 8:19 PM, Bruce Ravel bra...@bnl.gov wrote:


 Hi all,

 I have received a number of questions and bug reports about the
 software -- both over the mailing list and via personal mail -- in the
 last few days.

 Because of the recent storm here in the eastern part of North America
 I have fallen a little behind.  I will address all the issues sent to
 me, but I may not respond for several days as I get caught up both at
 work and at home.  If you are waiting for an answer to your question
 -- please be patient, I won't forget about you.

 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

  Homepage:http://xafs.org/BruceRavel
  Software:https://github.com/bruceravel
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Re: [Ifeffit] questions concerning paper

[Matt Newville]

Dear Eckhard,

On Thu, May 22, 2008 at 6:32 AM,  [EMAIL PROTECTED] wrote:
 Hello,

 i have some questions concerning the xafs-formula in this paper (attached):
 Theoretical approaches to x-ray absorption fine structure (July 2000).
 The author explained on page 625 and 626 the parameters of this formula.
 I think, most of you have read this paper.

 I don't understand the meaning of lambda(k), the author wrote ... and
 lambda(k) is the energy-dependent XAFS mean free path (not to be confused
 with the de Broglie wavelength).
 My question is, the mean free path whereof? The propagating
 photoelektron(wave) or the (back)scattered waves?

Yes (that is both). This lambda(k) is the mean-free-path for a
photo-electron of wavenumber k.
That is, it is the mean distance that a photo-electron will travel
before it scatters inelastically (and incoherently) from electrons (or
phonons, etc) in the material.   These scatterings are from the
low-energy electrons, and do not include the back-scattering from
the highly localized electrons of the cores of neighboring atoms:
those scattering events will be elastic and coherent, and give rise to
the XAFS.

This lamdba(k) is essentially the same mean-free-path for a
photo-electron used in other electron spectroscopies, and has a
classic U-shape when plotted as a function of k.  I say essentially
because we often fold into this term that the finite lifetime of the
core-hole, which also limits how far the photo-electron can travel and
still have an empty space at home to return to.

Odysseus, the photo-electron (an EveryParticle: though we like to
think of it as special, it is really indistinguishable from its
neighbors) leaves home for war, and has many adventures on his way
home which might prevent him from ever getting back.  Meanwhile, there
is a long line of people waiting to take his place at home.

 In the next sentence, what is the overall amplitude factor S_0^2? How is
 it defined?

S_0^2 accounts for the relaxation of ALL THE OTHER electrons in the
absorbing atom.   The other core electrons respond a bit to ripping
the 1s (or other) core electron out of the atom, which makes the atom
that the photo-electron sees on returning slightly different from when
it left.
S_0^2 is simply the overlap of the N-1 electrons in the ground state
atom with the N-1 electrons in the excited atom.  It has to be less
than 1, but is typically close to 1.0.   With this definition, S_0^2
should have no energy dependence, but there are other processes
(multi-electron excitations, for example) that can be considered as
relaxation of the other electrons in the atom that may have energy
dependence.

Odysseus is gone for a very long time: can he even recognize home when
he gets back?  Will they recognize him

 In conjunction with question one i don't understand the expression in the
 next paragraph for the term e^{-2R/lambda}. The author wrote: The decay
 of the wave (which wave does he mean?) due to the mean free path or finite
 lifetime (what does he mean?, finite lifetime of the emitted and
 propagating photoelektron wave?) [including core-hole lifetime] of the
 photoelectron is captured by ... Is it right, that the emitted
 photoelektron is detectable outside the sample?

The decay is of the photo-electron in that it may scatter into other
low-energy electron states.

The lifetime is the core-hole lifetime (how long the core-hole will
live before being filled, generally through an emission process such
as fluorescence.  This is typically in the femtosecond range.

The emitted photo-electron CAN escape the sample, though as the
mean-free-path is on the order of 5 to 30Ang, the photo-electrons
would only be from the top surface of the sample.   In fact, one can
(and some do!) measure XAFS using the emitted electrons.  Typically
the emitted electron current is dominated not by the primary
photo-electrons, but by the cascade of electrons the photo-electrons
and emitted Auger electrons cause as they scatter toward the sample
surface.  This is similar to the photo-currents measured with Auger
spectroscopy.


 Another parameter is the phase factor phi = arg f(k) ...reflects the
 quantum-mechanical wavelike nature of the backscattering. Please explain
 me the meaning of this parameter.

I'm not sure I can explain quantum mechanics.  The phi = arg f(k) here
(page 626, Fig 6b)  is the phase-shift of the photo-electron as it
scatters from the neighboring atom.   That is, scattering has a finite
effect on both the amplitude and phase of the photo-electron
wave-function.

The war changes Odysseus both physically and mentally.

 At the bottom of this page the author wrote: ...the Debye-Waller factor,
 which is given to a good approximation by e^{-2 sigma^2 k^2}. In this
 context he refers to figure 8, where k^2 chi(k) vs. k is plotted. I don't
 understand this context because there is no chi in the approximation for
 the Debye-Waller factor. Where comes the chi here?

chi(k)  is proportional to e^(-2 

Re: [Ifeffit] questions concerning paper

[Frenkel, Anatoly]

We should ask John Rehr to rename FEFF to Odysseus. It makes both physical and 
mythological sense. 

Anatoly


- Original Message -
From: [EMAIL PROTECTED] [EMAIL PROTECTED]
To: Ravel, Bruce; XAFS Analysis using Ifeffit 
ifeffit@millenia.cars.aps.anl.gov
Sent: Thu May 22 14:30:38 2008
Subject: Re: [Ifeffit] questions concerning paper

I loved it also,
thanks Matt :-)

May i cite your Odysseus explanation in my diploma thesis? ;)


 Original-Nachricht 
 Datum: Thu, 22 May 2008 12:40:01 -0400
 Von: Bruce Ravel [EMAIL PROTECTED]
 An: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
 Betreff: Re: [Ifeffit] questions concerning paper

 
 Matt,
 
 That was awesome!  I **loved** the Odysseus explanation of the exafs
 equation.  Quite possibly the best Ifeffit mailing list post ever.
 
 B
 
 
 
 -- 
  Bruce Ravel   [EMAIL PROTECTED]
 
  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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GMX startet ShortView.de. Hier findest Du Leute mit Deinen Interessen!
Jetzt dabei sein: http://www.shortview.de/[EMAIL PROTECTED]
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Re: [Ifeffit] questions concerning paper

[Barton, David (DG)]

Or maybe a prequel, describing his peaceful home life running around the
farm until the force, a bright light, came one day calling him to leave
home. 

  _ 
  David Barton, 

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Matt
Newville
Sent: Friday, May 23, 2008 4:04 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] questions concerning paper

Hi Eckhard,

On Thu, May 22, 2008 at 1:30 PM, E. Bosman [EMAIL PROTECTED] wrote:
 I loved it also,
 thanks Matt :-)

 May i cite your Odysseus explanation in my diploma thesis? ;)

Sure, that's what we're here for   Perhaps you could come up with
a better story, or write a sequel. ;).
Cheers,

--Matt
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[Ifeffit] Questions on EXAFS

[Rajasekaran S]

I have a couple of questions on the use of EXAFS:
1. How sensitive is EXAFS/XANES in determining ~ couple of ppm (up to
100ppm) of halogen content in solid content?
2. Also, are there lab-scale EXAFS/XANES equipments available towards this?
Anyone working on lab-scale equipments?

Thanks
Raja
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Re: [Ifeffit] Questions on EXAFS

[Matt Newville]

Raja,

On Sun, Mar 16, 2008 at 3:07 PM, Rajasekaran S [EMAIL PROTECTED] wrote:
 I have a couple of questions on the use of EXAFS:

 1. How sensitive is EXAFS/XANES in determining ~ couple of ppm (up to
 100ppm) of halogen content in solid content?

It depends, somewhat on what you mean.  Probably the simplest answer
is: EXAFS/XANES is terrible at telling the halogen content in solid
content. EXAFS/XANES studies one selected element, ignoring those
that are not directly bound to the element selected.   That it, it
would be pretty much useless at telling a Cl/Br ratio.

You may want to look into X-ray Fluorescence analysis, which can
non-destructively determine elemental abundances.

On the other hand, EXAFS/XANES can successfully measure the bonding of
Cl and Br when they are at 100ppm or so (perhaps less) in solid
content.  In my experience, EXAFS/XANES on elements at concentrations
of a few ppm is very challenging, though it does depend what the rest
of the system is.

 2. Also, are there lab-scale EXAFS/XANES equipments available towards this?
 Anyone working on lab-scale equipments?

There are lab-based EXAFS/XANES systems.  I believe Rigaku sells
machines for laboratory EXAFS.  They may be the only company to do so.

Hope that helps,

--Matt
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Re: [Ifeffit] Questions about Athena and XANES

[Jeff Terry]

Hi Jenny,

I just wanted to add a bit to Matt's answer on TEY vs FY and suggest a  
couple of reference for you.


There are three contributions to the TEY: photoelectrons, Auger  
Electrons, and secondary electrons. The secondary electrons will  
typically determine the maximum depth that you can observe in a TEY  
measurement. There is a good description of this in Jo Stohr's book,  
NEXAFS Spectroscopy which can be seen at google books.

http://tiny.cc/44VGq

There is also a quick synopsis of the book at: 
http://www-ssrl.slac.stanford.edu/stohr/nexafs.htm
At this site, there is a photoelectron spectrum showing the relative  
intensity of Auger and Photopeaks. The secondaries are roughly a  
factor of 100 more intense than the other contributions.


It is possible to measure both TEY and Auger electron yield (AEY) and  
you will see that the AEY is more surface sensitive that TEY.  
Measuring AEY requires an analyzer capable of discriminating the  
electron energy. AEY is typically performed at lower photon energies  
as there are not too many electron energy analyzers at hard x-ray  
facilities.


It is actually pretty difficult to try to calculate the maximum  
analysis depth for TEY because of the three different contributions.  
Here is an attempt to understand the probe depth of TEY but neglects  
secondary electrons: http://www.icdd.com/resources/axa/vol44/v44_058.pdf


For the K-edges in the hard x-ray regime, with TEY it would not be  
unrealistic to expect probe depths on the order of 1000 angstroms (100  
nm).


Jeff

On Feb 20, 2008, at 6:33 PM, Jenny Cai wrote:


Hi all,

Could someone please answer my questions? I would really appreciate  
your help.


1. For linear combination fitting, there are three indicators for  
the goodness of fitting: R-factor, chi-square and reduced chi- 
square. Could anyone tell me how they work?


2. Since TEY is sensitive for the surface and FY for the bulk (and  
surface?), species detected by TEY should be also detected by FY,  
right?


3. How to calculate the maximum analysis depths for TEY and FY?

Thank you in advance.


Jenny Cai




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Re: [Ifeffit] Questions about Athena and XANES

[Matt Newville]

Hi Jeff,

Thanks -- you're right.  I was only considering Auger electrons which
are more surface sensitive than the secondary electrons that actually
dominate most TEY measurements.

--Matt
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[Ifeffit] Questions about Athena and XANES

[Jenny Cai]

Hi all,

Could someone please answer my questions? I would really appreciate your help.

1. For linear combination fitting, there are three indicators for the goodness 
of fitting: R-factor, chi-square and reduced chi-square. Could anyone tell me 
how they work?

2. Since TEY is sensitive for the surface and FY for the bulk (and surface?), 
species detected by TEY should be also detected by FY, right? 

3. How to calculate the maximum analysis depths for TEY and FY? 

Thank you in advance.


Jenny Cai
 



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Re: [Ifeffit] Questions about Athena and XANES

[Matt Newville]

Hi Jenny,

 1. For linear combination fitting, there are three indicators for the
 goodness of fitting: R-factor, chi-square and reduced chi-square. Could
 anyone tell me how they work?

This is actually documented in Athena, and the Users Guide.  They are
also defined in the Feffit documentation.   In short, they are all
scaled measures ofSum [(data-fit)^2]

R-factor scales this my the data values, and chi-square scales by an
estimate of the noise in the data.
Reduced chi-square relates to chi-square through the usual statistical
definition, in that it is
chi-square / (number of free variables in the fit).

Of course, chi-square requires one to know the uncertainty in the data
-- generally we don't have a great estimate of this.  I mean no
offense of this, but if you're asking about these then you almost
certainly haven't put in an estimate of the uncertainty.  So
chi-square is probably scaled incorrectly.

On top of that, reduced chi-square needs to know the number of
independent measurements. Normally one assumes each datum to be
independent.  This is arguable, but it we can make that assumption for
now.  But if chi-square is scaled poorly, so is reduced chi-square.

If that's too vague, or I misunderstood the question, please ask again.

 2. Since TEY is sensitive for the surface and FY for the bulk (and
 surface?), species detected by TEY should be also detected by FY, right?

Yes, but TEY samples a much smaller volume of material than FY, so the
signal from the volume seen by TEY (that is, the surface) may be
insignificant compared to the signal from the volume seen by FY.

 3. How to calculate the maximum analysis depths for TEY and FY?

Google/Wikipedia might help here.  The sampling depth for TEY is
typically dominated by the mean-free-path for the Auger electrons,
which is in the range of 20 - 50 Angstroms.Sampling depths for FY
are typically set by the absorption length of fluorescence x-rays,
which is in the range of 2 to 50 microns (yes, a much more variable
range, depending on sample composition).

In both cases, you'd need to calculate the depth that the x-ray beam
penetrates the sample (depends strongly on matrix) too.  In my
experience, it's unusual for this to dominate the sampling depth, but
it can be significant for FY in high-Z matrices.

--Matt
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