headers
Anatoly I Frenkel | 10 Aug 2012 17:48
Favicon

XANES-2012 short course at Brookhaven

Dear IFEFFIT subscribers:

Please find below the information about the short course on X-ray absorption spectroscopy that will be
organized at Brookhaven National Laboratory on Nov. 8-10, 2012

Either follow the link in the bottom of the NSLS web page: http://www.nsls.bnl.gov
or go directly to the course web site: http://workshops.ps.bnl.gov/default.aspx?w=XANES2012

The short course in X-ray absorption near edge structure (XANES) spectroscopy will be offered on November
8-10 at the NSLS. To qualify for admission, participants should have prior background in XAS theory
and/or experiment and data analysis. The course will consist of lectures, in-class demonstrations and
hands-on data analysis sessions.  The lectures cover the XANES fundamentals, surveys recent
developments in theory and data analysis, the commonly used computer codes (FEFF and others), data
modeling techniques, and specific applications of XANES to research problems.  

The course enrollment is limited to 30 participants.
Application deadline: September 30, 2012. 

Best regards,
Anatoly Frenkel
Yeshiva University
Permalink | Reply |
headers
Huaming Guo | 20 Aug 2012 15:02
Picon
Favicon

Re: How to fit "N" number of Neigbors in (D)Artemis?


Dear Colleague,

I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to be a constant in the (D)Artemis. We can not set the variable for this parameter. How can I do that if I model non crystalline samples using (D)Artemis? Thanks a lot.

Regards

Huaming Guo 

-------------------------------------------
Prof.Dr. Huaming Guo
School of Water Resources & Environment
China University of Geosciences
Beijing 100083
P.R.China
Tel: 0086-10-82321366
Fax: 0086-10-82321081
Email: hmguo <at> cugb.edu.cn
-------------------------------------------



Anatoly I Frenkel 写:

> Dear IFEFFIT subscribers:
> 
> Please find below the information about the short course on X-ray absorption spectroscopy that will be organized at Brookhaven National Laboratory on Nov. 8-10, 2012
>  
> Either follow the link in the bottom of the NSLS web page: http://www.nsls.bnl.gov
> or go directly to the course web site: http://workshops.ps.bnl.gov/default.aspx?w=XANES2012
>  
> The short course in X-ray absorption near edge structure (XANES) spectroscopy will be offered on November 8-10 at the NSLS. To qualify for admission, participants should have prior background in XAS theory and/or experiment and data analysis. The course will consist of lectures, in-class demonstrations and hands-on data analysis sessions.  The lectures cover the XANES fundamentals, surveys recent developments in theory and data analysis, the commonly used computer codes (FEFF and others), data modeling techniques, and specific applications of XANES to research problems.  
> 
> The course enrollment is limited to 30 participants.
> Application deadline: September 30, 2012. 
> 
> Best regards,
> Anatoly Frenkel
> Yeshiva University
> 
> _______________________________________________
> Ifeffit mailing list
> Ifeffit <at> millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit 

_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Permalink | Reply |
headers
Bruce Ravel | 20 Aug 2012 15:44
Favicon
Gravatar

Re: How to fit "N" number of Neigbors in (D)Artemis?

On Monday, August 20, 2012 09:02:28 PM Huaming Guo wrote:
> I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to be a
> constant in the (D)Artemis. We can not set the variable for this parameter.
> How can I do that if I model non crystalline samples using (D)Artemis?
> Thanks a lot. 

In Artemis, N is a pure number, but S02 can take a math expression.

In the EXAFS equation, N and S02 are multiplied together.

Thus, you might consider parameterizing the amplitude by setting N to
1 and putting all of the parameterization in the math expression for
S02.

B

--

-- 

 Bruce Ravel  ------------------------------------ bravel@...

 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
Permalink | Reply |
headers
Wei Li | 20 Aug 2012 15:53
Picon
Favicon

Re: How to fit "N" number of Neigbors in (D)Artemis?

Hi, Bruce,


Does that mean each shell has a different S02 value?

Wei

On Mon, Aug 20, 2012 at 9:44 AM, Bruce Ravel <bravel-IGkKxAqZmp0@public.gmane.org> wrote:
On Monday, August 20, 2012 09:02:28 PM Huaming Guo wrote:
> I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to be a
> constant in the (D)Artemis. We can not set the variable for this parameter.
> How can I do that if I model non crystalline samples using (D)Artemis?
> Thanks a lot.

In Artemis, N is a pure number, but S02 can take a math expression.

In the EXAFS equation, N and S02 are multiplied together.

Thus, you might consider parameterizing the amplitude by setting N to
1 and putting all of the parameterization in the math expression for
S02.

B


--

 Bruce Ravel  ------------------------------------ bravel-IGkKxAqZmp0@public.gmane.org

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

 Homepage:    http://xafs.org/BruceRavel
 Software:    https://github.com/bruceravel
_______________________________________________
Ifeffit mailing list
Ifeffit-yJARRRr6MatzaV5c7wqwxA@public.gmane.orgaps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit



--
Wei Li

Postdoc researcher
Environmental Soil Chemistry Group
Delaware Environmental Institute
University of Delaware, Newark,19713
Tel:631-949-0663
http://ag.udel.edu/soilchem/li.html

_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Permalink | Reply |
headers
Bruce Ravel | 20 Aug 2012 16:13
Favicon
Gravatar

Re: How to fit "N" number of Neigbors in (D)Artemis?

On Monday, August 20, 2012 09:53:13 AM Wei Li wrote:
> Hi, Bruce,
> 
> Does that mean each shell has a different S02 value?

No.  It means that S02 must be evaluated for each path.  

Or, I suppose, I should say that the product of N and S02 must be
evaluated for each path.  

No!  No!  Actually, I should say that the product of N and S02 must be
evaluated correctly for each path where what I mean by "correctly"
depends upon the details of your fitting model.

That sounds right!

If you are fitting your copper foil data, then "correctly" probably
means to let N be the path degeneracy found by the path finder and to
use a single S02 parameter for all paths.

If you are fitting a crystal with different sites for the absorbing
atom -- say the super conductor YBa2Cu3O7, which has 1 Cu atom in the
Cu1 site and 2 Cu atoms in the Cu2 site -- then your parameterization
of S02 must be scaled accordingly depending on which Feff calculation
the path comes from.

If you are fitting an amorphous solid or a nanoparticle or something
else which unknown coordination, then you are probably best off
setting N to 1 and parameterizing S02 for each path in some manner
that captures the details of the coordination environment that you are
trying to measure.

Remember, N and S02 are multiplied together in the EXAFS equation.

HTH,
B

> Wei
> 
> On Mon, Aug 20, 2012 at 9:44 AM, Bruce Ravel <bravel@...> wrote:
> > On Monday, August 20, 2012 09:02:28 PM Huaming Guo wrote:
> > > I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to
> > 
> > be a
> > 
> > > constant in the (D)Artemis. We can not set the variable for this
> > 
> > parameter.
> > 
> > > How can I do that if I model non crystalline samples using (D)Artemis?
> > > Thanks a lot.
> > 
> > In Artemis, N is a pure number, but S02 can take a math expression.
> > 
> > In the EXAFS equation, N and S02 are multiplied together.
> > 
> > Thus, you might consider parameterizing the amplitude by setting N to
> > 1 and putting all of the parameterization in the math expression for
> > S02.
> > 
> > B
> > 
> > 
> > --
> > 
> >  Bruce Ravel  ------------------------------------ bravel@...
> >  
> >  National Institute of Standards and Technology
> >  Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
> >  Building 535A
> >  Upton NY, 11973
> >  
> >  Homepage:    http://xafs.org/BruceRavel
> >  Software:    https://github.com/bruceravel
> > 
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit@...
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

--

-- 

 Bruce Ravel  ------------------------------------ bravel@...

 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
Permalink | Reply |
headers
Huaming Guo | 20 Aug 2012 15:24
Picon
Favicon

Re: How to fit "N" number of Neigbors in (D)Artemis?


Thanks. In this case, is the number of neibors equal to N * SO2 in the model result? 

Regards

HM

Bruce Ravel 写:

> On Monday, August 20, 2012 09:02:28 PM Huaming Guo wrote:
>> I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to be a
>> constant in the (D)Artemis. We can not set the variable for this parameter.
>> How can I do that if I model non crystalline samples using (D)Artemis?
>> Thanks a lot. 
> 
> In Artemis, N is a pure number, but S02 can take a math expression.
> 
> In the EXAFS equation, N and S02 are multiplied together.
> 
> Thus, you might consider parameterizing the amplitude by setting N to
> 1 and putting all of the parameterization in the math expression for
> S02.
> 
> B
> 
> 
> -- 
> 
>  Bruce Ravel  ------------------------------------ bravel <at> bnl.gov
> 
>  National Institute of Standards and Technology
>  Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
>  Building 535A
>  Upton NY, 11973
> 
>  Homepage:    http://xafs.org/BruceRavel
>  Software:    https://github.com/bruceravel
> _______________________________________________
> Ifeffit mailing list
> Ifeffit <at> millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit 

_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Permalink | Reply |
headers
Scott Calvin | 20 Aug 2012 16:24

Re: How to fit "N" number of Neigbors in (D)Artemis?

Just to fill out some details about how this somewhat quirky aspect of Ifeffit/Artemis can be used:

Suppose you want to find the degeneracy of nearest-neighbors, represented by path 1, and next-nearest
neighbors, represented by path 2. To fit the degeneracy of one of the paths,

1. Set "N" to 1 for both paths.

2. Create parameters named, say, "amp," "N1," and "N2." 

3. Fill in the N box for both the first and second path with "1" (not "N1" and "N2"!)

4. Fill in the S02 box for path 1 with "amp*N1" and for path 2 with "amp*N2."

5. EXAFS does not contain enough information to guess all three parameters; one of them must be set. Often,
that is amp, perhaps because it is obtained from a standard. But maybe it's N1: you might know the
near-neighbor coordination, but not the next-nearest neighbors. In any case, you need to set at least one
of the three parameters to a known (or suspected) value.

6. All your named parameters now mean what you think they should mean in the log files: e.g., "N2" is the
coordination number for the next-nearest neighbors. But the "S02" path parameter in the log files is
amp*N1 for the first path and amp*N2 for the second path. That's kind of confusing, but because you've
designed your guess/def/set parameters effectively, it's not a problem!

Hope that helps...

--Scott Calvin
Sarah Lawrence College

On Aug 20, 2012, at 9:24 AM, Huaming Guo wrote:

> 
> Thanks. In this case, is the number of neibors equal to N * SO2 in the model result?  
> 
> Regards 
> 
> HM 
> 
> Bruce Ravel 写: 
> 
> > On Monday, August 20, 2012 09:02:28 PM Huaming Guo wrote: 
> >> I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to be a 
> >> constant in the (D)Artemis. We can not set the variable for this parameter. 
> >> How can I do that if I model non crystalline samples using (D)Artemis? 
> >> Thanks a lot.  
> >  
> > In Artemis, N is a pure number, but S02 can take a math expression. 
> >  
> > In the EXAFS equation, N and S02 are multiplied together. 
> >  
> > Thus, you might consider parameterizing the amplitude by setting N to 
> > 1 and putting all of the parameterization in the math expression for 
> > S02. 
> >  
> > B 
> >  
> >  
> > --  
> >  
> >  Bruce Ravel  ------------------------------------ bravel <at> bnl.gov 
> >  
> >  National Institute of Standards and Technology 
> >  Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 
> >  Building 535A 
> >  Upton NY, 11973 
> >  
> >  Homepage:    http://xafs.org/BruceRavel 
> >  Software:    https://github.com/bruceravel 
> > _______________________________________________ 
> > Ifeffit mailing list 
> > Ifeffit <at> millenia.cars.aps.anl.gov 
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit 
> 
> _______________________________________________
> Ifeffit mailing list
> Ifeffit <at> millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________
Ifeffit mailing list
Ifeffit <at> millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Permalink | Reply |

Gmane