Re: [Ifeffit] (no subject)

2023-04-25 Thread Kelly, Shelly Diane
Hello Joyti,

I'm not sure I know what your definition of 'exact' and 'average'.  The exafs 
signal comes from each atom that is probed by the x-ray beam. The total signal 
is exactly  an average of the local atomic environment of all atoms. If half 
the atoms have 4 carbon neighbors and the other half have 8 carbon neighbors at 
the same distance, the exafs signal will be that of 6 carbon neighbors.

Kind regards
Shelly



From: Ifeffit  on behalf of Anatoly 
Frenkel 
Sent: Monday, April 24, 2023, 11:06 AM
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] (no subject)

Joyti,

The coordination number of Rh-C bonds is defined as the total number of Rh-C 
bonds in the sample divided by the total number of Rh atoms in the sample.
Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary appointment)
Department of Chemistry (affiliate appointment)
Stony Brook University
Stony Brook, NY 11794
Email:  
anatoly.fren...@stonybrook.edu<https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0ybKTBGBlALcrWeszTCA..=mailto%3ajgchen%40columbia.edu>
http://you.stonybrook.edu/frenkel
Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2

Joint Appointment:
Senior Chemist
Chemistry Division, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov<mailto:fren...@bnl.gov>
https://www.bnl.gov/staff/frenkel
---


On Mon, Apr 24, 2023 at 12:25 PM Jyoti Pandey 
mailto:jyotipandey51...@gmail.com>> wrote:
Hello everyone,

I have a cluster of 13 Rh atoms above the graphene sheet. The first 
coordination number that I am getting is around 1.65 (which is obtained by 
choosing a Rh-C) path. I am curious to know whether this value is the "exact" 
or the "average" coordination number w.r.t all the Rh atoms.

Thanks

With Best Regards

Dr. Jyoti Pandey, Ph.D.
Postdoctoral Researcher
Department of Physics
Central Michigan University, MI, USA
Mobile No. +1-928-265-0599
.

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Re: [Ifeffit] (no subject)

2023-04-24 Thread Anatoly Frenkel
Joyti,

The coordination number of Rh-C bonds is defined as the total number of
Rh-C bonds in the sample divided by the total number of Rh atoms in the
sample.
Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary
appointment)
Department of Chemistry (affiliate appointment)
Stony Brook University
Stony Brook, NY 11794
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel
Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2

Joint Appointment:
Senior Chemist
Chemistry Division, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/staff/frenkel
---


On Mon, Apr 24, 2023 at 12:25 PM Jyoti Pandey 
wrote:

> Hello everyone,
>
> I have a cluster of 13 Rh atoms above the graphene sheet. The first
> coordination number that I am getting is around 1.65 (which is obtained by
> choosing a Rh-C) path. I am curious to know whether this value is the
> "exact" or the "average" coordination number w.r.t all the Rh atoms.
>
> Thanks
>
> With Best Regards
>
> Dr. Jyoti Pandey, Ph.D.
> Postdoctoral Researcher
> Department of Physics
> Central Michigan University, MI, USA
> Mobile No. +1-928-265-0599
> .
>
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Re: [Ifeffit] (no subject)

2019-05-20 Thread Ying Liu
Hi Sameh

I would recommend you to search in this website: https://xafs.org/Databases

Best wishes



 Ying LIU

223 G.O.Jones Building
Centre of Condensed Matter and Material Physics
Department of Physics and Astronomy
Queen Mary, University of London
327 Mile End Road, London, E1 4NS
United Kingdom
Tel: +44 (0) 7456740242
Email:  
ying@qmul.ac.uk



On 20 May 2019, at 11:46, Sameh Ibrahim Ahmed 
mailto:sameh2...@gmail.com>> wrote:

Dear collegues

I need the XAFS or XANES spectra for some material to use them in my analysis. 
Actually, I am not sure if there is a library for the XAFS spectra for 
different compounds available free online !. In fact, I need the spectra for 
the following elements and their oxides with different oxidation states as well
1- Ni
2- Fe
3- Mo
4- V
5- Co
6- Mn

Thank you in advance for your help.

Best regards


--
سامح إبراهيم أحمد
أستاذ مساعد الفيزياء
جامعة عين شمس
Sameh Ibrahim Ahmed
Associate professor of Physics
Ain-Shams University
Abbassia-11588
Cairo-EGYPT
email: sa...@sci.asu.edu.eg & 
sameh2...@gmail.com
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Re: [Ifeffit] (no subject)

2013-03-13 Thread Bruce Ravel
On Wednesday, March 13, 2013 08:24:41 PM davood dar wrote:
 1. *1*.What is the ideal value of R- factor for any fit.

R-factor is a way of expressing percentage misfit.  Smaller is
generally better, although smaller is not better if other aspects of
the fit are not defensible.  For instance, if one of the fitting
parameters is physically unreasonable, then getting a smaller R-factor
is not so useful.

R-factor is just one of the ways that the quality of the fit is
evaluated.

I discuss in some detail the statistical parameters reported by the
software here:

  https://speakerdeck.com/bruceravel/advanced-topics-in-exafs-analysis

 2.  *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

Making clever use of Feff calculation on known structures to
investigate unknown structures is something I talk about in 

  https://speakerdeck.com/bruceravel/modeling-non-crystalline-samples

Lots more information at

  http://xafs.org

and at

  http://bruceravel.github.com/demeter/

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] (no subject)

2012-05-06 Thread Anatoly I Frenkel
It sounds like a good idea but you will still need to know whether the best fit 
results for the bond length and third cumulant are correct. Since they are 
expected to vary widely for different cluster sizes and different substrates 
and different atmospheres, you should first try to see if your method will work 
for a more simple system where you know what the bond length and third cumulant 
should be, i.e. bulk Pt.
Besides, you may find something similar to what you are proposing in Bus and 
v.Bokhoven's article.

Anatoly

Sent from my mobile phone, please forgive typos


-Original message-
From: JeongEunSuk eunsuk1...@hotmail.com
To: ifeffit ifeffit@millenia.cars.aps.anl.gov
Sent: Mon, May 7, 2012 04:02:06 GMT+00:00
Subject: [Ifeffit] (no subject)

Hello
I measured temperature-dependent EXAFS at Pt L3 edge with Pt nanoparticles in 
room and high temperature(400 C). I have some questions about thermal vibration 
in EXAFS fit. I read that third and fourth culmulants related with phase and 
amplitude in anharmonic term, respectively. especially, I concerned third 
culmulant to relate with phase.
As you know, the phase also relates with bonding length. So that, the bonding 
length between Pt-Pt pair considerably correlated with third culmulant. So I 
can't decide exact bonding length and third culmulant because their 
correlation. I think that the relation of both bonding length and third 
culmulant is similar to that of number and debye-waller factor.
Is it right to find  bonding length and third culmulant like finding number and 
debye-waller factor using k-weight?
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Re: [Ifeffit] (no subject)

2010-01-19 Thread 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.
 



새로운 Windows 7: 여러분에게 맞는 최상의 PC를 찾으세요. 자세히 보기.   
  
_
새로운 Windows 7: 일상 작업을 단순화하세요. 여러분에게 맞는 최상의 PC를 찾으세요.
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Re: [Ifeffit] (no subject)

2010-01-19 Thread 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 eunsuk1...@hotmail.com

  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.


 --
 새로운 Windows 7: 여러분에게 맞는 최상의 PC를 찾으세요. 자세히 
 보기.http://windows.microsoft.com/shop

 --
 Windows 7: 일상 작업을 단순화하세요. 여러분에게 맞는 최상의 PC를 
 찾으세요.http://windows.microsoft.com/shop

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Re: [Ifeffit] (no subject)

2009-03-11 Thread Bruce Ravel
On Wednesday 11 March 2009 09:40:31 am Michael Jacob wrote:
 I measured Fe(II) edge EXAFS data for my protein that has two iron sites
 (Fe-Fe distance ~5A). My question is how to fit the model with the data?
 Can I discard the contribution of multiple scattering effects to the
 fitting? One most important information that I want to obtain is on the
 Fe-Fe distance. Is it enough to conclude from the raw data FT that the
 Fe-Fe distance
 in my protein sample has been changed in comparison to the Fe-Fe distance
 in the model (created with Feff using the crystal structure coordinates)? I
 try fitting using arthemis but got bad and weird results. is there any
 manual or step-by step guide that I can learn how to fit model of two metal
 sites to my data?

There is not a manual -- that is one of the great shortcomings of
Artemis compared to Athena.  There is, however, a LOT of useful
information among the Tutorials and Workshops pages at
http://xafs.org.  I don't know if you will find precisely what you are
looking for, but hopefully you will find enough that is relevant to
get you started.

Good luck,
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] (no subject)

2009-03-11 Thread Frenkel, Anatoly
I would like to be proven wrong but my feeling is, without even knowing 
anything about this particular system, that one cannot observe Fe-Fe pair at 
that distance in such complex case. 
However, to approach it more rigorously, the first step would be to examine the 
relative importance factors of different paths in the output of FEFF. If 
Fe-Fe path is well isolated in distance and importance from others (in reality, 
it probably is not the case) it can be done, otherwise - not. 

Anatoly




From: ifeffit-boun...@millenia.cars.aps.anl.gov 
ifeffit-boun...@millenia.cars.aps.anl.gov 
To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov 
Sent: Wed Mar 11 09:40:31 2009
Subject: [Ifeffit] (no subject) 


Hi all,

I measured Fe(II) edge EXAFS data for my protein that has two iron sites (Fe-Fe 
distance ~5A). My question is how to fit the model with the data? Can I discard 
the contribution of multiple scattering effects to the fitting? One most 
important information that I want to obtain is on the Fe-Fe distance. Is it 
enough to conclude from the raw data FT that the Fe-Fe  distance in my protein 
sample has been changed in comparison to the Fe-Fe distance in the model 
(created with Feff using the crystal structure coordinates)? I try fitting 
using arthemis but got bad and weird results. is there any manual or step-by 
step guide that I can learn how to fit model of two metal sites to my data? 

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? 

Any help will be appreciated,

MJacob

 

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Re: [Ifeffit] (no subject)

2007-11-27 Thread Bruce Ravel
On Tuesday 27 November 2007 09:12:33 Bindu R. wrote:
 could you tell me how does one tune the bond angles from the multiple
 scattreing paths?

Hi Bindu,

I don't quite understand the question.  Perhaps you can offer a few
more details about what you are trying to do  Are you doing EXAFS
analysis considering these MS paths?  Are you trying to explore the
effect of bond angles on your XANES calculations?

B



-- 
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Measurements Group, Beamlines X23A2, X24A, U7A

 Building 535A, Room M7
 Brookhaven National Laboratory
 Upton NY, 11973, USA

 My homepage:http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] (no subject)

2007-11-27 Thread Carlo Segre

Hi Bindu:

I am presuming that you mean that you want to tune the bond angle of the 
MS paths in your EXAFS fitting but, as Bruce notes, I might be wrong.

The bond angles for the multiple scattering paths are simply calculated 
from the positions of the atoms around the central atom in the FEFF input 
file.  In the refinement process used by Ifeffit, the overall path length
is slightly changed to fit the experimental data.  This implies 
that a 3-Dimensional geometry has been reduced to a 1-Dimensional 
fitting and all angular information is locked into the initial 
FEFF calculation.  Thus you can only tune angles by starting with a 
different local arrangement of atoms around the central atoms.

To my knowledge, there is no automatic way of doing this but there are 
manual ways of approaching the problem depending on the kind of system you 
are studying.  It would be helpful to have more information.

Cheers,

Carlo

On Tue, 27 Nov 2007, Bindu R. wrote:

 could you tell me how does one tune the bond angles from the multiple 
 scattreing paths?

 Bindu


 Dr.Bindu R.
 Visiting Scientist
 DCMPMS
 Tata Institute of Fundamental Research
 Homi Bhabha Road
 Colaba
 Mumbai-400 005
 India
 Mobile-919892536830

 -
 Chat on a cool, new interface. No download required. Click here.

-- 
Carlo U. Segre -- Professor of Physics
Associate Dean for Special Projects, Graduate College
Illinois Institute of Technology
Voice: 312.567.3498Fax: 312.567.3494
[EMAIL PROTECTED]   http://www.iit.edu/~segre   [EMAIL PROTECTED]
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Re: [Ifeffit] (no subject)

2007-11-27 Thread Bruce Ravel
On Tuesday 27 November 2007 09:33:20 Carlo Segre wrote:
 The bond angles for the multiple scattering paths are simply calculated
 from the positions of the atoms around the central atom in the FEFF input
 file.  In the refinement process used by Ifeffit, the overall path length
 is slightly changed to fit the experimental data.  This implies
 that a 3-Dimensional geometry has been reduced to a 1-Dimensional
 fitting and all angular information is locked into the initial
 FEFF calculation.  Thus you can only tune angles by starting with a
 different local arrangement of atoms around the central atoms.

 To my knowledge, there is no automatic way of doing this but there are
 manual ways of approaching the problem depending on the kind of system you
 are studying.  It would be helpful to have more information.

Carlo is right.  There is no automated way of doing so with Feff and
Ifeffit at this time.  (This is one of the many things I am working
towards with my Demeter effort, but that is quite a ways off and is a
topic for a different email message.)

There are a number of ways of approaching the problem within the
context of Feff and Ifeffit.  One that I came up with is discussed in
Chapter 9 of this thing that I wrote several years ago:
http://cars9.uchicago.edu/~ravel/talks/course/notes.pdf.

Way back when, Anatoly came up with a somewhat different approach for
his work on mixed salts.  I think this is the right reference: Solid
State Commun., 99, 67 (1996). I am sure Anatoly will pipe up if I got
that wrong.

Also way back when, Dani Haskel came up with yet another approach.
This one appears to be the correct reference: Phys. Rev. B 61, 7055
(2000).  Look also at his other papers on the structure of the
lanthanum copper oxides.

Finally, you might find my paper on barium tantalum oxinitride
relevant: Physical Review B73, p. 184121 (2006).

HTH,
B



-- 
 Bruce Ravel  --- [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Measurements Group, Beamlines X23A2, X24A, U7A

 Building 535A, Room M7
 Brookhaven National Laboratory
 Upton NY, 11973, USA

 My homepage:http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




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Re: [Ifeffit] (no subject)

2007-02-15 Thread Scott Calvin
Hi Ruwn,

Using a different S02 for each path effectively means that you're 
using a different coordination number for each path. In some cases, 
that may be appropriate--for example, small nanoparticles with 
unknown morphology. It should be noted, however, that S02 often 
correlates highly with sigma2, and a fit that prefers different S02's 
may be getting mixed up with sigma2's...although in a case like 
that Artemis/Ifeffit will give high uncertainties to the S02's it finds.

More fundamentally, just because a fit matches the data well, it 
doesn't mean it's good. The choice of parameters to fit must also 
be physically justifiable. If you can justify each path having a 
different coordination number than in your model, you can try 
different S02's; otherwise, your fit is unconvincing.

--Scott Calvin
Sarah Lawrence College


At 02:31 AM 2/15/2007, you wrote:

Dear Bruce



We have used Athena and Artemis software to analyses the EXAFS. When 
we do the analysis, we used different S2o for each path for fitting 
of Cu2O data. I succeeded to obtain good fitting by this way. 
Documents related to percent EXAFS analysis have been mentioned S2o 
is one value for all paths. What I want to know is our fittings are 
correct or not. I am looking forward early response.

?xml:namespace prefix = o ns = urn:schemas-microsoft-com:office:office /

About 10 years ago we had being using another program made by 
?xml:namespace prefix = st1 ns = 
urn:schemas-microsoft-com:office:smarttags /Tokyo University in 
Japan. In this program, the refined parameters also included S2oj 
and Nj to the each cells



Thanks



Ruwn
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Re: [Ifeffit] (no subject)

2007-02-15 Thread Bruce Ravel
On Thursday 15 February 2007 01:31, Ruwan Wijesundera wrote:
 We have used Athena and Artemis software to analyses the EXAFS. When we do
 the analysis, we used different S2o for each path for fitting of Cu2O data.
 I succeeded to obtain good fitting by this way. Documents related to
 percent EXAFS analysis have been mentioned S2o is one value for all paths.
 What I want to know is our fittings are correct or not. I am looking
 forward early response.

 About 10 years ago we had being using another program made by Tokyo 
 University in Japan. In this program, the refined parameters also included 
 S2oj and Nj to the each cells

Questions 8 and 9 on this FAQ page:
   http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling
are, I think, relevant to your question.  In particular, read the
first link under question 9, keeping in mind that it was written 3 and
1/2 years ago and Artemis has changed somewhat since then.


B


-- 
 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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