To ifeffit community,
If suppose I am able to see C and O contributions to the EXAFS in my sample(CO chemisorbed on copper),and suppose i need to fit Cu-C,Cu-O and Cu-Cu EXAFS signal, then how can I construct my feff.inp file?Will it be enough to just consider a simple structure includes only 4 atoms since EXAFS only considers single scattering from the nearest neighbors?
for example,
ipot Z element
0 29 Cu
1 29 Cu
2 6 C
3 8 O

x y z potential_label Tag
0 0 0 0 Cu
0 0 2.5 1 Cu
1.9 0 0 2 C
3.0 0 0 3 O

so will this simple dimers enough to generate feff paths which can be used to fit my data including Cu-C,Cu-O and Cu-Cu contributions?Or do I need to consider more atoms and their coordinates in the range of RMAX?

Thanks a million.

------------ Original Message ------------
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1. Re: How to write feff.inp file for CO adsorbed Cu?
(Matthew Marcus)
2. Re: Importing Multiple Data Sets into Athena (Daniel Whittaker)


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

Message: 1
Date: Wed, 05 Sep 2012 21:54:24 -0700
From: Matthew Marcus
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] How to write feff.inp file for CO adsorbed Cu?
Message-ID: <50482C80.3030105@lbl.gov>
Content-Type: text/plain; Zharset=ISO-8859-1; format=flowed

I don't know about surface CO, but I do know that in metal carbonyls, you get a very strong scattering from the distal atom, let's
say the O in M-C=O, due to the focusing from the intermediate atom. Thus, if you really have a monolayer-selective method for
doing EXAFS, e.g. partial Auger yield, then you may be able to see the CO.
mam

On 9/5/2012 8:12 PM, Zhaomo Tian wrote:
> Hi,Jason!
> I think you are really professional and pointed out the most important point at the beginning !
>
> Actually I am really worried about my experiment too, I also have a doubt about whether I can see C or O contributions to the EXAFS in my sample.But I think maybe no one can give the answer for sure. So at least I need to try first and see. Actually the originality of my work is to study the electrochemical reduction of CO2 on metal electrodes. Since CO is noticed as an important adsorbed intermediate in the multistep reaction and only copper has been found to be unique among the metals in its ability to produce a high quantities of hydrocarbon fuels, i start to first investigate the interaction between adsorbed CO and copper.Thats why I believe that using EXAFS to study the chemisorbed CO gas-copper system will contribute to some reasonable explanation.
>
> I sent you two references, in the first one there is evidence for CO adsorbed Ru taken at Ru k-edge,where CO is observed in EXAFS, and the second one SEXAFS study on CO adsorbed on Cu, but it is taken at oxygen K edge.I think even if there is not exact the same evidence with my system which is EXAFS on Cu k-edge of CO adsorbed Cu, but it may still work. Why do you think my experiment is not promising? Could you please explain some reasons to me? Is there any conditions for metal and adsorbed gas that their EXAFS signal can be detected? If there are,would you please to give me some modification of my experiment?
>
> Thanks a million.
>
> Best Regards,
>
>
>
> ------------ Original Message ------------
> From : ifeffit-request@millenia.cars.aps.anl.gov
> To : ifeffit@millenia.cars.aps.anl.gov
> Mail Subject : Ifeffit Digest, Vol 115, Issue 2
> Sent : Wed, 05 Sep 2012 08:25:57 -0500
>
> Send Ifeffit mailing list submissions to
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> or, via email, send a message with subject or body 'help' to
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> than "Re: Contents of Ifeffit digest..."
>
>
> Today's Topics:
>
> 1. Ratio of peak amplitudes in R-space (Rana, Jatinkumar Kantilal)
> 2. Re: Ratio of peak amplitudes in R-space (Christopher Patridge)
> 3. Re: Ratio of peak amplitudes in R-space (Scott Calvin)
> 4. How to write feff.inp file for CO adsorbed Cu? (Zhaomo Tian)
> 5. Re: How to write feff.inp file for CO adsorbed Cu? (Jason Gaudet)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 5 Sep 2012 12:01:01 +0000
> From: "Rana, Jatinkumar Kantilal"
>
> To: "ifeffit@millenia.cars.aps.anl.gov"
>
> Subject: [Ifeffit] Ratio of peak amplitudes in R-space
> Message-ID:
> Content-Type: text/plain; Zharset="us-ascii"
>
> Dear Ifeffit community,
>
> I was wondering If I can make a qualitative comparison about the amplitude ratio of first two shells for various states of same sample ?
>
> For example, I have a sample which is measured at various states, say A, B, C, D and E during any physical or chemical process.
>
> I get systematic change in the ratio of first two peaks at each state. This could be interpreted either as change in disorder or as change in number of atoms associated with first two shells as a result of any physical or chemical change material has undergone.
>
> As we know that amplitude of peak decreases with increase in distance from central absorber.
>
> Can I compare the amplitude ratio of first two peaks for various states of same sample ??
>
> Many thanks in advance !!!
>
> With best regards,
> Jatin
>
>
>
> ________________________________
>
> Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH
>
> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.
>
> Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph
> Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking
>
> Sitz Berlin, AG Charlottenburg, 89 HRB 5583
>
> Postadresse:
> Hahn-Meitner-Platz 1
> D-14109 Berlin
>
> http://www.helmholtz-berlin.de
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 2
> Date: Wed, 5 Sep 2012 08:28:27 -0400
> From: Christopher Patridge
> To: XAFS Analysis using Ifeffit
> Subject: Re: [Ifeffit] Ratio of peak amplitudes in R-space
> Message-ID:
>
> Content-Type: text/plain; Zharset="iso-8859-1"
>
> Jatin,
>
> If these changes are systematic and you somewhat understand the physical or
> chemical process associated with the sample, then why not just build a
> model and do a structural fitting? A simple peak ratio comparison maybe
> helpful but a much stronger argument and interpretation can be made if you
> use a structural model to extract these comparisons....
>
> several methods for building a model are available.
>
> buena salud,
>
> Chris Patridge
>
> On Wed, Sep 5, 2012 at 8:01 AM, Rana, Jatinkumar Kantilal <
> jatinkumar.rana@helmholtz-berlin.de> wrote:
>
> > Dear Ifeffit community,
> >
> >
> >
> > I was wondering If I can make a qualitative comparison about the amplitude
> > ratio of first two shells for various states of same sample ?
> >
> >
> >
> > For example, I have a sample which is measured at various states, say A,
> > B, C, D and E during any physical or chemical process.
> >
> >
> >
> > I get systematic change in the ratio of first two peaks at each state.
> > This could be interpreted either as change in disorder or as change in
> > number of atoms associated with first two shells as a result of any
> > physical or chemical change material has undergone.
> >
> >
> >
> > As we know that amplitude of peak decreases with increase in distance from
> > central absorber.
> >
> >
> >
> > Can I compare the amplitude ratio of first two peaks for various states of
> > same sample ??
> >
> >
> >
> > Many thanks in advance !!!
> >
> >
> >
> > With best regards,
> >
> > Jatin
> >
> >
> >
> >
> >
> > ------------------------------
> >
> > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH
> >
> > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher
> > Forschungszentren e.V.
> >
> > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv.
> > Vorsitzende Dr. Beatrix Vierkorn-Rudolph
> > Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking
> >
> > Sitz Berlin, AG Charlottenburg, 89 HRB 5583
> >
> > Postadresse:
> > Hahn-Meitner-Platz 1
> > D-14109 Berlin
> >
> > http://www.helmholtz-berlin.de
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit@millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> >
>
>
> --
> Christopher J. Patridge PhD.
> Contact: (315)-529-0501
> -------------- next part --------------
> An HTML attachment was scrubbed...
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>
> ------------------------------
>
> Message: 3
> Date: Wed, 5 Sep 2012 08:32:27 -0400
> From: Scott Calvin
> To: XAFS Analysis using Ifeffit
> Subject: Re: [Ifeffit] Ratio of peak amplitudes in R-space
> Message-ID: <59B5117D-3960-4548-A617-9EA4022AF78E@slc.edu>
> Content-Type: text/plain; Zharset="iso-8859-1"
>
> Hi Jatin,
>
> It's really best to model such a system using Ifeffit or similar software. There's a lot that goes into peak height. For one thing, I'm assuming you're looking at the peak height in the magnitude of the Fourier transform. But the Fourier transform of the individual scattering paths is complex-valued, not positive-definite. Thus, two paths contributing at some value of R can sometimes result in less amplitude than either path alone. Depending on data ranges and windowing, there's likely to be some contribution from the path that you're thinking of as corresponding to the first peak at the R of the second, and vice-versa, and that contribution is not additive when viewed in the magnitude.
>
> In addition, for the peak at higher-R there may be a significant contribution from multiple scattering.
>
> It should also be noted that a single peak may be due to unresolved splitting. For example, a nearest-neighbor octahedron might be distorted, with different axial and radial distances. In a case like that, a change in the amount of distortion can have a dramatic effect on the height of the peak.
>
> Having said that, you can make qualitative comparisons in a series like the one you describe. If you have a suspicion of what might be happening (change in coordination, change in disorder, change in splitting, etc.), then you can see it progress by just inspecting the graphs in the way you suggest, and could probably identify, e.g., a phase change. But for quantitative determinations, you really need to model the system.
>
> --Scott Calvin
> Sarah Lawrence College
>
> On Sep 5, 2012, at 8:01 AM, Rana, Jatinkumar Kantilal wrote:
>
> Dear Ifeffit community,
>
> I was wondering If I can make a qualitative comparison about the amplitude ratio of first two shells for various states of same sample ?
>
> For example, I have a sample which is measured at various states, say A, B, C, D and E during any physical or chemical process.
>
> I get systematic change in the ratio of first two peaks at each state. This could be interpreted either as change in disorder or as change in number of atoms associated with first two shells as a result of any physical or chemical change material has undergone.
>
> As we know that amplitude of peak decreases with increase in distance from central absorber.
>
> Can I compare the amplitude ratio of first two peaks for various states of same sample ??
>
> Many thanks in advance !!!
>
> With best regards,
> Jatin
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 05 Sep 2012 21:47:14 +0900
> From: Zhaomo Tian
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: [Ifeffit] How to write feff.inp file for CO adsorbed Cu?
> Message-ID: <1346849234137.75822.postech@postech.ac.kr>
> Content-Type: text/plain; Zharset="us-ascii"
>
> An HTML attachment was scrubbed...
> URL:
>
> ------------------------------
>
> Message: 5
> Date: Wed, 5 Sep 2012 09:25:53 -0400
> From: Jason Gaudet
> To: XAFS Analysis using Ifeffit
> Subject: Re: [Ifeffit] How to write feff.inp file for CO adsorbed Cu?
> Message-ID:
>
> Content-Type: text/plain; Zharset="iso-8859-1"
>
> Hi Tian,
>
> What leads you to believe you'd be able to see C or O contributions to the
> EXAFS in your sample? CO probing of a catalyst during XAS measurements is
> a pretty common experiment (although CO is often not a good probe molecule
> for Cu...) but I'm having difficulty coming up with an example where the CO
> itself was directly observed in EXAFS. Sulfur, sure, but CO? If your Cu
> was monodisperse I suppose it would be less of a stretch to try, but if
> you're talking about a Cu surface and expecting to separate Cu-C and Cu-Cu
> contributions I'd be worried you may be far overestimating the capabilities
> of your experiment.
>
> If you have a cite that suggests this is feasible, it'd be news to me and
> I'd be happy to read it.
>
> -Jason
>
> On Wed, Sep 5, 2012 at 8:47 AM, Zhaomo Tian wrote:
>
> > Dear All!
> >
> > I am a beginner in this field and I have a difficulty in writing feff.inp
> > file for my system.
> >
> > My system is CO gas adsorbed on metal (such as copper)surface and the
> > experiment data will be taken on Cu k edge, since it is not crystalline
> > structure, I may need to write my own feff.inp file instead of getting it
> > from atoms.inp file. Is there anyone who knows how to create a structure
> > for my system and how to calculate atomic coordinates of so many atoms?Or a
> > simple structure includes only 4 atoms(2 Cu,1 C and 1 O is enough?) Then I
> > am asking help for generating feff.inp file(especially all necessary atomic
> > coordinates) for Cu-CO. If someone knows it, would you please give me a
> > hand?
> >
> > Thanks a million
> >
> > Best Regards,
> >
> >
> >
> > *Tian Zhaomo*
> >
> > *M.S. candidate*
> >
> >
> >
> >
> >
> > *Lab. For Photosynthesis Materials and Devices*
> >
> > Department of Materials Science and Engineeing,POSTECH
> >
> > san 31, Hyoja-Dong, Nam-Gu,
> > Pohang, 790-784, Republic of Korea
> >
> >
> >
> > office: +82-54-279-2827
> >
> > mobile: +82-10-7747-3790
> >
> > e-mail: zhaomo1989@postech.ac.kr
> >
> >
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit@millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> >
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------------------------------

Message: 2
Date: Thu, 6 Sep 2012 10:29:43 +0200
From: "Daniel Whittaker"
To: "XAFS Analysis using Ifeffit"
Subject: Re: [Ifeffit] Importing Multiple Data Sets into Athena
Message-ID: <333028C7AAE84063AC157620985143B0@DWLAPTOP>
Content-Type: text/plain; Zharset="iso-8859-1"; Format="flowed"

Hi Scott,

I have attached 3 of the data files and the Zr foil ref scan (already
calibrated). I first import the reference Zr foil scan and then the 3 files.
The Numerator for the data is column 30 and i also import the ref channel
where the numerator is column 7. If i choose to set ref to standard values
(as you would expect that to work) it fails and makes processing difficult.
The only way round it i see is to import each data set individually and set
the element, edge and value of E0 manually (for the reference - the data is
read correctly) before then using the "align marked groups" function to
align all the data to the standard Zr foil i imported at the start.

Having played with the setting on the preprocess tab if you check the "align
to standard" radio button it aligns the data (not the reference channel)
despite the fact the "same element" radio is not checked - should the
preprocessing not apply to the reference channel (if present) before the
data channel?

As i say it is not a huge problem and i only report it in the interest of
bug removal.

Thanks,
Dan

--------------------------------------------------
From: "Scott Calvin"
Sent: Wednesday, September 05, 2012 6:13 PM
To: "XAFS Analysis using Ifeffit"
Subject: Re: [Ifeffit] Importing Multiple Data Sets into Athena

> Hi Dan,
>
> Could you attach the data files you are trying to import? We can see if
> the problem is reproducible on our systems.
>
> --Scott Calvin
> Sarah Lawrence College
>
> On Sep 5, 2012, at 10:50 AM, Daniel Whittaker wrote:
>
> Hello all,
>
> I am having a small issue when importing multiple data sets into Athena
> all of which have a reference channel.
>
> The issue i am experiencing is that when importing multiple data sets
> together they do not all import correctly. The first data set (of all
> selected) imports fine (The data is Np and the reference Zr foil) - it
> imports the reference file which can be aligned to the calibration Zr foil
> file. However, the remainder of the files do not work at all, the
> reference channel does not import correctly at all. I have tried (best as
> i can tell) all of the pre-process options to no avail. When i import them
> individually it works although I have to tell it what element the ref
> channel is and the edge and E0 (couldn't the edge and E0 be linked such
> that selection of one filled the other?) but this isn't too much of an
> issue.
> It is by no means a massive problem but i thought i would ask if there is
> a way around it or if it is a real bug?
> All other multiple data processing - such as "align marked groups" - works
> fine.
> Regards,
> Dan Whittaker
>
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
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