[Ifeffit] Ifeffit Digest, Vol 68, Issue 3

Thu Oct 2 02:30:37 CDT 2008

Hi Renske,

I still think your problem is related to the potentials. If you unzip your artemis project and look in one of the feffXXXX.dat files in the folder data0.feff3 (this calculations was done with the solvent_O) you will find the calculated R_MTs in the first lines - for ipot3 (O) this is 1.6. Do the same with the data0.feff7 folder (apparently this calculation was done without the solvent O - even though the feff.inp says something different) and you will find 0.728. FEFF (always?) uses the closest atom (relative to the ipot=0-atom) to determine the unique potentials to be used for all atoms with the same ipot (in the manual it is stated that FEFF takes the first atom in the atoms-list but in your case just changing the position in the list did change nothing whereas increasing the distance to 3.3 (the O_t_1 atoms are at 3.266) did yield a different R_MT - but maybe I am wrong).  

HTH

Jakob

___________________________________________________ 
Jakob Frommer 
Soil Chemistry Group 
Institute of Biogeochemistry and Pollutant Dynamics, 
ETH Zürich 
Universitätstrasse 16, 
CHN F19 
CH - 8092 Zürich 
Tel: +41 44 632 87 58 
Fax: +41 44 633 11 18 
web: http://www.ibp.ethz.ch/research/soilchemistry

________________________________

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Subject: Ifeffit Digest, Vol 68, Issue 3

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Today's Topics:

   1. Re: Athena Peak Fitting (Matt Newville)
   2. Re: Independence of scattering paths? (van der Veen Renske)

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Message: 1
Date: Wed, 1 Oct 2008 16:23:34 -0500
From: "Matt Newville" <newville at cars.uchicago.edu>
Subject: Re: [Ifeffit] Athena Peak Fitting
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
        <b8522e3d0810011423g68bb1b81g143ed34a0569a471 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Jenny,

I would say that method 2 looks better, as the fit over the whole of
the specified fitting range is clearly better.   I wouldn't
necessarily say that "peak 1" in this fit -- I'm assuming you mean the
highest energy peak at ~2488.3eV -- is  too broad.  At that high
energy (definitely into the EXAFS region),  the idea of peaks coming
from specific electronic transitions breaks down, and EXAFS
oscillations can be that broad in energy.

It seems that you need this "broad peak" because you're fitting out
past 2500 eV.    I think that's OK (that third broad peak may not be a
single electronic transition but is still useful for identifying
species).  But, if you'd rather not have to use the broader peak, you
might also try fitting just the two sharper peaks at lower energy, say
out to 2485 eV.

Hope that helps,

--Matt

On Wed, Oct 1, 2008 at 1:31 PM, Jenny Cai <jennyh_cai at yahoo.ca> wrote:
> Hi Everyone,
>
> I am using Athena peak fitting function to fit the sulfur spectrum of my
> coke sample. I checked everywhere, but couldn't get detailed instruction for
> using this function. So, I attached a file with this email to get help.
> Could you please take a look at it, and tell me if I did the fitting right
> (in terms of fitting procedure only)?
>
> I did the fitting in two ways, and I know both of them have problems. For
> instance, in the first case, I can't get a good step line and have to cut
> off the tail of the spectrum. In the second one, peak 1 is way too broad,
> but if I cut it off, the fitting will be very poor. So, please tell me which
> way is better, or you have some ideas to improve the fitting.
>
> Thank you in advance!
>
>
> Best,
>
> Jenny
>
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------------------------------

Message: 2
Date: Thu, 2 Oct 2008 06:36:48 +0200
From: "van der Veen Renske" <Renske.vanderveen at psi.ch>
Subject: Re: [Ifeffit] Independence of scattering paths?
To: <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
        <67F374811ED3544C8543E6C0EE5EAA4B02AFEC8E at MAILBOX0B.psi.ch>
Content-Type: text/plain; charset="us-ascii"

Dear Bruce and Jakob

Thanks for your replies. I realize that I should have been a bit more
precise in where I actually put this extra atom: it is placed outside
the molecule at an axial position of the absorbing Pt atom, representing
an ethanol solvent molecule that coordinates. It is not placed between
any other atoms that are included in the fit/sum, so the MT potentials
should not be disturbed.

Thanks to the nice presentation of scattering paths in Artemis, I am
sure that I chose the same scattering paths involving the same atoms for
both sums.

I attached an Artemis project to make things more clear.

Thanks a lot & best wishes,
Renske

>
> On Friday 26 September 2008 22:38:58 van der Veen Renske wrote:
> > I have a question concerning the independence of scattering
> pathways.
> > I fitted the EXAFS signal of a molecule consisting of 30 atoms (the
> > related FEFF calculation is called calc 1). To see the
> effect of the
> > surrounding solvent molecules in the chi(k) data, I added
> an O-atom in
> > the coordinate list of the FEFF input file at an arbitrary distance
> > from the absorbing atom (in this case Pt) and I re-ran FEFF
> (calc 2).
> > As a check within calc 2, I generated the sum of the same
> scattering
> > paths that were used in the fitting model of calc 1 using
> the therein
> > obtained structural fit parameters. The new O-atom was not
> included in this sum.
> > I expected the sum within calc 2 to be identical to the fit
> of calc 1
> > based on the fact that the original atoms can not sense the
> presence
> > of the new O-atom (independence of scattering paths). BUT: the
> > resulting sum was significantly different from the fit!
>
> It is a little hard to answer this question since you
> described it to us rather than showing it to us with project
> file(s).  I have a couple of suggestions, but without being
> able to examine what you did, I cannot be sure that either is
> relevant.  (You can insert here my standard diatribe on the
> topic of how to ask questions.)
>
> One suggestion is to be very careful that you are including
> the same set of paths in the calculation.  When you add an
> atom to a feff.inp file, the indexing of the paths change in
> a way that may be hard to predict.  Just blindly summing up
> the first N paths may not do what you want.
>
> The other suggestion is to check that you did not place the
> oxygen atom in a position that dramatically altered the
> muffin tin radii.
> The potantials calculation can change quite if you insert an
> atom at an arbitrary loctation such that the muffin tin radii
> have to be very different for some atoms.
>
> 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
>
>  My homepage:    http://xafs.org/BruceRavel
>  EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>

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