[Ifeffit] FEff (Joshua Kas)

Joshua Kas joshua.j.kas at gmail.com
Tue Sep 30 13:03:44 CDT 2014


Hi Carlos and Matt,
Matt is correct that the CFAVERAGE card averages over a variety of
absorbing atoms specified within the input file, with amplitude fixed to 1.
In addition, CFAVERAGE only works in FEFF8.4 and earlier, and only if you
have the monolithic version (i.e., feff is a single executable, not a
script that runs several executables). We intend to improve the
capabilities of feff9/jfeff to include more possibilities in terms of
averaging over the absorption of different sites within a feff.inp file, or
averaging over multiple input files, but for now, you will have to perform
the averaging yourself.
Cheers,
Josh Kas

On Tue, Sep 30, 2014 at 10:00 AM, <ifeffit-request at millenia.cars.aps.anl.gov
> wrote:

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> Today's Topics:
>
>    1. Re: FEff (Matt Newville)
>    2. Trouble creating feff input file for NaTiO3 cubic perovskite
>       structure (Badari Rao)
>    3. Re: Trouble creating feff input file for NaTiO3 cubic
>       perovskite structure (Bruce Ravel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 29 Sep 2014 12:47:57 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] FEff
> Message-ID:
>         <
> CA+7ESbqpUvDtwnjXumeqWo2DMwvw15nyUOfjPq5jnV8t5EJviw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Mon, Sep 29, 2014 at 11:48 AM, Bruce Ravel <bravel at bnl.gov> wrote:
>
> > On 09/29/2014 11:44 AM, Carlos Triana Estupinan wrote:
> >
> >> Dear
> >> Feff group
> >>
> >> I am Carlos Triana, and I want ask you the following.
> >> I am trying to calculate the feff.inp file for a theoretical amorphous
> >> structure composed by a supercell with 24 Ti atoms surrounding by 48
> >> oxygen atoms with different coordination. In amorphous materials or
> >> materials with distortions from regular crystals, the absorbing atoms
> >> may have different surroundings.
> >> My question is how can I build the feff.inp file in this case, shall I
> >> define the 24 Ti atoms like absorbing atoms, because in this case the
> >> feff does not works.
> >> What can I do in this case, how can I build the feff.inp file with
> >> different environments
> >>
> >> I will be very grateful for your help
> >>
> >
> > I'd like to follow up on Matt's comment.
> >
> > I presume you have some way of knowing a list of Cartesian coordinates
> for
> > the atoms in your cluster.  If so, the discussion on pages 7-10 of this
> > talk should be helpful, with the caveat that your input file needs to be
> > appropriate to the version of Feff you intend to use.
> >
> > https://speakerdeck.com/bruceravel/modeling-non-
> > crystalline-samples?slide=9
> >
> > Make one input file for each Ti atom serving as the absorber.  As Matt
> > said, take care not to overwrite your results.
> >
> > Were this my problem, I would prefer to organize and perform N
> > calculation, then add them up myself.  That said, Feff does provide a
> > simple sort of configuration average.  Look up "CFAVERAGE" in the Feff
> > document.
> >
> > B
> >
>
>
> I believe CFAVERAGE does not work as advertised.  I haven't checked this
> recently, but my recollection is that using CFAVERAGE always ends up giving
> a coordination number that is a whole number, which cannot always be the
> case.  That might depend on versions of Feff, and I'd be happy to shown to
> be wrong about this.
>
> Can anyone else verify or shed light on this?
>
>  --Matt
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> ------------------------------
>
> Message: 2
> Date: Tue, 30 Sep 2014 15:15:12 +0530
> From: Badari Rao <badari.rao at gmail.com>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] Trouble creating feff input file for NaTiO3 cubic
>         perovskite structure
> Message-ID:
>         <CAM=6XwBpwofyOJGk8pRpR6H=xA=
> DzKWOhHEG3-qgDKPaHE-yvw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear All,
> When I try to feed the following data into the atoms input and run the feff
> calculations, the software just automatically closes.
> space group no: 221
> a = b = c = 3.88; alpha = beta = gamma = 90;
> atomic coordinates:
> Na: 0.5, 0.5 , 0.5
> Ti:   0,    0,    0
> O:   0,    0,    0.5
>
> Core: Ti
>
> I don't think it is a bug because the calculation works perfectly when I
> replace Na with heavier atoms like K, Mg etc. I would like to know why I am
> not able to create the feff input file using Na.
>
> -- Yours Sincerely
> Badari Narayana. A. R.
> Ph.D Student, Nanoscience and Nanotechnology,
> c/o Prof Rajeev Ranjan,
> Electroceramics Lab,
> Department of Materials Engineering,
> Indian Institute of Science.
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> ------------------------------
>
> Message: 3
> Date: Tue, 30 Sep 2014 08:21:18 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Trouble creating feff input file for NaTiO3
>         cubic perovskite structure
> Message-ID: <542AA03E.8070701 at bnl.gov>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> On 09/30/2014 05:45 AM, Badari Rao wrote:
> > Dear All,
> > When I try to feed the following data into the atoms input and run the
> > feff calculations, the software just automatically closes.
> > space group no: 221
> > a = b = c = 3.88; alpha = beta = gamma = 90;
> > atomic coordinates:
> > Na: 0.5, 0.5 , 0.5
> > Ti:   0,    0,    0
> > O:   0,    0,    0.5
> >
> > Core: Ti
> >
> > I don't think it is a bug because the calculation works perfectly when I
> > replace Na with heavier atoms like K, Mg etc. I would like to know why I
> > am not able to create the feff input file using Na.
>
> I cannot reproduce your problem using the information you've given.
> That structural data runs just fine and gives sensible output on both
> Windows and linux.
>
> When making a bug report, you should include the information discussed
> in http://bruceravel.github.io/demeter/pods/bugs.pod.html.  Without the
> information in the error log and without an actionable recipe for
> replicating the problem, there is simply nothing that I can do to help.
>
> B
>
>
> --
>   Bruce Ravel  ------------------------------------ bravel at 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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