[Ifeffit] Trouble creating feff input file for NaTiO3 cubic perovskite structure
badari.rao at gmail.com
Wed Oct 8 02:44:22 CDT 2014
Dear Dr. Bruce,
Thank you for spending time on this problem.
I did realize that that the simple perovskite structure I created may be
physically unreasonable which is why feff was crashing. I tried modifying
the lattice parameter to see if at some point it would start working, but
it didn't help.
I needed this particular simple perovskite structure as I am trying to
analyze an A-site disordered perovskite Na0.5Bi0.5TiO3. Since 'atoms' does
not allow us to input disordered structure (due to obvious reasons), I
wanted to create two separate structure files namely: NaTiO3 and BiTiO3,
and thus I encountered this problem.
However, I also found that the problem with NaTiO3 occurs only when the
atomic coordinates are at the cubic positions. If I incorporate some
distortion into the structure (say tetragonal or rhombohedral), then feff
seems to be working fine.
With best regards,
Date: Fri, 03 Oct 2014 14:48:20 -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: <542EEF74.5000702 at bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed
In your original email you said "I am not able to create the feff
input file using Na." That is certainly not true. Artemis is able to
make the feff input file from your crystal data.
Your problem appears to be that, when you then run feff, feff crashes.
At the risk of sounding like a jerk, if you ask the wrong question,
there's very little chance that I will give you the right answer.
So, let's discuss the actual problem.
The input data you provide fails (as identified in the "datoms.log"
file that you should have attached in the first place) in a place in
Feff where Feff is attempting to compute the muffin tin radii.
I concur with your observation that Feff is able run to completion so
long as the A site in your crystal data has a high enough Z number.
In your case, that seems to be 12 (Mg). Anything 11 or less results
in that error.
The error message from Feff is confusing. I don't understand why that
particular error message is issued given what's at line 90 of
istprm.f. I also don't understand that part of Feff well enough to
know why a light element in the A site is causing a problem with the
calculation of muffin tin radii.
I've never seen this problem before, which is why Demeter is not smart
enough to recognize it and offer a more useful error message.
So, I don't actually have a solution for you. Your crystal data with
Na in the A site simply doesn't work with Feff. Well done! That's a
very strange problem you've found.
I did a brief search for minerals with Na, Ti, and O at
crystallography.net. It would seem that those three elements don't
actually have a perovskite phase. The nearest thing
stoichiometrically is trigonal Na4Ti5O12. Feff runs just fine on all
the Ti sites in that material. Given that, my conclusion is that your
simple pervoskite is simply not close enough to a phsically reasonable
assembly of those three atoms that Feff can find a suitable solution
for the muffin tin radii.
That is, Feff crashes (taking Demeter down with it) on that structure,
but that structure seems to be unphysical anyway.
Maybe not the most helpful of answers, but it's the best I can do.
On 10/01/2014 05:32 AM, Badari Rao wrote:
> Dear Dr. Bruce,
> I have attached the datoms.log file and the .inp file used. I am using
> windows platform. I hope you can get to the root of the problem with this.
> On Tue, Sep 30, 2014 at 10:30 PM,
> <ifeffit-request at millenia.cars.aps.anl.gov
> <mailto:ifeffit-request at millenia.cars.aps.anl.gov>> wrote:
> Date: Tue, 30 Sep 2014 08:21:18 -0400
> From: Bruce Ravel <bravel at bnl.gov <mailto:bravel at bnl.gov>>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov
> <mailto: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 <mailto: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
> information in the error log and without an actionable recipe for
> replicating the problem, there is simply nothing that I can do to
> Bruce Ravel ------------------------------
------ bravel at bnl.gov
> <mailto: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/
> 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.
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
Bruce Ravel ------------------------------------ bravel at bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
Upton NY, 11973
Badari Narayana. A. R.
Ph.D Student, Nanoscience and Nanotechnology,
c/o Prof Rajeev Ranjan,
Department of Materials Engineering,
Indian Institute of Science.
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