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Re: Question about cluster size in Atoms3.0
Dear Feffusers
I have a question concerning the use of ATOMS (vers. 2.5) for doping
purposes.
When I introduce the doping ion by repeating the coordinates
of the host atom I get the following error messagge:
* * * * WARNING * * * *
Your input file has generated atoms overlapping in space.
All redundant atoms have been removed from the atom list.
Feff.inp has been written and the atom list may be correct
but the atom labels and McMaster calculations are incorrect.
The most likely causes of this are:
1: Specifying a unique crystallographic site more than once. (See
section 3.1 of the ATOMS document.)
2: Constructing a basis list that overlaps itself when translated.
3: Specifying incorrect unique crystallographic positions.
feff.inp overwritten.
Here is my input file:
------------------------------------
title name: FeO
space f m 3 m
a = 4.2774
alpha= 90
rmax = 10.00
core = Fe
atom
Fe 0.00000 0.00000 0.00000 Fe 0.2
Mg 0.00000 0.00000 0.00000 Mg 0.8
O 0.50000 0.50000 0.50000 O 1.0
------------------------------------
Am I doing something wrong in setting the input file?
Any comments will be highly appriciated.
Cheers
Maurizio
Bruce Ravel wrote:
>Dr. Jian,
>
>I hope you don't mind if I CC my response to your questions to the
>feffusers mailing list. I think that you questions are of sufficiently
>general interest that other may appreciate seeing this.
>
>On Wednesday 24 September 2003 07:59 am, Jian DING wrote:
>
>
>
>>I have a question about the cluster size in TKAtoms 3.0 Obeta7. It
>>is said in your documentation that, the cluster size defaults to the
>>smaller of 7 A and 1.1 times the length of the largest lattice
>>constant. However, when I tried to enter the cluster size smaller
>>than the lattice constant, there is no error happened. For example,
>>I enter the cluster size as 3.5A, or even 3A,althouth the lattce
>>constant of SiC is 4.358A. When I run TKAtoms 3.0, The normal
>>feff.inp files could be generated.
>>
>>
>
>I suppose I should have said that the cluster radius defaults to 7 A
>*or* 1.1 times the largest lattice constant, which ever is larger,
>unless a cluster radius is specified, in which case that is used. So,
>if you specify a shorter cluster radius, that shorter value will be
>used. Indeed, whatever cluster radius you specify will be used.
>The default only comes into play if you leave the little box for the
>cluster radius empty.
>
>
>
>>I am going to do some EXAFS calculation about dopants, for example,
>>replacing several Si atoms by Al atoms in SiC. The atom number
>>included in a cluster increases much more with the cluster size
>>increasing. Because I think it should be more effective to
>>investigate the dopant effect in a cluster with fewer atoms, so I
>>hope to calculate the smaller cluster if possible. I wonder if there
>>is any effect on the calculation result if I use smaller cluster
>>size mentioned above.
>>
>>
>
>You have hit upon one of the essential issues in understanding how to
>use feff8. One wants to use as small a cluster as possible so the
>calculation goes quickly. On the other hand one wants to use a large
>cluster so as not to neglect any important contributions to the
>scattering. For a material like SiC, I suspect that one will need a
>rather large cluster because I suspect that the mean free path is
>quite long, especially in the XANES region.
>
>A good strategy for balancing the desire for a small cluster with the
>need for a large cluster is run a sequence of feff calculations,
>increasing the cluster size each time. The best way to do this would
>be to run Atoms with a large cluster radius. Then set the radius
>parameter to the SCF and FMS cards to successively larger values.
>Eventually increasing the cluster size will not change the
>calculation. This tells you what size cluster you need to fully
>represent the material.
>
>The issue of introducing dopants into the feff calculation is a tricky
>one. I have written about this before. Here is a link to a
>discussion of this topic in the ifeffit mailing list archives. It is
>mostly about EXAFS, but I discuss XANES calculations on doped
>materials at the end.
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2002-July/000092.html
>
>Note that convergence in cluster size may be different for a doped
>cluster as for undoped SiC due to the introduced disorder. Or it may
>not be. The only way to know is to develop your strategy for
>computing the doped material and then investigating cluster size
>convergence using that strategy.
>
>
>I hope that helps. If you have any further questions, your best bet
>would be to subscribe to the FEFFUSERS mailing list. See
> http://leonardo.phys.washington.edu/feff/Notes_comments/feffusers.html
>and post your questions there.
>
>Hope that helps,
>Bruce
>
>
>
>
>
--
Maurizio Mattesini
Condensed Matter Theory Group
Department of Physics, Uppsala University
Box 530 SE-751 21 (Sweden)
Tel. +46 18 471 58 58
Mobile +46 73 970 08 66
Fax +46 18 471 35 24
E-mail: m_mattesini@yahoo.com
http://maurizio.freeservers.com