[Ifeffit] Fwd: Icosahedral cluster coordinates
Frenkel, Anatoly
frenkel at bnl.gov
Mon Jun 27 12:29:33 CDT 2011
Perhaps, some problems with constructing atomic coordinates? It appears that they were obtained by modifying the hcp structure... but I am not sure if that algorithm listed in the input file was correct (from the input file: "*c and a have been chosen to give 5% expansion between layers and 10% within the layer in the first shell as per Farges (1982).This thus roughly simulates a relaxed icosohedron").
In a regular icosahedron all distances in the radial direction are the same, and all distances within the shell are about 5% longer. This program can be used to generate atomic coordinates in an icosahedron, up to the 10th order (for larger icosahedral clusters you may contact me directly).
http://www3.bnl.gov/frenkel/coords.html
FEFF works on these coordinates (it has been tested).
Regards,
Anatoly
________________________________
From: ifeffit-bounces at millenia.cars.aps.anl.gov on behalf of Scott Calvin
Sent: Mon 6/27/2011 1:06 PM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] Fwd: Icosahedral cluster coordinates
Hi Zohair,
I'm posting this back to the list, because I couldn't solve the problem. I did experiment with your file for a bit; it works fine for the atoms up to 4 angstroms, but ones much past that make feff fail. Maybe someone else can suggest why feff is choking on what appears on inspection to be a valid file. (Note to others on the list: the attached feff.inp file is the one that doesn't work; the pasted one is my original, and does work.)
As for atoms being able to work with icosahedral structures, that will probably never be possible. Atoms is designed to work with crystal structures, and icosahedral clusters are not crystals; i.e. they don't have translational symmetry. A separate helper application would have to be written for this kind of cluster.
--Scott Calvin
Sarah Lawrence College
Begin forwarded message:
From: <Zohair.Hussain at csiro.au>
Date: June 27, 2011 1:12:06 AM PDT
To: <dr.scott.calvin at gmail.com>
Subject: Re: [Ifeffit] Icosahedral cluster coordinates
Dear Scott,
I came across an e-mail exchange from 2005 between you and Patrick Kluth regarding icosahedral clusters and feff files as below.
I'm trying to fit data collected at the Cu k-edge for Mg65Cu25Gd10 bulk metallic glass(BMG). It has been reported that BMGs have an icosahedral structure. A recent paper (attached) gives a demonstration of that. What I've tried to do is to modify the feff file you made for Patrick to my MgCuGd structure. I attach the feff.inp file I made for that.
The problem I'm running into is that when I try and run this modified feff file through artemis I get an error message (file attached). I should point out that when I run your feff file for Fe it runs without any errors.
I'm wondering if you can either tell me what I'm doing wrong or guide me to make a feff file from an atoms input file for the MgCuGd material.
In the long run, it would be good to know how to make Feff files for icosahedral structures starting from an atoms input file (I usually use webatoms for this) as I would be working with various BMG materials (Al, Ti and Mg based) that should potentially have this structure.
I'd be grateful for your help.
Kind Regards,
Zohair Hussain
Postdoctoral Fellow
CPSE - CSIRO
Private Bag 33
Clayton South MDC
Clayton VIC 3169
Australia
e-mail: zohair.hussain at csiro.au
Phone +61 3 9545 7891
Fax +61 3 9544 1128
[Ifeffit] Icosahedral cluster coordinates
Scott Calvin SCalvin at slc.edu <mailto:ifeffit%40millenia.cars.aps.anl.gov?Subject=Re%3A%20%5BIfeffit%5D%20Icosahedral%20cluster%20coordinates&In-Reply-To=%3Ca06230900bf034551d19b%40%5B192.168.10.2%5D%3E>
Tue Jul 19 19:06:17 CDT 2005
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________________________________
Hi Patrick,
Hopefully this will do it. A disclaimer: I never actually tested this
on an icosahedral material, and I did the coordinates by hand, so I
can't guarantee it.
--Scott Calvin
Sarah Lawrence College
>
>
>I am working with metal clusters and would like to do some FEFF
>calculations on icosahedral clusters. Is there anyone out there who
>has a FEFF input file (or equivalently a list of coordinates) for an
>icosahedral cluster (147 atoms is probably sufficient for my
>purpuses).
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* This feff.inp file generated by ATOMS, version 2.50
* ATOMS written by and copyright (c) Bruce Ravel, 1992-1999
* -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
* total mu = 2764.1 cm^-1, delta mu = 2397.0 cm^-1
* specific gravity = 6.899, cluster contains 147 atoms.
* -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
* mcmaster corrections: 0.00065 ang^2 and 0.812E-06 ang^4
* -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
TITLE Fe hcp
%c and a have been chosen to give 5% expansion between layers and 10%
within the
%layer in the first shell as per Farges (1982).
%This thus roughly simulates a relaxed icosohedron
HOLE 1 1.0 Fe K edge ( 7.112 keV), second number is S0^2
* mphase,mpath,mfeff,mchi
CONTROL 1 1 1 1
PRINT 1 0 0 0 0 3
RMAX 7.50193
*CRITERIA curved plane
*DEBYE temp debye-temp
*NLEG 8
SCF 5.0
POTENTIALS
* ipot z label
0 26 Fe
1 26 Fe
ATOMS
0.00000 0.00000 0.00000 0 Fe1 0.00000
-1.57817 -0.00003 -2.07750 1 Fe1 2.60895
-1.57817 -0.00003 2.07750 1 Fe1 2.60895
0.78911 1.36672 2.07750 1 Fe1 2.60895
0.78911 -1.36678 -2.07750 1 Fe1 2.60898
0.78911 -1.36678 2.07750 1 Fe1 2.60898
0.78911 1.36672 -2.07750 1 Fe1 2.60895
-2.36728 1.36675 0.00000 1 Fe1 2.73350
-2.36728 -1.36675 0.00000 1 Fe1 2.73350
0.00000 -2.73350 0.00000 1 Fe1 2.73350
0.00000 2.73350 0.00000 1 Fe1 2.73350
2.36728 1.36675 0.00000 1 Fe1 2.73350
2.36728 -1.36675 0.00000 1 Fe1 2.73350
-1.57817 -2.73353 2.07750 1 Fe1 3.77873
-1.57817 -2.73353 -2.07750 1 Fe1 3.77873
-1.57817 2.73347 2.07750 1 Fe1 3.77869
-1.57817 2.73347 -2.07750 1 Fe1 3.77869
3.15639 -0.00003 -2.07750 1 Fe1 3.77873
3.15639 -0.00003 2.07750 1 Fe1 3.77873
0.00000 0.00000 4.15500 1 Fe1 4.15500
0.00000 0.00000 -4.15500 1 Fe1 4.15500
-3.94545 -1.36678 2.07750 1 Fe1 4.66376
-3.94545 -1.36678 -2.07750 1 Fe1 4.66376
-3.94545 1.36672 2.07750 1 Fe1 4.66375
-3.94545 1.36672 -2.07750 1 Fe1 4.66375
0.78911 4.10022 2.07750 1 Fe1 4.66375
0.78911 4.10022 -2.07750 1 Fe1 4.66375
0.78911 -4.10028 2.07750 1 Fe1 4.66379
0.78911 -4.10028 -2.07750 1 Fe1 4.66379
3.15639 2.73347 2.07750 1 Fe1 4.66376
3.15639 -2.73353 -2.07750 1 Fe1 4.66379
3.15639 2.73347 -2.07750 1 Fe1 4.66376
3.15639 -2.73353 2.07750 1 Fe1 4.66379
-4.73456 0.00000 0.00000 1 Fe1 4.73456
-2.36728 -4.10025 0.00000 1 Fe1 4.73456
-2.36728 4.10025 0.00000 1 Fe1 4.73456
2.36728 4.10025 0.00000 1 Fe1 4.73456
2.36728 -4.10025 0.00000 1 Fe1 4.73456
4.73456 0.00000 0.00000 1 Fe1 4.73456
-2.36728 -1.36675 -4.15500 1 Fe1 4.97353
-2.36728 1.36675 -4.15500 1 Fe1 4.97353
-2.36728 1.36675 4.15500 1 Fe1 4.97354
-2.36728 -1.36675 4.15500 1 Fe1 4.97354
0.00000 2.73350 -4.15500 1 Fe1 4.97354
0.00000 -2.73350 4.15500 1 Fe1 4.97354
0.00000 -2.73350 -4.15500 1 Fe1 4.97353
0.00000 2.73350 4.15500 1 Fe1 4.97354
2.36728 1.36675 -4.15500 1 Fe1 4.97354
2.36728 -1.36675 -4.15500 1 Fe1 4.97354
2.36728 -1.36675 4.15500 1 Fe1 4.97353
2.36728 1.36675 4.15500 1 Fe1 4.97353
-4.73456 -2.73350 0.00000 1 Fe1 5.46700
-4.73456 2.73350 0.00000 1 Fe1 5.46700
0.00000 5.46700 0.00000 1 Fe1 5.46700
0.00000 -5.46700 0.00000 1 Fe1 5.46700
4.73456 2.73350 0.00000 1 Fe1 5.46700
4.73456 -2.73350 0.00000 1 Fe1 5.46700
-3.94545 -4.10028 -2.07750 1 Fe1 6.05763
-3.94545 4.10022 -2.07750 1 Fe1 6.05759
-3.94545 4.10022 2.07750 1 Fe1 6.05759
-3.94545 -4.10028 2.07750 1 Fe1 6.05763
-1.57817 -5.46703 -2.07750 1 Fe1 6.05764
-1.57817 -5.46703 2.07750 1 Fe1 6.05764
-1.57817 5.46697 -2.07750 1 Fe1 6.05759
-1.57817 5.46697 2.07750 1 Fe1 6.05759
5.52367 -1.36678 -2.07750 1 Fe1 6.05764
5.52367 1.36672 2.07750 1 Fe1 6.05763
5.52367 1.36672 -2.07750 1 Fe1 6.05763
5.52367 -1.36678 2.07750 1 Fe1 6.05764
-4.73456 0.00000 4.15500 1 Fe1 6.29921
-4.73456 0.00000 -4.15500 1 Fe1 6.29921
-2.36728 -4.10025 -4.15500 1 Fe1 6.29921
-2.36728 -4.10025 4.15500 1 Fe1 6.29921
-2.36728 4.10025 -4.15500 1 Fe1 6.29921
-2.36728 4.10025 4.15500 1 Fe1 6.29921
2.36728 -4.10025 -4.15500 1 Fe1 6.29921
2.36728 4.10025 4.15500 1 Fe1 6.29921
2.36728 -4.10025 4.15500 1 Fe1 6.29921
2.36728 4.10025 -4.15500 1 Fe1 6.29921
4.73456 0.00000 -4.15500 1 Fe1 6.29921
4.73456 0.00000 4.15500 1 Fe1 6.29921
-1.57817 -0.00003 6.23250 1 Fe1 6.42921
-1.57817 -0.00003 -6.23250 1 Fe1 6.42921
0.78911 1.36672 6.23250 1 Fe1 6.42921
0.78911 -1.36678 6.23250 1 Fe1 6.42922
0.78911 -1.36678 -6.23250 1 Fe1 6.42922
0.78911 1.36672 -6.23250 1 Fe1 6.42921
-6.31273 -0.00003 -2.07750 1 Fe1 6.64580
-6.31273 -0.00003 2.07750 1 Fe1 6.64580
3.15639 -5.46703 -2.07750 1 Fe1 6.64584
3.15639 -5.46703 2.07750 1 Fe1 6.64584
3.15639 5.46697 2.07750 1 Fe1 6.64579
3.15639 5.46697 -2.07750 1 Fe1 6.64579
-4.73456 -2.73350 4.15500 1 Fe1 6.86674
-4.73456 -2.73350 -4.15500 1 Fe1 6.86674
-4.73456 2.73350 -4.15500 1 Fe1 6.86674
-4.73456 2.73350 4.15500 1 Fe1 6.86674
0.00000 5.46700 -4.15500 1 Fe1 6.86674
0.00000 -5.46700 -4.15500 1 Fe1 6.86674
0.00000 5.46700 4.15500 1 Fe1 6.86674
0.00000 -5.46700 4.15500 1 Fe1 6.86674
4.73456 -2.73350 -4.15500 1 Fe1 6.86674
4.73456 2.73350 -4.15500 1 Fe1 6.86674
4.73456 2.73350 4.15500 1 Fe1 6.86674
4.73456 -2.73350 4.15500 1 Fe1 6.86674
-1.57817 2.73347 6.23250 1 Fe1 6.98617
-1.57817 -2.73353 6.23250 1 Fe1 6.98619
-1.57817 -2.73353 -6.23250 1 Fe1 6.98619
-1.57817 2.73347 -6.23250 1 Fe1 6.98617
3.15639 -0.00003 6.23250 1 Fe1 6.98619
3.15639 -0.00003 -6.23250 1 Fe1 6.98619
-6.31273 -2.73353 -2.07750 1 Fe1 7.18601
-6.31273 2.73347 -2.07750 1 Fe1 7.18599
-6.31273 -2.73353 2.07750 1 Fe1 7.18601
-6.31273 2.73347 2.07750 1 Fe1 7.18599
0.78911 -6.83378 2.07750 1 Fe1 7.18604
0.78911 -6.83378 -2.07750 1 Fe1 7.18604
0.78911 6.83372 -2.07750 1 Fe1 7.18599
0.78911 6.83372 2.07750 1 Fe1 7.18599
5.52367 -4.10028 -2.07750 1 Fe1 7.18604
5.52367 4.10022 -2.07750 1 Fe1 7.18601
5.52367 -4.10028 2.07750 1 Fe1 7.18604
5.52367 4.10022 2.07750 1 Fe1 7.18601
-7.10184 -1.36675 0.00000 1 Fe1 7.23216
-7.10184 1.36675 0.00000 1 Fe1 7.23216
-4.73456 -5.46700 0.00000 1 Fe1 7.23216
-4.73456 5.46700 0.00000 1 Fe1 7.23216
-2.36728 -6.83375 0.00000 1 Fe1 7.23216
-2.36728 6.83375 0.00000 1 Fe1 7.23216
2.36728 -6.83375 0.00000 1 Fe1 7.23216
2.36728 6.83375 0.00000 1 Fe1 7.23216
4.73456 5.46700 0.00000 1 Fe1 7.23216
4.73456 -5.46700 0.00000 1 Fe1 7.23216
7.10184 1.36675 0.00000 1 Fe1 7.23216
7.10184 -1.36675 0.00000 1 Fe1 7.23216
-3.94545 -1.36678 6.23250 1 Fe1 7.50191
-3.94545 -1.36678 -6.23250 1 Fe1 7.50191
-3.94545 1.36672 -6.23250 1 Fe1 7.50190
-3.94545 1.36672 6.23250 1 Fe1 7.50191
0.78911 4.10022 -6.23250 1 Fe1 7.50190
0.78911 -4.10028 -6.23250 1 Fe1 7.50194
0.78911 4.10022 6.23250 1 Fe1 7.50190
0.78911 -4.10028 6.23250 1 Fe1 7.50194
3.15639 2.73347 6.23250 1 Fe1 7.50191
3.15639 -2.73353 -6.23250 1 Fe1 7.50194
3.15639 -2.73353 6.23250 1 Fe1 7.50194
3.15639 2.73347 -6.23250 1 Fe1 7.50192
END
________________________________
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