[Ifeffit] Fwd: Icosahedral cluster coordinates
Scott Calvin
dr.scott.calvin at gmail.com
Mon Jun 27 12:06:56 CDT 2011
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
> Tue Jul 19 19:06:17 CDT 2005
> Previous message: [Ifeffit] Icosahedral cluster coordinates
> Next message: [Ifeffit] Icosahedral cluster coordinates
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
> 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).
> -------------- next part --------------
> * 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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