[Wien] RE: Partial Occupancy problem

[Siew Wei Goh]

Thank you so much for the explanation!  Really appreciate it!

I've checked the Pn1.struct created against the original pentlandite
structure and they do look to be the same with shifted origin.  However, I
have one more question.  

Following the change in the space group to accommodate for the new
assignment of metal atoms to specific sites, Wien split one of the S sites
into two inequivalent sitesRegards,
 
Siew Wei Goh
School of Chemistry
University of New South Wales
Sydney NSW 2052, Australia
Tel: +61 (2) 9385 5519
 
 

-----Original Message-----
From: Peter Blaha [mailto:pblaha at theochem.tuwien.ac.at] 
Sent: Thursday, January 05, 2006 8:41 PM
To: sw.goh at unsw.edu.au
Cc: WIEN mailing-list
Subject: Re: Partial Occupancy problem

I've not checked your struct files in detail, but the procedure leading to
Pn1.struct seems perfectly all right.

Experimentally this seems to be a random alloy between Fe and Ni in this 
second site. Only in the "model of random (partial) occupation" this has 
cubic symmetry. (This is NOT the truth either, because of course in nature 
at one particular point in space there can be only Fe OR Ni and not half 
of them). It is just saying that there is NO long range order but 
(complete ?) deisorder.

Whithin a "bandstructure" model you must put specific atoms on specific 
sites and this MUST break symmetry leading to lower symmetry. Thus your 
Pn1.struct file is most likely ok.

A "shift" of positions is not a problem (one can in principle always shift 
the origin of the unitcell - these are just conventions). Just check 
within nn if the distances remain the same (or with xcrysden if your 
structure looks the same (with shifted origin).

Of course your model is now ONE ordered "superstructure" and certain 
properties may depend on how one introduces the long range order 
(necessary in WIEN2k). You could select different sites as Ni (leading to 
a different spacegroup !), or you 
could create a "supercell" with more atoms and introduce some more 
randomness. (For S-XANES spectra I'd NOT expect too much influence, but I 
might be wrong)

Regards

> I am trying to simulate S K-edge NEXAFS spectra on pentlandite (Fe,Ni)9S8.
> I am having major problem with simulating this structure because of the
> partial occupancy of its Ni and Fe atoms!  I have been searching for
> possible guide in how to deal with partial occupancy in WIEN2k from the
User
> Forum. There had been a few entries on Partial Occupancy and I followed
the
> link through, but still found no solution to my problem.  In the forum, it
> says to "try combination of sites"!  In my attempted to do this, I could
not
> get WIEN to run my modified structures.  I will describe below what I had
> attempted.
> 
>  
> 
> I thought to simplify the calculation by attempting to calculate for
> Fe5Ni4S8.  First I generated the pentlandite structure by using only Fe
> atoms on both the metal sites, octahedral and tetrahedral sites (see
> attached structure file, "Pn_Fe.struct"). This gives 48 symmetry.
> 
>  
> 
> Next I took out 4 of the 8 atoms from the Fe tetrahedral sites {ATOM -2}
and
> put Ni atoms into those coordinate.  I then change the ATOMS number
> accordingly (see attached "Pn_FeNi edited.struct".  When attempting to run
> WIEN on this modified structure without running pass StructGen session, it
> tells me that I've got the wrong inequivalent atoms and asked me to select
> the suggested space group - this would change the cubic structure (space
> group 225) into tetragonal (space group 216)! See attached "Pn1.struct".
I
> do not think simulations obtained from this alternative suggested space
> group is appropriate to describe pentlandite!  It would have altered the
> positions or the atoms itself and so the absorption spectra would also be
> affected! Am I right?
> 
>  
> 
> If I forced WIEN to continue without changing the space group, it soon ran
> into SYMMETRY problem during initialization stage!  
> 
>  
> 
> I'd also tried running the modified structure pass StrucGen first.
However,
> this doesn't help because it simply generate identical multiplicity metal
> coordinates for both the Fe and Ni atoms!  And. WIEN ran into error!
> 
>  
> 
> Obviously I had been going about the wrong way in getting WIEN to work on
> this structure.  Please advice what can I do to get WIEN to run the
> structure with the correct space group.  Many thanks in advance.  Once
> again, Happy New Year!
> 
>  
> 
>  
> 
> Fm3m  225
> 
> a = 10.03 Angstrom
> 
> alpha = 90 deg
> 
>  
> 
> atom                 x          y          z
occupancy
> 
> Fe (Oct)            0.5        0.5        0.5                    1.0
> 
> Fe (Tet)             0.125    0.125    0.125                0.5
> 
> Ni (Tet)             0.125    0.125    0.125                0.5
> 
> S 1                    0.25      0.25      0.25                  1.0
> 
> S2                     0.25      0          0                      1.0
> 
>  
> 
>  
> 
> Regards,
> 
>  
> 
> Siew Wei Goh
> 
> School of Chemistry
> 
> University of New South Wales
> 
> Sydney NSW 2052, Australia
> 
> Tel: +61 (2) 9385 5519
> 
>  
> 
>  
> 
>  
> 
> 


                                      P.Blaha
--------------------------------------------------------------------------
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-15671             FAX: +43-1-58801-15698
Email: blaha at theochem.tuwien.ac.at    WWW:
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