[Wien] (no subject)

[Oleg Rubel]

Your warnings are completely natural. The initial set of equivalent 
atoms will be broken by defects introduced. My suggestion will be

(1) run "x nn" and accept the structure file it proposes instead of the 
original one, then

(2) run "x sgroup" and accept the structure file in case there will be a 
warning like you have had [warning: !!! Struct file is not consistent 
with space group found.]

(3) try to avoid labeling the atoms (Se1, Se2) unless you would like to 
reduce the symmetry on purpose.

(4) There is likely more than one possible arrangements for the pair of 
impurities in your structure. I would recommend to optimize forces for 
several alternatives, compare total energies and decide which 
configuration is likely to form in an alloy.

Oleg

On 20/08/2013 9:08 PM, Israel Pérez wrote:
> Hi Prof. P. Blaha
>
> I need some help with supercell calculations. I'd like to investigate
> the effect of replacing Se with Te in the system FeSe. Structure file is
> as shown below.
>
>
> FeSe
> P   LATTICE,NONEQUIV.ATOMS:  2129_P4/nmm
> MODE OF CALC=RELA unit=ang
>    7.119735  7.119735 10.364585 90.000000 90.000000 90.000000
> ATOM  -1: X=0.25000000 Y=0.75000000 Z=0.00000000
>            MULT= 2          ISPLIT=-2
>        -1: X=0.75000000 Y=0.25000000 Z=0.00000000
> Fe     NPT=  781  R0=0.00005000 RMT=    2.1900   Z: 26.0
> LOCAL ROT MATRIX:    0.7071068-0.7071068 0.0000000
>                       0.7071068 0.7071068 0.0000000
>                       0.0000000 0.0000000 1.0000000
> ATOM  -2: X=0.25000000 Y=0.25000000 Z=0.23720000
>            MULT= 2          ISPLIT=-2
>        -2: X=0.75000000 Y=0.75000000 Z=0.76280000
> Se         NPT=  781  R0=0.00005000 RMT=    1.9400   Z: 34.0
> LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
>                       0.0000000 1.0000000 0.0000000
>                       0.0000000 0.0000000 1.0000000
>    16      NUMBER OF SYMMETRY OPERATIONS
> -1 0 0 0.00000000
>   0-1 0 0.00000000
>   0 0-1 0.00000000
>         1
>   0-1 0 0.00000000
> -1 0 0 0.00000000
>   0 0-1 0.00000000
>         2
>   0 1 0 0.00000000
>   1 0 0 0.00000000
>   0 0 1 0.00000000
>         3
>   1 0 0 0.00000000
>   0 1 0 0.00000000
>   0 0 1 0.00000000
>         4
> -1 0 0 0.50000000
>   0 1 0 0.00000000
>   0 0 1 0.00000000
>       5
> -1 0 0 0.50000000
>   0-1 0 0.50000000
>   0 0 1 0.00000000
>         6
>   0-1 0 0.50000000
> -1 0 0 0.50000000
>   0 0 1 0.00000000
>         7
>   0 1 0 0.50000000
> -1 0 0 0.00000000
>   0 0-1 0.00000000
>         8
>   0 1 0 0.00000000
> -1 0 0 0.50000000
>   0 0 1 0.00000000
>         9
>   0-1 0 0.00000000
>   1 0 0 0.50000000
>   0 0-1 0.00000000
>        10
>   0-1 0 0.50000000
>   1 0 0 0.00000000
>   0 0 1 0.00000000
>        11
>   0 1 0 0.50000000
>   1 0 0 0.50000000
>   0 0-1 0.00000000
>        12
> -1 0 0 0.00000000
>   0 1 0 0.50000000
>   0 0-1 0.00000000
>        13
>   1 0 0 0.50000000
>   0-1 0 0.00000000
>   0 0-1 0.00000000
>        14
>   1 0 0 0.00000000
>   0-1 0 0.50000000
>   0 0 1 0.00000000
>        15
>   1 0 0 0.50000000
>   0 1 0 0.50000000
>   0 0-1 0.00000000
>        16
>
> Then I copy it to a new session and create a supercell 2X2X1 with
> lattice F. The program recognizes 8 inequivalent atoms, each with two
> positions (total of 16 atoms). Then I replace the last atom of Se by Te
> so that I have a doping of 25% and set its RMT to 2 and the atomic
> number to 52. RMT_Fe=2.1 and RMT_Se=1.96. Here I have a couple of
> questions. First, I wonder if we have to label all inequivalent atoms
> (for instance, Fe1, Fe2, Se1, Se2, etc.) because when I compute xnn, I
> got a warning like this
>
>   WARNING: Mult not equal. PLEASE CHECK outputnn-file
>   WARNING: ityp not equal. PLEASE CHECK outputnn-file
>   WARNING: ityp not equal. PLEASE CHECK outputnn-file
>
>    NN created a new SFeSeTe.struct_nn file
> NN created a new CASE.STRUCT_NN FILE
> 0.016u 0.000s 0:00.01 100.0%	0+0k 0+160io 0pf+0w
>
> If I continue to x group I got another warning such as this:
>
> warning: !!! Number of inequivalent atoms has changed. !!! Old value= 8
> New value= 6 warning: !!! Bravais lattice has changed.
> sgroup found: 12 (C 2/m) [unique axis c] cell choice 2
>
> Why? And then the program suggests to change the sgroup. If I don't
> accept and continue I get an error in editinst step:
>
> error: SFeSeTe.inst not consistent with Z
> edit SFeSeTe.inst and rerun lstart afterwards or change Z in StructGen!
>
> On the other hand, if I labeled the atoms, the warnings after xnn is
> executed don't appear anymore. However, when I run  sgroup, I got a warning:
>
> warning: !!! Struct file is not consistent with space group found.
> sgroup found: !!! Struct file is not consistent with space group found.
> Number and name of space group: 2 (P -1)
>
> which causes errors in forthcoming steps. Should I labeled them and why?
> What is the correct procedure to avoid these warnings and perform
> supercell calculations successfully. I'm a beginner with supercell
> calculations.
>
> I have already read the manual but the information is not enough to
> solve this problem. I also checked the wien list of problems. There are
> some similar to mine but the warnings and errors are different. I'd
> appreciate any assistance you may have.
>
> Regards
>
> Thanks
>
> Israel  Perez
>
> <http://www.mda.cinvestav.mx/>
>
>
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