The ABINIT Users Mailing List ( CLOSED )

[mmikami@rc.m-kagaku.co.jp]

Hello Xianghjun,

I corrected my crystal data (thanks to your caution).
Then the following data will be OK for the ABINIT to recognize the 
structure as P3 (#143) which I have obtained by symmetrizing your 
original data (see below, marked with *) with Cerius2.  With this 
input,  ABINIT will reply, "Symmetries : space group P3 (#143); Bravais 
hP (primitive hexag.)" So I believe that your original geometry was 
needed to be more symmetrized before the ABINIT job submission. (Please 
check the slight difference in detail. I do not have time now to go 
into detail ...)

Otherwise, the effective digits for xred should be as many as possible, 
so I used 1/3 or 2/3 in the below. In the original data, the digits 
might have been fewer than the ABINIT expects.
(Please read again: 
http://www.abinit.org/wws/arc/forum/2003-08/msg00000.html
The space group 194 may be reagard as the lower-symmetry 51, if the 
effective digits for xred are few.)
For the rprim, please see also,
http://www.abinit.org/ABINIT/Infos_v4.1/varbas.htm#rprim
(As Xavier mentioned, sqrt(0.75) will be OK)

Thus, in the previous e-mails, we just meant that the input for the 
structure should be highly symmetrized before ABINIT job submission, if 
one wants ABINIT to recognize the geometry as high symmetry. In my 
opinion, this should be called as a "specification", not a "bug"...

Regards,
Masayoshi

acell   6.59831    6.59831   18.66285   angstrom
angdeg 90.00000   90.00000  120.00000   # Note that 120, not 60
ntypat 3
natom 21
typat 15*1 3*2 3*3   # 15Si, 3Ag, 3H
xred
1/3              2/3              0.32442
0.00000    0.00000    0.31844
0.78105    0.78105    0.99267
0.65918   -0.00000    0.15695
2/3              1/3              0.32442
0.67867    0.67867    0.11440
0.66143    0.00000    0.28194
0.21895    0.00000    0.99267
0.00000    0.65918    0.15695
0.32133    0.00000    0.11440
0.00000    0.66143    0.28194
0.00000    0.21895    0.99267
0.34082    0.34082    0.15695
0.00000    0.32133    0.11440
0.33857    0.33857    0.28194
1/3              2/3              0.40508
0.00000    0.00000    0.39922
2/3              1/3              0.40508
0.45359    0.40169    0.95348
0.59831    0.05190    0.95348
0.94810    0.54641    0.95348

(*) Your original data, where the gamma = 60, not 120.
acell 3*12.46900941390533980495
rprim
         0.8660254037 -0.500 0.000
         0.8660254037  0.500 0.000
         0.000000  0.000 2.82842712474619009760
ntypat 3               # There are three types of atom
natom 21
typat 15*1 3*2 3*3
xred
0.218950  0.0000000000000000 0.9926660702015143
0.000000  0.7810504209763201 0.9926660702015143
0.340823  0.6591768987078352 0.1569544844852325
0.000000  0.3408231012921648 0.1569544844852325
0.333333  0.3333333333333357 0.3244222690927250
0.000000  0.0000000000000000 0.3184370406339494
0.321330  0.0000000000000000 0.1144023099468491
0.000000  0.6786691791771417 0.1144023099468491
0.338570  0.6614299606199239 0.2819440365858185
0.000000  0.3385700791165035 0.2819440415528746
0.781050  0.2189495790236799 0.9926660702015143
0.659177  0.0000000000000000 0.1569544844852325
0.666667  0.6666666666666643 0.3244222690927250
0.678669  0.3213308208228654 0.1144023099468491
0.661430  0.0000000000000000 0.2819440415528746
0.333333  0.3333333333333357 0.4050793316269057
0.000000  0.0000000000000000 0.3992189417566484
0.666667 0.6666666666666643 0.4050793316269057
-0.401693960  -0.0519003712    0.9534800216094036
-0.0519003712 0.4535941     0.9534800216094036
0.4535941000 -0.40169396  0.9534800191258791

On 2003.9.1, at 22:22 Asia/Tokyo, xhongjun wrote:

> Dear Masayoshi:
>   The system I studied is Si(111)sqrt(3)*sqrt(3)
> Ag surface(IET structure).From the ref PHYSICAL REVIEW B 68, 
> 085407(2003)(see also H. Aizawa, M. Tsukada,
> N. Sato, and S. Hasegawa, Surf. Sci. 429, L509(1999)).
> I know that this system should belong to P3 space group.
> Your geometry is not that I want to study.
> The system I study is given in BIOSYM car format,which
> should be recognized by Cerius2 or molden.
> cat 1.car
> !BIOSYM archive 3
> PBC=ON
>
> !DATE     Jul 28 21:16:26 2002
> PBC 6.5983 6.5983 18.6628 90.0000 90.0000 60.0000
> Si1      1.444700630    0.000000000   18.525975439 dmol 1      ??? Si  
> 0.000
> Si2      2.576807571    4.463161634   18.525975439 dmol 1      ??? Si  
> 0.000
> Si3      4.423584577    3.766738953    2.929217601 dmol 1      ??? Si  
> 0.000
> Si4      1.124428749    1.947567723    2.929217601 dmol 1      ??? Si  
> 0.000
> Si5      3.299154297    1.904768892    6.054643318 dmol 1      ??? Si  
> 0.000
> Si6      0.000000000    0.000000000    5.942941912 dmol 1      ??? Si  
> 0.000
> Si7      2.120235914    0.000000000    2.135072859 dmol 1      ??? Si  
> 0.000
> Si8      2.239035832    3.878123821    2.135072859 dmol 1      ??? Si  
> 0.000
> Si9      4.416151782    3.779613639    5.261878545 dmol 1      ??? Si  
> 0.000
> Si10     1.116995676    1.934693263    5.261878637 dmol 1      ??? Si  
> 0.000
> Si11     5.875961290    1.251145041   18.525975439 dmol 1      ??? Si  
> 0.000
> Si12     4.349456165    0.000000000    2.929217601 dmol 1      ??? Si  
> 0.000
> Si13     6.598315193    3.809537784    6.054643318 dmol 1      ??? Si  
> 0.000
> Si14     5.538191146    1.836182854    2.135072859 dmol 1      ??? Si  
> 0.000
> Si15     4.364322164    0.000000000    5.261878637 dmol 1      ??? Si  
> 0.000
> H16      3.299154297    1.904768892    7.559933772 dmol 1      ???     
> H   0.000
> H17      0.000000000    0.000000000    7.450562210 dmol 1      ???     
> H   0.000
> H18      6.598315193    3.809537784    7.559933772 dmol 1      ???     
> H   0.000
> Ag19    -2.821729923   -0.296574638   17.794652191 dmol 1      ??? Ag  
> 0.000
> Ag20     1.154023028    2.591975794   17.794652191 dmol 1      ??? Ag  
> 0.000
> Ag21     1.667704606   -2.295402477   17.794652145 dmol 1      ??? Ag  
> 0.000
> end
> end
> -------------------------------------
> Are there any errors in my input file?
> Regards
> xianghjun
>
> >mmikami@rc.m-kagaku.co.jp wrote:
> > Hello Xianghjun,
> > Are you confident with your geometry ?
> > Which kind of symmetry are you expecting ??
> > (You might know the answer. If so, why not give us the information ?)
> > I tried your input file from the original e-mail :
> > http://www.abinit.org/wws/arc/forum/2003-09/msg00003.html
> > Then I look into your geometry ... seems the slab model ??
> > (I also tried to find the geometry with Cerius2, then I did not find
> >  any high symmetries, but just "P1", even with the tolerance
> >  deviation of 0.50 angstrom. So the same answer ...)
> > Could you please check your structure carefully again ?
> > Regards,
> > Masayoshi
> > P.S. The attachment is the picture file of your model... (temp.gif)
> > Does this have any high symmetries ?