Two comments in addition to what Stefan said:
i) You started with a P cell, and want a 2x2x1 supercell. With such a
cell a F-centering is not possible (and supercell neglects your request
and creates a P cell anyway). (You would need 2x2x2 to allow for F-cells)
ii) Since you got 8 positions, each 2 fold degenerate, you probably want
to FIRST "split" one of those Se positions (either in w2web or manually)
and have "9 non-equivalent atoms". Only then you replace one of the
single Se by Te.
iii) And then, as Stefan said, the 3 programs nn, sgroup and symmetry,
help you to setup a proper struct file with correct symmetries. Of
course you always have to accept their suggestions. (We put that as
"WARNINGS", because it is NOT always true that you should accept it, but
you should THINK about it. Suppose you enter a "known structure", but
you mistype something in the input. Then nn or sgroup will also complain
and put WARNINGS, but in this case you must NOT accept it, but find your
input error .....
On 08/21/2013 03:08 AM, 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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P.Blaha
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Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: [email protected] WWW:
http://info.tuwien.ac.at/theochem/
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