[Wien] Bug in StructGen
Peter Blaha
pblaha at theochem.tuwien.ac.at
Sat Jan 24 16:43:10 CET 2009
a) I don't think there is a "problem" in the structeditor with the
format (number of atoms). Instead, I remember that I had once similar
problems before when using some specific web-browser. While I cannot
remember exactly, I think it happened with some version if the
MS-windows internet-explorer. The problems did not appear (for the same
case) when using my default (Linux firefox) browser.
b) I tried to put in your struct file and my structeditor gives me an
error message that the cell parameters are not ok. It returns into the
edit-mode with 14 positions, but of course without generation of the 2nd
equivalent position for atoms 10-14. This behavior is consistent with
the previous mail by Perez-Mato, that for a "monoclinic spacegroup you
have to put of of the angles .ne. 90 degrees.
c) I just made a fix in the SRC_spacegroup programm to overcome this
restriction. In principle this fix works, however, I think there is a
fundamental problem for many monoclinic sg which one cannot overcome
unless one does specify a monoclinic angle himself:
Eg. for spacegroup P2 there can be several settings, depending on the
monoclinic angle (the "unique" axis. Take your desired position 14:
ATOM 14: X=0.75000000 Y=0.75000000 Z=0.75000000
MULT= 2 ISPLIT= 8
14: X=0.25000000 Y=0.25000000 Z=0.75000000
This can only be achieved, when gamma .ne. 90; but for eg. beta .ne. 90
one would get:
ATOM 14: X=0.75000000 Y=0.75000000 Z=0.75000000
MULT= 2 ISPLIT= 8
14: X=0.25000000 Y=0.75000000 Z=0.25000000 y-z interchanged
So when you put all angles to 90 degree, no program can know which
coordinates it should generate for the P2 spacegroup. Of course I could
assume you "mean" gamma.ne.90 .... but I'm not sure if this does not
lead to undesired atomic positions in some cases.
wmppemam at lg.ehu.es schrieb:
> I do not know if it has been changed in the last versions, but in previous
> versions StructGen did not "like" monoclinic structures with the
> monoclinic angle equal to 90.00 degrees. If you were interested in doing
> calculations with a monoclinic exactly equal to 90 degrees, you had to
> generate the struct file puting some false value of 90.01 or whatever, and
> correct it afterwards by hand. maybe this is your problem
>
> regards,
> *************************************************
> J. Manuel Perez-Mato
> Fac. Ciencia y Tecnologia,
> Universidad del Pais Vasco, UPV
> 48080 BILBAO,
> Spain
>
> tel. +34 946012473
> fax. +34 946013500
> *************************************************
>
> On Fri, 23 Jan 2009, D.A. Tompsett wrote:
>
>> Dear All,
>> I believe that I have come across a bug in StructGen.
>>
>> I am attempting to input the following .struct file. There are 14 ineqiv
>> atoms. However when I click "Save Structure" in w2web it hangs. When I look
>> at the file .struc_i it only has 4 atoms. Any advice would be greatly
>> appreciated. It seems that some part of the program is reading the NAT
>> field of line 2 of the .struct file with the wrong character width.
>>
>> Thanks for any help,
>> David Tompsett.
>>
>> Title P LATTICE,NONEQUIV.ATOMS: 14 3 P2
>> RELA
>> 10.487602 10.487602 23.396708 90.000000 90.000000 90.000000
>> ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000
>> MULT= 1 ISPLIT= 8
>> Fe1 NPT= 781 R0=0.00005000 RMT= 2.2400 Z: 26.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 2: X=0.00000000 Y=0.50000000 Z=0.00000000
>> MULT= 1 ISPLIT= 8
>> Fe2 NPT= 781 R0=0.00005000 RMT= 2.2400 Z: 26.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 3: X=0.50000000 Y=0.50000000 Z=0.00000000
>> MULT= 1 ISPLIT= 8
>> Fe3 NPT= 781 R0=0.00005000 RMT= 2.2400 Z: 26.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 4: X=0.50000000 Y=0.00000000 Z=0.00000000
>> MULT= 1 ISPLIT= 8
>> Fe4 NPT= 781 R0=0.00005000 RMT= 2.2400 Z: 26.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 5: X=0.00000000 Y=0.00000000 Z=0.50000000
>> MULT= 1 ISPLIT= 8
>> Fe5 NPT= 781 R0=0.00005000 RMT= 2.2400 Z: 26.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 6: X=0.00000000 Y=0.50000000 Z=0.50000000
>> MULT= 1 ISPLIT= 8
>> Fe6 NPT= 781 R0=0.00005000 RMT= 2.2400 Z: 26.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 7: X=0.50000000 Y=0.50000000 Z=0.50000000
>> MULT= 1 ISPLIT= 8
>> Fe7 NPT= 781 R0=0.00005000 RMT= 2.2400 Z: 26.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 8: X=0.50000000 Y=0.00000000 Z=0.50000000
>> MULT= 1 ISPLIT= 8
>> Fe8 NPT= 781 R0=0.00005000 RMT= 2.2400 Z: 26.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 9: X=0.75000000 Y=0.25000000 Z=0.60780300
>> MULT= 2 ISPLIT= 8
>> 9: X=0.25000000 Y=0.75000000 Z=0.60780300
>> As1 NPT= 781 R0=0.00005000 RMT= 1.9900 Z: 33.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 10: X=0.75000000 Y=0.25000000 Z=0.89219000
>> MULT= 2 ISPLIT= 8
>> 10: X=0.25000000 Y=0.75000000 Z=0.89219000
>> As2 NPT= 781 R0=0.00005000 RMT= 1.9900 Z: 33.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 11: X=0.25000000 Y=0.25000000 Z=0.39219700
>> MULT= 2 ISPLIT= 8
>> 11: X=0.75000000 Y=0.75000000 Z=0.39219700
>> As3 NPT= 781 R0=0.00005000 RMT= 1.9900 Z: 33.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 12: X=0.25000000 Y=0.25000000 Z=0.10780300
>> MULT= 2 ISPLIT= 8
>> 12: X=0.75000000 Y=0.75000000 Z=0.10780300
>> As4 NPT= 781 R0=0.00005000 RMT= 1.9900 Z: 33.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 13: X=0.75000000 Y=0.25000000 Z=0.25000000
>> MULT= 2 ISPLIT= 8
>> 13: X=0.25000000 Y=0.75000000 Z=0.25000000
>> Sr1 NPT= 781 R0=0.00005000 RMT= 2.1500 Z: 38.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM 14: X=0.75000000 Y=0.75000000 Z=0.75000000
>> MULT= 2 ISPLIT= 8
>> 14: X=0.25000000 Y=0.25000000 Z=0.75000000
>> Sr2 NPT= 781 R0=0.00005000 RMT= 2.1500 Z: 38.0
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> 2 NUMBER OF SYMMETRY OPERATIONS
>> 1 0 0 0.00000000
>> 0 1 0 0.00000000
>> 0 0 1 0.00000000
>> 1
>> -1 0 0 0.00000000
>> 0-1 0 0.00000000
>> 0 0 1 0.00000000
>> 2
>>
>> --
>> David A. Tompsett
>> Quantum Matter Group
>> Cavendish Laboratory
>> J. J. Thomson Avenue
>> Cambridge CB3 0HE
>> U.K.
>> Tel: +44 7907 566351 (mobile)
>> Fax: +44 1223 337351
>> http://www-qm.phy.cam.ac.uk/
>>
>>
>>
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>
>>
>>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
--
-----------------------------------------
Peter Blaha
Inst. Materials Chemistry, TU Vienna
Getreidemarkt 9, A-1060 Vienna, Austria
Tel: +43-1-5880115671
Fax: +43-1-5880115698
email: pblaha at theochem.tuwien.ac.at
-----------------------------------------
More information about the Wien
mailing list