[Wien] Bug in StructGen
wmppemam@lg.ehu.es
wmppemam at lg.ehu.es
Sun Jan 25 12:54:24 CET 2009
A structure can be monoclinic even if the monoclinic angle is 90 degrees
due to the atomic positions within the cell, and this can often occur when
dealing with frozen phonon calculations. Of course, the program should
know which of the three directions is the monoclinic one, to construct the
structure. The menu/list of space groups in StructGen has each monoclinic
group repeated three times (although with the same label). Probably this
was originally intended to indicate to the program the desired monoclinic
setting, in the same way that for instance the group 66 can be introduced
as Cccm, Amaa or Bbmb. This would solve the ambiguity when the monoclinic
angle is 90 degrees. But these three possible apparent choices of setting
in the menu for all monoclinic space groups (for P2 for instance) are not
working.
Regards,
J. Manuel Perez-Mato
*************************************************
On Sat, 24 Jan 2009, Peter Blaha wrote:
> 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
>>>
>>>
>>>
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>
> --
> -----------------------------------------
> 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
> -----------------------------------------
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