[Wien] Change of structure symmetry
delamora
delamora at unam.mx
Thu Oct 13 00:35:43 CEST 2016
Thank you for all your comments.
Two more comments;
Here is the cell with the orthorhombic symmetry, 90 degree angles, which I think is correct
sgroup does not accept it and changes one angle to; 135.000500, with the corresponding arrangements of atoms
With this new structure XCrySDen gives an error
but if I change this angle by little: 135.000000 or 136.00 then I can see it with XCrySDen
This is not the first time that these two problems happen
Now I am running with the unchanged, orthorhombic, cell no error seems to appear as long as I ignore sgroup
________________________________
De: Wien <wien-bounces at zeus.theochem.tuwien.ac.at> en nombre de JUAN MANUEL PEREZ <jm.perez-mato at ehu.eus>
Enviado: miércoles, 12 de octubre de 2016 12:37:11 p. m.
Para: A Mailing list for WIEN2k users
Asunto: Re: [Wien] Change of structure symmetry
C11m does not exist. It includes a gratuit centering that can be
elliminated by changing the unit cell within the same convention (one unit
cell direction perpendicular to the mirror plane).
But, as said in the previous message, the symmetry of the discussed
structure keeping the original unit cell would be given rather by the label
Cm11 with the monoclinic axis along a (the alpha angle may be different
from 90 but it is not forced to be different!), and therefore it does not
correspond to none of the two possible standard settings (monoclinic axis
along b or c) that you have in the Wikipedia.
In any case, it is true that sgroup does not propose the more reasonable
unit cell among those possible in
the standard description of the symmetry as C1m1, and coud have just
interchanged the axes, keeping the three 90 degrees angles. BUT the
identification of symmetries is an algebraic problem where the specific
metrics of the unit cell does not play a role, and all this type of
programs do not care about it. To find the “nicest” unit cell among the
possible ones is beyond them, and if one wants to consider all the possible
cases that one can encounter this unit cell “embellishment process is not
trivial. The best is to identify the “normalizer” of the space group in
the listings available (see for instance the Bilbao server), which defines
the unit cell changes that are possible, and find by hand the one with with
which we are happy.
best regards,
J. Manuel Perez-Mato
Fac. Ciencia y Tecnologia,
Universidad del Pais Vasco, UPV
48080 BILBAO,
Spain
***************************************************
> El 12/10/2016, a las 17:51, Laurence Marks <L-marks at northwestern.edu>
> escribió:
>
> I meant "correct" when the cell is C11m, which is better for Wien.
>
> On Wed, Oct 12, 2016 at 10:50 AM, Laurence Marks
> <L-marks at northwestern.edu> wrote:
>
>> My two cents worth. If you look at, for
>> instance, https://en.wikipedia.org/wiki/List_of_space_groups, Cm #8 is
>> a monoclinic spacegroup which (in the B11m setting) has beta .ne. 90.
>> It is "correct" to have gamma .ne. 90 for the standard convention.
>> However, this is inconvenient and it would be nice if sgroup made an
>> exception for Wien.
>>
>> On Wed, Oct 12, 2016 at 10:14 AM, Peter Blaha
>> <pblaha at theochem.tuwien.ac.at> wrote:
>>
>>> ===================================================================
>>>
>>> The structure that you have attached does NOT have Cmm2 as space group
>>> symmetry, but only Cm, which is the one that sgroup correctly finds.
The
>>> mirror plane of the Cm group is perpendicular to the original a axis,
>>> and
>>> in the standard description of Cm it should be perpendicular to the b
>>> axis.
>>> That is the reason why it interchanges the axes, to make the old a axis
>>> become
>>> the new b one. It is however true that it could have however kept the
>>> original
>>> unit cell metrics, with the axes interchanged. The program indeed does
>>> not
>>> seem to have any particular criterion to optimize the choice of the
unit
>>> cell within the standard description of the space group, and as Peter
>>> Blaha
>>> says there are many possible choices for monoclinic space groups. The
>>> program just chooses one, the reason being that your structure is
>>> monoclinic
>>> with Cm symmetry and not Cmm2.
>>>
>>> J. Manuel Perez-Mato
>>> Fac. Ciencia y Tecnologia,
>>> Universidad del Pais Vasco, UPV
>>> 48080 BILBAO,
>>> Spain
>>> ***************************************************
>>>
>>> On 10/12/2016 04:50 AM, delamora wrote:
>>>> I want to see how Cu interacts with the TiO2 surface, so I construct
>>>> with 'supercell' an enlarged cell, with
>>>> SG 35 (C m m 2)
>>>> then I attach Cu and O on the surface in a way that I break the
>>>> symmetry
>>>> in the b direction
>>>> The cell is orthorhombic
>>>>
>>>> CXY LATTICE,NONEQUIV.ATOMS: 21
>>>> MODE OF CALC=RELA unit=bohr
>>>> 11.187184 23.838706 23.838290 90.0 90.0 90.0
>>>>
>>>> if I run initialize calculation and then sgroup the new cell changes
to
>>>>
>>>> CXZ LATTICE,NONEQUIV.ATOMS: 28 8 Cm
>>>> MODE OF CALC=RELA unit=bohr
>>>> 23.838706 33.712727 11.187184 90.0 90.0 135.000500
>>>>
>>>> which is correct, but it is no longer orthogonal which is awkward, one
>>>> angle changes from
>>>> 90 to 135.0005
>>>> also the a, b, c => c, a, b
>>>>
>>>> Also I cannot see the structure with XCrySDen, unless I change the
>>>> 135.0005 angle by little.
>>>>
>>>> With the new structure and the old one I managed to make a new
>>>> TiO2.struct with orthorhombic and can be seen with XCrySDen
>>>>
>>>> It would be nice that sgroup would generate a structure with the
>>>> orthorhombic symmetry
>>>>
>>>> Saludos
>>>>
>>>> Pablo de la Mora
>>>>
>>>>
>>>>
>>>
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>>>
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>>>
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>>>
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>>
>> --
>> Professor Laurence Marks
>>
>> "Research is to see what everybody else has seen, and to think what
>> nobody else has thought", Albert Szent-Gyorgi
>> www.numis.northwestern.edu[1] <http://www.numis.northwestern.edu[1] > ; Corrosion in 4D:
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>> Co-Editor, Acta Cryst A
>
> --
> Professor Laurence Marks
>
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought", Albert Szent-Gyorgi
> www.numis.northwestern.edu[1] <http://www.numis.northwestern.edu[1] > ; Corrosion in 4D:
> MURI4D.numis.northwestern.edu[2]Partner of the CFW 100% program for
> gender equity, www.cfw.org/100-percent[3<http://www.cfw.org/100-percent[3>]
> Co-Editor, Acta Cryst A
>
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