[Wien] Change of structure symmetry
Laurence Marks
laurence.marks at gmail.com
Thu Oct 13 14:35:42 CEST 2016
Sometimes changing the 90 to 92 before sgroup, then changing it back works.
To be used with extreme care.
---
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
http://www.numis.northwestern.edu
Corrosion in 4D http://MURI4D.numis.northwestern.edu
Partner of the CFW 100% gender equity project, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
On Oct 12, 2016 17:36, "delamora" <delamora at unam.mx> wrote:
> 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
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_List-5Fof-5Fspace-5Fgroups&d=CwMF-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=x89rhJoaNoZvL4TggKrrel0P3TQIcL6QF7ROlB8oyzs&s=UjRf_fqc-qYdKi9V79WaiW2VQM-j_J6jHqrY-a3nlLA&e=>,
> 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
> >>>>
> >>>>
> >>>>
> >>>
> >>>> _______________________________________________
> >>>> Wien mailing list
> >>>> Wien at zeus.theochem.tuwien.ac.at
> >>>>
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> >>>>
> >>>
> >>> --
> >>>
> >>> P.Blaha
> >>>
> --------------------------------------------------------------------------
> >>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> >>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> >>> Email: blaha at theochem.tuwien.ac.at WIEN2k:
> >>>
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> >>> WWW:
> >>>
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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]
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.numis.northwestern.edu-5B1-5D-26nbsp-3B&d=CwMF-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=x89rhJoaNoZvL4TggKrrel0P3TQIcL6QF7ROlB8oyzs&s=DJ2pC6LvPoWtiUgC3xrhTCam74JG2dM9kxj47UoORUo&e=>; Corrosion
> in 4D:
> >> MURI4D.numis.northwestern.edu[2]Partner of the CFW 100% program for
> >> gender equity, www.cfw.org/100-percent[3
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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]
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.numis.northwestern.edu-5B1-5D-26nbsp-3B&d=CwMF-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=x89rhJoaNoZvL4TggKrrel0P3TQIcL6QF7ROlB8oyzs&s=DJ2pC6LvPoWtiUgC3xrhTCam74JG2dM9kxj47UoORUo&e=>; Corrosion
> in 4D:
> > MURI4D.numis.northwestern.edu[2]Partner of the CFW 100% program for
> > gender equity, www.cfw.org/100-percent[3
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> ]
> > Co-Editor, Acta Cryst A
> >
> > _______________________________________________
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