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" <delam...@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-boun...@zeus.theochem.tuwien.ac.at> en nombre de JUAN > MANUEL PEREZ <jm.perez-m...@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-ma...@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-ma...@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 > >> <pbl...@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@zeus.theochem.tuwien.ac.at > >>>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus. > theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwICAg&c= > yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=UIz_ > tYDpioGmLaxB1CnCBXVDaiikF8Qxt6cbXR08z-k&s=ojPWMOGoECaqOg0dia6WDukTKYKxyt > eOD0snF0XRq2c&e= > >>>> SEARCH the MAILING-LIST at: > >>>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_ > index.html&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=UIz_ > tYDpioGmLaxB1CnCBXVDaiikF8Qxt6cbXR08z-k&s=KpDTJaINh510H34fxM- > m22vfHGfg73K2pgVk44pH4p8&e= > >>>> > >>> > >>> -- > >>> > >>> P.Blaha > >>> > -------------------------------------------------------------------------- > >>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna > >>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 > >>> Email: bl...@theochem.tuwien.ac.at WIEN2k: > >>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > wien2k.at&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=UIz_ > tYDpioGmLaxB1CnCBXVDaiikF8Qxt6cbXR08z-k&s=0oQkNDJGymzhfb_ > mzl3xLJsoQIaFIiNng--nVnGykuQ&e= > >>> WWW: > >>> > https://urldefense.proofpoint.com/v2/url?u=http- > 3A__www.imc.tuwien.ac.at_TC-5FBlaha&d=CwICAg&c= > yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=UIz_ > tYDpioGmLaxB1CnCBXVDaiikF8Qxt6cbXR08z-k&s=lcZJan3wcIPgY1FQmVkBAdIADIr6Px > lwAmKWqx3_6xI&e= > >>> > -------------------------------------------------------------------------- > >>> _______________________________________________ > >>> Wien mailing list > >>> Wien@zeus.theochem.tuwien.ac.at > >>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus. > theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwICAg&c= > yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=UIz_ > tYDpioGmLaxB1CnCBXVDaiikF8Qxt6cbXR08z-k&s=ojPWMOGoECaqOg0dia6WDukTKYKxyt > eOD0snF0XRq2c&e= > >>> SEARCH the MAILING-LIST at: > >>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_ > index.html&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=UIz_ > tYDpioGmLaxB1CnCBXVDaiikF8Qxt6cbXR08z-k&s=KpDTJaINh510H34fxM- > m22vfHGfg73K2pgVk44pH4p8&e= > >> > >> -- > >> 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cfw.org_100-2Dpercent-5B3&d=CwMF-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=x89rhJoaNoZvL4TggKrrel0P3TQIcL6QF7ROlB8oyzs&s=T_Cfa7Rr9RiEQlbeyXxkW2ph84pyaMOzjppWosz8VIg&e=> > ] > >> 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cfw.org_100-2Dpercent-5B3&d=CwMF-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=x89rhJoaNoZvL4TggKrrel0P3TQIcL6QF7ROlB8oyzs&s=T_Cfa7Rr9RiEQlbeyXxkW2ph84pyaMOzjppWosz8VIg&e=> > ] > > Co-Editor, Acta Cryst A > > > > _______________________________________________ > > Wien mailing list > > Wien@zeus.theochem.tuwien.ac.at > > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > <https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwMF-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=x89rhJoaNoZvL4TggKrrel0P3TQIcL6QF7ROlB8oyzs&s=xmmGdW2bcyQb24QFX3qJipgSgumHFteTrfZ5HXFUqtY&e=> > > SEARCH the MAILING-LIST at: > > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html&d=CwMF-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=x89rhJoaNoZvL4TggKrrel0P3TQIcL6QF7ROlB8oyzs&s=MNathsfsYax5f7mRs8Zc306AJjpx6Ky7C86A-RAVZDY&e=> > > > > Vínculos: > --------- > [1] http://www.numis.northwestern.edu/ > [2] http://muri4d.numis.northwestern.edu/ > [3] http://www.cfw.org/100-percent > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cfw.org_100-2Dpercent&d=CwMF-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=x89rhJoaNoZvL4TggKrrel0P3TQIcL6QF7ROlB8oyzs&s=so8BafD2dGxP2A2hrZ6ZRCCUSuHpHqWw886SMnbAzcw&e=> > > > _______________________________________________ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > <https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwMF-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=x89rhJoaNoZvL4TggKrrel0P3TQIcL6QF7ROlB8oyzs&s=xmmGdW2bcyQb24QFX3qJipgSgumHFteTrfZ5HXFUqtY&e=> > SEARCH the MAILING-LIST at: http://www.mail-archive.com/ > wien@zeus.theochem.tuwien.ac.at/index.html > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html&d=CwMF-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=x89rhJoaNoZvL4TggKrrel0P3TQIcL6QF7ROlB8oyzs&s=MNathsfsYax5f7mRs8Zc306AJjpx6Ky7C86A-RAVZDY&e=> >
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