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<p>Thanks, I tried but it did not work for this case<br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De:</b> Wien <wien-bounces@zeus.theochem.tuwien.ac.at> en nombre de Laurence Marks <laurence.marks@gmail.com><br>
<b>Enviado:</b> jueves, 13 de octubre de 2016 07:35:42 a. m.<br>
<b>Para:</b> A Mailing list for WIEN2k users<br>
<b>Asunto:</b> Re: [Wien] Change of structure symmetry</font>
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<p dir="ltr">Sometimes changing the 90 to 92 before sgroup, then changing it back works. To be used with extreme care.</p>
<p dir="ltr">---<br>
Professor Laurence Marks<br>
"Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi<br>
<a href="http://www.numis.northwestern.edu">http://www.numis.northwestern.edu</a><br>
Corrosion in 4D <a href="http://MURI4D.numis.northwestern.edu">http://MURI4D.numis.northwestern.edu</a><br>
Partner of the CFW 100% gender equity project, <a href="http://www.cfw.org/100-percent">
www.cfw.org/100-percent</a><br>
Co-Editor, Acta Cryst A<br>
</p>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Oct 12, 2016 17:36, "delamora" <<a href="mailto:delamora@unam.mx">delamora@unam.mx</a>> wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p>Thank you for all your comments.</p>
<p>Two more comments;</p>
<p>Here is the cell with the orthorhombic symmetry, 90 degree angles, <span>which I think is correct</span></p>
<p>sgroup does not accept it and changes one angle to; <span>135.000500, with the corresponding arrangements of atoms</span></p>
<p><span>With this new structure XCrySDen gives an error<br>
</span></p>
<p>but if I change this angle by little: 135.000000 or 136.00 then I can see it with XCrySDen<br>
</p>
<p><br>
</p>
<p>This is not the first time that these two problems happen</p>
<p><br>
</p>
<p>Now I am running with the unchanged, orthorhombic, cell no error seems to appear as long as I ignore sgroup <br>
</p>
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<div id="m_2552039603786916245x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De:</b> Wien <<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.<wbr>tuwien.ac.at</a>>
en nombre de JUAN MANUEL PEREZ <jm.perez-mato@ehu.eus><br>
<b>Enviado:</b> miércoles, 12 de octubre de 2016 12:37:11 p. m.<br>
<b>Para:</b> A Mailing list for WIEN2k users<br>
<b>Asunto:</b> Re: [Wien] Change of structure symmetry</font>
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<div class="m_2552039603786916245PlainText"><br>
C11m does not exist. It includes a gratuit centering that can be<br>
elliminated by changing the unit cell within the same convention (one unit<br>
cell direction perpendicular to the mirror plane).<br>
<br>
But, as said in the previous message, the symmetry of the discussed<br>
structure keeping the original unit cell would be given rather by the label<br>
Cm11 with the monoclinic axis along a (the alpha angle may be different<br>
from 90 but it is not forced to be different!), and therefore it does not<br>
correspond to none of the two possible standard settings (monoclinic axis<br>
along b or c) that you have in the Wikipedia.<br>
<br>
In any case, it is true that sgroup does not propose the more reasonable<br>
unit cell among those possible in <br>
the standard description of the symmetry as C1m1, and coud have just<br>
interchanged the axes, keeping the three 90 degrees angles. BUT the<br>
identification of symmetries is an algebraic problem where the specific<br>
metrics of the unit cell does not play a role, and all this type of<br>
programs do not care about it. To find the “nicest” unit cell among the<br>
possible ones is beyond them, and if one wants to consider all the possible<br>
cases that one can encounter this unit cell “embellishment process is not<br>
trivial. The best is to identify the “normalizer” of the space group in<br>
the listings available (see for instance the Bilbao server), which defines<br>
the unit cell changes that are possible, and find by hand the one with with<br>
which we are happy.<br>
<br>
best regards,<br>
<br>
J. Manuel Perez-Mato<br>
Fac. Ciencia y Tecnologia,<br>
Universidad del Pais Vasco, UPV<br>
48080 BILBAO,<br>
Spain<br>
<br>
******************************<wbr>*********************<br>
<br>
> El 12/10/2016, a las 17:51, Laurence Marks <<a href="mailto:L-marks@northwestern.edu" target="_blank">L-marks@northwestern.edu</a>><br>
> escribió:<br>
><br>
> I meant "correct" when the cell is C11m, which is better for Wien.<br>
><br>
> On Wed, Oct 12, 2016 at 10:50 AM, Laurence Marks<br>
> <<a href="mailto:L-marks@northwestern.edu" target="_blank">L-marks@northwestern.edu</a>> wrote:<br>
><br>
>> My two cents worth. If you look at, for<br>
>> instance, <a href="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=" target="_blank">https://en.<wbr>wikipedia.org/wiki/List_of_<wbr>space_groups</a>,
Cm #8 is<br>
>> a monoclinic spacegroup which (in the B11m setting) has beta .ne. 90.<br>
>> It is "correct" to have gamma .ne. 90 for the standard convention.<br>
>> However, this is inconvenient and it would be nice if sgroup made an<br>
>> exception for Wien.<br>
>><br>
>> On Wed, Oct 12, 2016 at 10:14 AM, Peter Blaha<br>
>> <<a href="mailto:pblaha@theochem.tuwien.ac.at" target="_blank">pblaha@theochem.tuwien.ac.at</a>> wrote:<br>
>><br>
>>> ==============================<wbr>==============================<wbr>=======<br>
>>><br>
>>> The structure that you have attached does NOT have Cmm2 as space group<br>
>>> symmetry, but only Cm, which is the one that sgroup correctly finds.<br>
The<br>
>>> mirror plane of the Cm group is perpendicular to the original a axis,<br>
>>> and<br>
>>> in the standard description of Cm it should be perpendicular to the b<br>
>>> axis.<br>
>>> That is the reason why it interchanges the axes, to make the old a axis<br>
>>> become<br>
>>> the new b one. It is however true that it could have however kept the<br>
>>> original<br>
>>> unit cell metrics, with the axes interchanged. The program indeed does<br>
>>> not<br>
>>> seem to have any particular criterion to optimize the choice of the<br>
unit<br>
>>> cell within the standard description of the space group, and as Peter<br>
>>> Blaha<br>
>>> says there are many possible choices for monoclinic space groups. The<br>
>>> program just chooses one, the reason being that your structure is<br>
>>> monoclinic<br>
>>> with Cm symmetry and not Cmm2.<br>
>>><br>
>>> J. Manuel Perez-Mato<br>
>>> Fac. Ciencia y Tecnologia,<br>
>>> Universidad del Pais Vasco, UPV<br>
>>> 48080 BILBAO,<br>
>>> Spain<br>
>>> ******************************<wbr>*********************<br>
>>><br>
>>> On 10/12/2016 04:50 AM, delamora wrote:<br>
>>>> I want to see how Cu interacts with the TiO2 surface, so I construct<br>
>>>> with 'supercell' an enlarged cell, with<br>
>>>> SG 35 (C m m 2)<br>
>>>> then I attach Cu and O on the surface in a way that I break the<br>
>>>> symmetry<br>
>>>> in the b direction<br>
>>>> The cell is orthorhombic<br>
>>>><br>
>>>> CXY LATTICE,NONEQUIV.ATOMS: 21<br>
>>>> MODE OF CALC=RELA unit=bohr<br>
>>>> 11.187184 23.838706 23.838290 90.0 90.0 90.0<br>
>>>><br>
>>>> if I run initialize calculation and then sgroup the new cell changes<br>
to<br>
>>>><br>
>>>> CXZ LATTICE,NONEQUIV.ATOMS: 28 8 Cm<br>
>>>> MODE OF CALC=RELA unit=bohr<br>
>>>> 23.838706 33.712727 11.187184 90.0 90.0 135.000500<br>
>>>><br>
>>>> which is correct, but it is no longer orthogonal which is awkward, one<br>
>>>> angle changes from<br>
>>>> 90 to 135.0005<br>
>>>> also the a, b, c => c, a, b<br>
>>>><br>
>>>> Also I cannot see the structure with XCrySDen, unless I change the<br>
>>>> 135.0005 angle by little.<br>
>>>><br>
>>>> With the new structure and the old one I managed to make a new<br>
>>>> TiO2.struct with orthorhombic and can be seen with XCrySDen<br>
>>>><br>
>>>> It would be nice that sgroup would generate a structure with the<br>
>>>> orthorhombic symmetry<br>
>>>><br>
>>>> Saludos<br>
>>>><br>
>>>> Pablo de la Mora<br>
>>>><br>
>>>><br>
>>>><br>
>>><br>
>>>> ______________________________<wbr>_________________<br>
>>>> Wien mailing list<br>
>>>> <a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.<wbr>at</a><br>
>>>><br>
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>>>><br>
>>><br>
>>> --<br>
>>><br>
>>> P.Blaha<br>
>>><br>
------------------------------<wbr>------------------------------<wbr>--------------<br>
>>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna<br>
>>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982<br>
>>> Email: <a href="mailto:blaha@theochem.tuwien.ac.at" target="_blank">blaha@theochem.tuwien.ac.at</a> WIEN2k:<br>
>>><br>
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>>> WWW: <br>
>>><br>
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>>><br>
------------------------------<wbr>------------------------------<wbr>--------------<br>
>>> ______________________________<wbr>_________________<br>
>>> Wien mailing list<br>
>>> <a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.<wbr>at</a><br>
>>><br>
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>><br>
>> --<br>
>> Professor Laurence Marks<br>
>><br>
>> "Research is to see what everybody else has seen, and to think what<br>
>> nobody else has thought", Albert Szent-Gyorgi<br>
>> <a href="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=" target="_blank">
www.numis.northwestern.edu[1] </a><wbr>; Corrosion in 4D:<br>
>> <a href="http://MURI4D.numis.northwestern.edu" target="_blank">MURI4D.numis.northwestern.edu</a>[<wbr>2]Partner of the CFW 100% program for<br>
>> gender equity, <a href="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=" target="_blank">www.cfw.org/100-<wbr>percent[3</a>]<br>
>> Co-Editor, Acta Cryst A<br>
><br>
> --<br>
> Professor Laurence Marks<br>
><br>
> "Research is to see what everybody else has seen, and to think what<br>
> nobody else has thought", Albert Szent-Gyorgi<br>
> <a href="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=" target="_blank">
www.numis.northwestern.edu[1] </a><wbr>; Corrosion in 4D:<br>
> <a href="http://MURI4D.numis.northwestern.edu" target="_blank">MURI4D.numis.northwestern.edu</a>[<wbr>2]Partner of the CFW 100% program for<br>
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> Co-Editor, Acta Cryst A<br>
><br>
> ______________________________<wbr>_________________<br>
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