[xcrysden] How to display a whole molecule in unit cell with good connection?

[Matic Poberznik]

Modifying this in the pwscf output file is impossible, so I suggest you 
convert the output file to xsf format using the pwo2xsf.sh tool. It can 
be found in the Quantum Espresso installation directory in my case it is in

/esspreso-5.1.1/PW/tools/pwo2xsf.sh

To write the optimized coordinates to the xsf file the syntax would be :

bash pwo2xsf.sh -oc name_of_pwout.out > name_of_xsf.xsf

Once you have the xsf file I suggest you shift the coordinates of the 
atoms so that the molecule is in the center of the cell; If the molecule 
atoms are , for instance, at 0.0, 0.0, 0.0 you should shift them so that 
the coordinates correspond to 1/2a+1/2b+1/2c where a,b,c are vectors of 
the unit cell. You should shift all atomic positions accordingly and the 
result will hopefully be better.

Best regards,

Matic

On 10/27/2015 11:25 AM, liyincumt at gmail.com wrote:
> Dear Matic,
>
> Thanks for your kind help!
> After setting the number of units drawn, some molecules inside the 
> supercell are displayed correctly. But there are too many molecules 
> inside the supercell. The figure would be hardly accepted by journal.
> Is it possible to just display the molecules correctly in one unit 
> cell? I have tried buttons of the display which are located in the 
> bottom center of the screen, none of them can work properly.
>
> Best Regards,
> Yin
> ------------------------------------------------------------------------
> Dr. Yin Li
> Department of Biophysics,Medical School, University of Pecs,
> No.12 Szigeti Street, Pecs, H-7624, HUNGARY
> Phone: +36-72-535271/36271
>
>     *From:* Matic Poberznik <mailto:matic.poberznik at gmail.com>
>     *Date:* 2015-10-27 12:14
>     *To:* XCrySDen mailing list <mailto:xcrysden at democritos.it>
>     *Subject:* Re: [xcrysden] How to display a whole molecule in unit
>     cell with good connection?
>     Dear Yin,
>
>     If I understood your problem correctly, I think the best solution
>     is to open the Modify menu and choose the Atomic Radius (Shift+R)
>     option. Once there you can modify the Covalent Radius and
>     Connectivity Factor for each atom type to suit your needs.
>
>     In order to load your custom parameters when xcrysden starts you
>     should add a line in $HOME/.xcrysden/custom-definitions file, an
>     example:
>
>     #
>     # this line changes the default atomic radius for aluminum to 1.6
>     #
>
>     set atmRad(13) 1.6
>
>     The custom definitions file is described on this link:
>     http://www.xcrysden.org/doc/custom.html
>
>     If the problem stems from the periodic boundary conditions then
>     first try the different display modes of unit cells, i. e. click
>     the button for the display of the translational asymmetric unit
>     (bottom center of the screen).  Then try Modify => Number of units
>     drawn (Shift+N), if the covalent radius is correct at least some
>     molecules should be displayed correctly. If that is not enough let
>     me know, there is one more workaround but it is a bit more
>     complicated.
>
>     Best regards,
>
>     Matic
>
>
>
>     On 10/27/2015 09:19 AM, liyincumt at gmail.com wrote:
>>     Dear Xcrysden developers,
>>
>>     Thanks for sharing this excellent visualization software for free!
>>     I am using xcrysden to visualize the input and output files of
>>     quantum espresso. I have a problem with visualization of
>>     crystals. Due to the presence of periodic boundary condition,
>>     some of atoms which are outside of the boundary look like being
>>     non-covalently connected. Is it possible to display a whole
>>     molecule with good covalent connections in Xcrysden.
>>
>>     Thank you very much!
>>
>>     Best Regards,
>>     Yin
>>
>>     ------------------------------------------------------------------------
>>     Dr. Yin Li
>>     Department of Biophysics,Medical School, University of Pecs,
>>     No.12 Szigeti Street, Pecs, H-7624, HUNGARY
>>     Phone: +36-72-535271/36271
>>
>>
>>     _______________________________________________
>>     XCrySDen mailing list
>>     XCrySDen at democritos.it
>>     http://www.democritos.it/mailman/listinfo/xcrysden
>
>
>
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-- 
Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia

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