[DFTB-Plus-User] Fragmented optimized structure

[Ben Hourahine]

Hello Alessandro,

If you need to see the connections, then repeating the structure might
also help (repeatgen in the dp_tools package).

Regards

Ben


On 07/05/2020 09:02, Alessandro LANDI via DFTB-Plus-User wrote:
> Dear Balint,
> if you read the input file that I provided at the end of my previous
> e-mail, you will notice that I already have included
>  
> Options {
>   ShowFoldedCoords       =       Yes
> }
>
> in the input file, but still, I get a fragmented geometry. Any idea
> what is going on? 
> I can provide my starting and optimized geometry if needed.
>
>
> Best regards,
> Alessandro
>
>
>
>
>
>
>
> Il giorno gio 7 mag 2020 alle ore 09:47 Bálint Aradi via
> DFTB-Plus-User <dftb-plus-user at mailman.zfn.uni-bremen.de
> <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>> ha scritto:
>
>     Dear Alessandro,
>
>     > Problem is, I need to reconstruct the "connected" molecules starting
>     > from the fragments obtained after the optimization, to perform other
>     > calculations on them. Does the DFTB+ suite provide a utility to
>     do this?
>
>     You could specify ShowFoldedCoords = Yes in the Option block, which
>     would always fold the coordinates into the central cell, even if atoms
>     move over the boundary.
>
>     Best regards,
>
>     Bálint
>
>
>     -- 
>     Dr. Bálint Aradi
>     Bremen Center for Computational Materials Science, University of
>     Bremen
>     http://www.bccms.uni-bremen.de/cms/people/b-aradi/
>     <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.bccms.uni-bremen.de%2Fcms%2Fpeople%2Fb-aradi%2F&data=02%7C01%7Cbenjamin.hourahine%40strath.ac.uk%7C0f5ee13a311347692a8c08d7f25d1e84%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637244354070171870&sdata=JbRxsnvVzLsr8BVsXzeS82c45CJcAnQovK3xByoqKLc%3D&reserved=0>
>
>
>     _______________________________________________
>     DFTB-Plus-User mailing list
>     DFTB-Plus-User at mailman.zfn.uni-bremen.de
>     <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
>     https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>     <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.zfn.uni-bremen.de%2Fcgi-bin%2Fmailman%2Flistinfo%2Fdftb-plus-user&data=02%7C01%7Cbenjamin.hourahine%40strath.ac.uk%7C0f5ee13a311347692a8c08d7f25d1e84%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637244354070171870&sdata=VegDHgSgtTn%2BjkGn5BMcyoAR1SE%2BuADcMKjDZ6KWyCs%3D&reserved=0>
>
>
>
> -- 
> Alessandro Landi, Assegnista di Ricerca
> Dipartimento di Chimica e Biologia "Adolfo Zambelli"
> Università degli Studi di Salerno
> Via Giovanni Paolo II, 132 - 84084 - Fisciano (SA)
> Phone number 089969390
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.zfn.uni-bremen.de%2Fcgi-bin%2Fmailman%2Flistinfo%2Fdftb-plus-user&data=02%7C01%7Cbenjamin.hourahine%40strath.ac.uk%7C0f5ee13a311347692a8c08d7f25d1e84%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637244354070191860&sdata=dHpft%2FsDxnKnoKEvOZF7L4vu80IZVTF667aKAAV3sds%3D&reserved=0

-- 
        Dr.  B.  Hourahine,  Senior  lecturer
            SUPA, Department  of  Physics,
             University  of  Strathclyde,
              John  Anderson  Building,
          107 Rottenrow, Glasgow G4 0NG, UK.                    
  +44 141 548 2325, benjamin.hourahine at strath.ac.uk

The  Department is  a partner  in SUPA,  the Scottish
            Universities Physics Alliance

The University  of Strathclyde  is a  charitable body,
       registered in Scotland, number SC015263

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20200507/542d257d/attachment.htm>