[DFTB-Plus-User] Fragmented optimized structure

[Alessandro LANDI]

Dear Ben,
thank you for the tip.
I actually need to obtain a connected geometry to perform other
calculations on it, not simply to see the connections. I have already
written my own code to repeat the gen file structure, but thank you for
having pointed out that a utility is already provided by DFTB+ itself. From
now on, I will use that utility instead of my code for extra safety.

Best regards,
Alessandro

Il giorno gio 7 mag 2020 alle ore 10:12 Ben Hourahine via DFTB-Plus-User <
dftb-plus-user at mailman.zfn.uni-bremen.de> ha scritto:

> 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> 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/
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>
> --
> 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
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> --
>         Dr.  B.  Hourahine,  Senior  lecturer
>             SUPA, Department  of  Physics,
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>
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-- 
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
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