[DFTB-Plus-User] running MD from xyz file

[Arun Sharma]

Dear Prof. Aradi,
Thank you so much for your detailed response. I intend to run MD with
periodic boundary conditions using PME. However, I suspect that because my
initial geometry is a xyz file and probably that causes these warnings. I
am building my simulation using dftb_in.hsd file that I located from a
recent publication. However, they started with a .gen input file. Does dftb
come with a tool to convert xyz files to gen files? I tried the one located
at https://github.com/itamblyn/scripts/blob/master/dftb/dptools/bin/xyz2gen.
However, it does not compile for me. Or, is there a way to add the box
information in some other way using a regular xyz file? I have attached the
input hsd file.

Thank you so much.


On Fri, Jun 23, 2023 at 3:00 AM <
dftb-plus-user-request at mailman.zfn.uni-bremen.de> wrote:

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>    1. Re: 4 nodes ignored in input file (Bálint Aradi)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Fri, 23 Jun 2023 08:52:57 +0200
> From: Bálint Aradi <aradi at uni-bremen.de>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: Re: [DFTB-Plus-User] 4 nodes ignored in input file
> Message-ID: <215420ec-726d-4eec-de73-148975d9e2e0 at uni-bremen.de>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Dear Arun,
>
> I guess, you geometry is non-periodic. The keywords which the parser
> complains about only make sense for periodic structures. Just comment
> them out.
>
> Best regards,
>
> Bálint
>
>
> On 20.06.23 14:40, Arun Sharma wrote:
> > Hello,
> > I am trying to run MD using DFTB+ v 22.2, however, my input fails with
> > the following errors:
> > WARNING!
> > -> The following 4 node(s) have been ignored by the parser:
> > (1)
> > Path: dftbplusinput/Hamiltonian/DFTB/KPointsAndWeights
> > Line: 37-42 (File: dftb_in.hsd)
> > (2)
> > Path: dftbplusinput/Hamiltonian/DFTB/Filling/Fermi/IndependentKFilling
> > Line: 63-63 (File: dftb_in.hsd)
> > (3)
> > Path: dftbplusinput/Hamiltonian/DFTB/EwaldParameter
> > Line: 86-86 (File: dftb_in.hsd)
> > (4)
> > Path: dftbplusinput/Hamiltonian/DFTB/EwaldTolerance
> > Line: 87-87 (File: dftb_in.hsd)
> >
> > ERROR!
> > -> Code halting due to the presence of errors in dftb_in file.
> >
> > However, there are no errors specified apart from the 4 mentioned above.
> > I wonder if someone could take a look at the input file and advise. I
> > sincerely appreciate your help.
> >
> > _______________________________________________
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> --
> 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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