[CP2K-user] [CP2K:15286] Re: Need help in running AIMD simulations on Ta2 dimer supported on C2N monolayer

[Fabian Ducry]

Dear Manzoor,

a very simple way is to use ASE (a python package). If you have it 
installed (e.g. "pip install ase" or if you use conda "conda install -c 
conda-forge ase") just run the following two lines in python:

from ase import io

io.read('CONTCAR').write('C2NTa2.xyz')

This will convert the CONTCAR to C2NTa2.xyz. The second line of c2n.xyz 
contains Lattice="xx xy xz yx yy yz zx zy zz" which are the 9 numbers 
that define the lattice. You can use these to set A xx xy xz B yx yy yz 
and C zx zy zz in the &CELL section of the input file. If you explicitly 
set A, B,and C then ANGLE is not needed anymore.

Cheers,

Fabian

On 03.05.2021 17:49, Rizwan Nabi wrote:
> Dear Manzoor,
> Please send me your CONTCAR, I will Send you XYZ format.
>
>
> Regards
> Rizwan
>
>
> -------
> *Dr Rizwan Nabi*
> Research Associate "European Research Council Fellow"
> Department of Chemistry, The University of Manchester
> Oxford Road, Manchester, M13 9PL, United Kingdom
> t: +44 (0)742 447 4940
> e: rizwa... at manchester.ac.uk <mailto:rizwa... at manchester.ac.uk>
> w: http://nfchilton.com/people.html <http://nfchilton.com/people.html>
>
>
> On Mon, May 3, 2021 at 4:21 PM DAR MANZOOR <mann... at gmail.com 
> <mailto:mann... at gmail.com>> wrote:
>
>     Dear Dr. Rizwan,
>
>     I don't think there is a problem with the structure of C2N
>     monolayer. Its structure is well documented in literature.
>     However, I feel I may be making some mistake in terms of the
>     format of the xyz file and cell parameters in the input file. If
>     you know how generate the xyz coordinates for VASP CONTCAR in the
>     CP2K format, that might help me troubleshoot this problem.
>
>     Manzoor
>
>     On Mon, May 3, 2021 at 7:19 PM Rizwan Nabi
>     <rizwan... at gmail.com <mailto:rizwan... at gmail.com>> wrote:
>
>         Dear Manzoor,
>         Can you just add H atoms on all the C atoms and Re-run the
>         calculations. I guess the problem is with the Carbon valency.
>         Please let me know if this works?
>
>
>         Regards
>         Rizwan
>         -------
>         *Dr Rizwan Nabi*
>         Research Associate "European Research Council Fellow"
>         Department of Chemistry, The University of Manchester
>         Oxford Road, Manchester, M13 9PL, United Kingdom
>         t: +44 (0)742 447 4940
>         e: rizwa... at manchester.ac.uk
>         <mailto:rizwa... at manchester.ac.uk>
>         w: http://nfchilton.com/people.html
>         <http://nfchilton.com/people.html>
>
>
>         On Mon, May 3, 2021 at 2:15 PM DAR MANZOOR
>         <mann... at gmail.com <mailto:mann... at gmail.com>> wrote:
>
>             Dear Rizwan,
>
>             Thanks for your reply. I am using an overall charge of
>             zero. I have run the same system in VASP and it relaxes
>             smoothly. However here I faced the same problem even when
>             I tried to relax the structure. The structure just breaks
>             away whether I run the geometry optimization or MD.
>
>             Best wishes,
>             Manzoor
>
>             On Mon 3 May, 2021, 6:36 PM Rizwan Nabi,
>             <rizwan... at gmail.com <mailto:rizwan... at gmail.com>>
>             wrote:
>
>                 Dear Manzoor,
>                 Please check If the charges are correct. From Your
>                 Coordinate file, the valency seems unsatisfied.
>                 I can not see any double bonds in the structure.
>
>                 Regards
>                 Rizwan
>
>                 On Monday, May 3, 2021 at 1:34:58 PM UTC+1
>                 ma... at gmail.com <mailto:ma... at gmail.com> wrote:
>
>                     Dear Users,
>
>                     I will be extremely grateful if anyone can take
>                     some time to look into the above problem.
>
>                     Best wishes,
>                     Manzoor
>
>                     On Sat 1 May, 2021, 11:06 PM DAR MANZOOR,
>                     <ma... at gmail.com> wrote:
>
>                         Dear CP2K developers,
>
>                         I am new to CP2K and am trying to run abinitio
>                         MD simulation on a Ta2 dimer supported on C2N
>                         monolayer. However, as i run the calculation
>                         the structure completely breaks and looks too
>                         weird. I am attaching the input and output
>                         files here. I will be grateful if someone can
>                         look into the files and help me troubleshoot
>                         the issue. Thanks in advance.
>
>                         -- 
>                         Regards & best wishes
>                         Dr. Manzoor A. Dar,
>                         Assistant Professor,
>                         Dept. of Chemistry,
>                         IUST Awantipora.
>
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>     -- 
>     Regards & best wishes
>     Dr. Manzoor A. Dar,
>     Assistant Professor,
>     Dept. of Chemistry,
>     IUST Awantipora.
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