[CP2K-user] [CP2K:15287] Re: Need help in running AIMD simulations on Ta2 dimer supported on C2N monolayer

[DAR MANZOOR]

Dear Fabian,

Thanks for your suggestions. I will try it out your suggestions and get
back to you on this. Thanks again.

Best wishes,
Manzoor

On Mon, May 3, 2021 at 9:35 PM Fabian Ducry <fabia... at gmail.com> wrote:

> 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
> w: http://nfchilton.com/people.html
>
>
> On Mon, May 3, 2021 at 4:21 PM DAR MANZOOR <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>
>> 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
>>> w: http://nfchilton.com/people.html
>>>
>>>
>>> On Mon, May 3, 2021 at 2:15 PM DAR MANZOOR <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>
>>>> 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 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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-- 
Regards & best wishes
Dr. Manzoor A. Dar,
Assistant Professor,
Dept. of Chemistry,
IUST Awantipora.
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