[CP2K-user] [CP2K:20337] Conversion output file.xyz to cif file with periodic conditions

[贾建峰]

Hi, K. AK, 

You should provide the cell parameters, i.e. A, B, C, and Alpha, Beta, Gamma. 




Jianfeng Jia
















At 2024-05-24 02:23:26, "K.AK" <koshima02 at gmail.com> wrote:

Thank you,  Krack Matthias.


I tried to search the conversion from non-periodic primitive cell .xyz file to periodic file cif file such as VESTA software, mercury, avogadro 1.2, or pymatgen python code, 


but the atoms did not break apart in the cell or repeat structure well.



I would like to know how to convert xyz to cif in detail.


xyz file was attached below.


Best regards, 
K.AK.
2024年5月23日木曜日 16:24:06 UTC+9 Krack Matthias:


Hi

 

Just google for «convert xyz to cif” to get hints. I suggest to have a look at the VESTA code.

 

M.

 

From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of K.AK <kosh... at gmail.com>
Date: Thursday, 23 May 2024 at 06:26
To: cp2k <cp... at googlegroups.com>
Subject: [CP2K:20227] Conversion output file.xyz to cif file with periodic conditions

Dear cp2k experts,

 

I simulated the optimization of MOF structure with periodic condition boundary.

 

MOF has a big cell, so I convert conventional cell to primitive cell of MOF.

 

The optimization by cp2k was successful, but I cannot convert xyz foutput file to cif file with periodic conditions. I would like to utilize this optimizaed structure to simulated MC method.

 

How should I convert xyz file to cif file? I would like to know the recommended software or python script.

 

xyz file was attached below.

 

Best regards, 

K.AK.


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