[CP2K-user] [CP2K:20230] Conversion output file.xyz to cif file with periodic conditions

[Joshua Edz]

Hi K. AK,

you can use the Python library ase. With ase you read the file .xyz and 
write an output as .cif. You might need to add the cell vectors manually, 
but I am not sure about that. Here is the link to the 
library https://wiki.fysik.dtu.dk/ase/ and the link to the functions 
https://wiki.fysik.dtu.dk/ase/ase/io/io.html.

All the best
Josh


K.AK schrieb am Donnerstag, 23. Mai 2024 um 20:23:26 UTC+2:

> 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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>>
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