Conversion output file.xyz to cif file with periodic conditions

[K.AK]

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.

[Krack Matthias]

Hi

 

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

 

M.

 

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[K.AK]

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:

[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

[Tian Lu]

Hello,

After performing geometry optimization by CP2K you will have a .restart file, which contains atomic coordinates and cell information of the last step. You can use Multiwfn (http://sobereva.com/multiwfn) to load the .restart file, and then choose subfunction 2 of main function 100, you will find an option to export .cif file. This is the easiest way.

[K.AK]

Thank you for  Joshua Edz, Tian Lu.

I will try to operate the recommended software and python code.

Thank you very much for your help.

Best regards, 

K.AK.

2024年5月25日土曜日 13:03:08 UTC+9 Tian Lu:

[贾建峰]

Hi, K. AK, 

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

Jianfeng Jia