<div>Hi K. AK,</div><div><br /></div><div>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.</div><div><br /></div><div>All the best</div><div>Josh</div><br /><br /><div class="gmail_quote"><div dir="auto" class="gmail_attr">K.AK schrieb am Donnerstag, 23. Mai 2024 um 20:23:26 UTC+2:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Thank you,
<span style="color:rgb(32,33,36);font-family:Roboto,Arial,sans-serif;letter-spacing:0.25px">Krack Matthias.</span><div><font color="#202124" face="Roboto, Arial, sans-serif"><span style="letter-spacing:0.25px"><br></span></font></div><div><font color="#202124" face="Roboto, Arial, sans-serif"><span style="letter-spacing:0.25px">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, </span></font></div><div><font color="#202124" face="Roboto, Arial, sans-serif"><span style="letter-spacing:0.25px"><br></span></font></div><div><font color="#202124" face="Roboto, Arial, sans-serif"><span style="letter-spacing:0.25px">but t</span></font>he atoms did not break apart in the cell or repeat structure well.<br></div><div><br></div><div>I would like to know how to convert xyz to cif in detail.</div><div><br></div><div><div>xyz file was attached below.</div><div><br></div><div>Best regards, </div><div>K.AK.</div></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">2024年5月23日木曜日 16:24:06 UTC+9 Krack Matthias:<br></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word">
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Hi<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Just google for «convert xyz to cif” to get hints. I suggest to have a look at the VESTA code.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">M.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p>
<div>
<div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt">
<b><span style="color:black">From: </span></b><span style="color:black"><a rel="nofollow">cp...@googlegroups.com</a> <<a rel="nofollow">cp...@googlegroups.com</a>> on behalf of K.AK <<a rel="nofollow">kosh...@gmail.com</a>><br>
<b>Date: </b>Thursday, 23 May 2024 at 06:26<br>
<b>To: </b>cp2k <<a rel="nofollow">cp...@googlegroups.com</a>><br>
<b>Subject: </b>[CP2K:20227] Conversion output <a href="http://file.xyz" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=de&q=http://file.xyz&source=gmail&ust=1716629036264000&usg=AOvVaw1DQicyNL2WX25QbuxBwtMD">file.xyz</a> to cif file with periodic conditions<u></u><u></u></span></p>
</div>
<p class="MsoNormal" style="margin-left:36.0pt">Dear cp2k experts,<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">I simulated the optimization of MOF structure with periodic condition boundary.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">MOF has a big cell, so I convert conventional cell to primitive cell of MOF.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">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.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">How should I convert xyz file to cif file? I would like to know the recommended software or python script.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">xyz file was attached below.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">Best regards, <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">K.AK.<u></u><u></u></p>
</div>
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