<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div id="spnEditorContent"><p style="margin: 0;">Hi, K. AK, </p><p style="margin: 0;">You should provide the cell parameters, i.e. A, B, C, and Alpha, Beta, Gamma. </p><p style="margin: 0;"><br></p><p style="margin: 0;">Jianfeng Jia</p><p style="margin: 0;"><br></p><p style="margin: 0;"><br></p><p style="margin: 0;"><br></p><p style="margin: 0;"><br></p></div><div style="position:relative;zoom:1"></div><div id="divNeteaseMailCard"></div><p style="margin: 0;"><br></p><p>At 2024-05-24 02:23:26, "K.AK" <koshima02@gmail.com> wrote:</p><blockquote id="isReplyContent" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thank you,
<span style="color: rgb(32, 33, 36); font-family: Roboto, Arial, sans-serif; letter-spacing: 0.25px; text-wrap: nowrap;">Krack Matthias.</span><div><font color="#202124" face="Roboto, Arial, sans-serif"><span style="letter-spacing: 0.25px; text-wrap: nowrap;"><br></span></font></div><div><font color="#202124" face="Roboto, Arial, sans-serif"><span style="letter-spacing: 0.25px; text-wrap: nowrap;">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; text-wrap: nowrap;"><br></span></font></div><div><font color="#202124" face="Roboto, Arial, sans-serif"><span style="letter-spacing: 0.25px; text-wrap: nowrap;">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><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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<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>
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<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>
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<b><span style="color:black">From: </span></b><span style="color:black"><a href="" data-email-masked="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" data-email-masked="" rel="nofollow">cp...@googlegroups.com</a>> on behalf of K.AK <<a href="" data-email-masked="" rel="nofollow">kosh...@gmail.com</a>><br>
<b>Date: </b>Thursday, 23 May 2024 at 06:26<br>
<b>To: </b>cp2k <<a href="" data-email-masked="" rel="nofollow">cp...@googlegroups.com</a>><br>
<b>Subject: </b>[CP2K:20227] Conversion output <a href="http://file.xyz" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=ja&q=http://file.xyz&source=gmail&ust=1716574368999000&usg=AOvVaw02Y-l16i7mJFR66kiy51MR">file.xyz</a> to cif file with periodic conditions<u></u><u></u></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Dear cp2k experts,<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt">I simulated the optimization of MOF structure with periodic condition boundary.<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
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<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>
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<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
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<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>
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<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
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<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>
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<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt">xyz file was attached below.<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Best regards, <u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt">K.AK.<u></u><u></u></p>
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