<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="EN-US" link="blue" vlink="purple"> <div class="WordSection1"> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Yes, try multiple unit cells in b direction. There is a keyword for that in the <a href="https://manual.cp2k.org/cp2k-6_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#MULTIPLE_UNIT_CELL"> &CELL section</a>.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p> <p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> cp...@googlegroups.com <...@googlegroups.com> <b>On Behalf Of </b>Nimali Rathnayake<br> <b>Sent:</b> Mittwoch, 8. Mai 2019 09:54<br> <b>To:</b> cp...@googlegroups.com<br> <b>Subject:</b> Re: [CP2K:11685] Geometry Optimization of Graphene<o:p></o:p></span></p> <p class="MsoNormal"><o:p> </o:p></p> <div> <p class="MsoNormal">Hi Krack,<o:p></o:p></p> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">Since I am new to the field I am bit confuse with your suggestion. <o:p></o:p></p> </div> <div> <p class="MsoNormal">What do you mean by lattice constant is short? Do you suggest me to add 3-4 graphene layers or to increase the cell size (i.e 3.35*3)? <o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">Please explain it to me.<o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">I am very grateful for your suggestion.<o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">Regards,<o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">Nimali<o:p></o:p></p> </div> </div> <p class="MsoNormal"><o:p> </o:p></p> <div> <div> <p class="MsoNormal">On Wed, May 8, 2019 at 5:45 PM Krack Matthias (PSI) <<a href="mailto:matthi...@psi.ch">matthi...@psi.ch</a>> wrote:<o:p></o:p></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Nimali</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The lattice constant b of your simulation cell is quite short with just 3.35 Angstrom for a gamma point calculation (no k points). I suggest to replicate your simulation cell at least 3 or 4 times in b direction.</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">HTH</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Matthias</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a> <<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>> <b>On Behalf Of </b>Nimali Rathnayake<br> <b>Sent:</b> Mittwoch, 8. Mai 2019 08:01<br> <b>To:</b> <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a><br> <b>Subject:</b> [CP2K:11683] Geometry Optimization of Graphene</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Dear All,<o:p></o:p></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am trying to run a geometry optimization calculation for graphene sheet. I have attached the INPUT file herewith.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">After completing the program I visualized the structure using VMD with the generated .XYZ coordinates. But, I couldn't see a nice structure and it has lost the hexagonal shape in the benzene rings, I have attached a image of the graphene structure.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am expecting all your help to fix this. I am really grateful for your help. <br clear="all"> <o:p></o:p></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">-- <o:p></o:p></p> <div> <div> <div> <div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#073763">Thank you,</span><o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#073763">Best Regards,</span><o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#073763">Nimali</span><o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsu...@googlegroups.com" target="_blank">cp2k+unsu...@googlegroups.com</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank"> cp...@googlegroups.com</a>.<br> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank"> https://groups.google.com/group/cp2k</a>.<br> To view this discussion on the web visit <a 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To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/FCDF8CAC6EF2504E85F16873A7DF161A4916B270%40MBX114.d.ethz.ch?utm_medium=email&utm_source=footer" target="_blank"> https://groups.google.com/d/msgid/cp2k/FCDF8CAC6EF2504E85F16873A7DF161A4916B270%40MBX114.d.ethz.ch</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank"> https://groups.google.com/d/optout</a>.<o:p></o:p></p> </blockquote> </div> <p class="MsoNormal"><br clear="all"> <o:p></o:p></p> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <p class="MsoNormal">-- <o:p></o:p></p> <div> <div> <div> <div> <div> <div> <div> <div> <p class="MsoNormal"><span style="color:#073763">Thank you,</span><o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal"><span style="color:#073763">Best Regards,</span><o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal"><span 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