<div dir="ltr">Hi Krack,<div><br></div><div>Thank you very much. I will try.</div><div><br></div><div>Kind Regards,</div><div><br></div><div>Nimali</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, May 8, 2019 at 6:04 PM Krack Matthias (PSI) <<a href="mailto:matthi...@psi.ch">matthi...@psi.ch</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> <div lang="EN-US"> <div class="gmail-m_-3648262254029199375WordSection1"> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">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" target="_blank"> &CELL section</a>.<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p> <p class="MsoNormal"><b><span style="font-size:11pt;font-family:Calibri,sans-serif">From:</span></b><span style="font-size:11pt;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 09:54<br> <b>To:</b> <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a><br> <b>Subject:</b> Re: [CP2K:11685] Geometry Optimization of Graphene<u></u><u></u></span></p> <p class="MsoNormal"><u></u> <u></u></p> <div> <p class="MsoNormal">Hi Krack,<u></u><u></u></p> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">Since I am new to the field I am bit confuse with your suggestion. <u></u><u></u></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)? <u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">Please explain it to me.<u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">I am very grateful for your suggestion.<u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">Regards,<u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">Nimali<u></u><u></u></p> </div> </div> <p class="MsoNormal"><u></u> <u></u></p> <div> <div> <p class="MsoNormal">On Wed, May 8, 2019 at 5:45 PM Krack Matthias (PSI) <<a href="mailto:matthi...@psi.ch" target="_blank">matthi...@psi.ch</a>> wrote:<u></u><u></u></p> </div> <blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin-left:4.8pt;margin-right:0cm"> <div> <div> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Hi Nimali</span><u></u><u></u></p> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">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><u></u><u></u></p> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">HTH</span><u></u><u></u></p> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Matthias</span><u></u><u></u></p> <p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p> <p class="MsoNormal"><b><span style="font-size:11pt;font-family:Calibri,sans-serif">From:</span></b><span style="font-size:11pt;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><u></u><u></u></p> <p class="MsoNormal"> <u></u><u></u></p> <div> <p class="MsoNormal">Dear All,<u></u><u></u></p> <div> <p class="MsoNormal"> <u></u><u></u></p> </div> <div> <p class="MsoNormal">I am trying to run a geometry optimization calculation for graphene sheet. I have attached the INPUT file herewith.<u></u><u></u></p> </div> <div> <p class="MsoNormal"> <u></u><u></u></p> </div> <div> <p class="MsoNormal">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.<u></u><u></u></p> </div> <div> <p class="MsoNormal"> <u></u><u></u></p> </div> <div> <p class="MsoNormal">I am expecting all your help to fix this. I am really grateful for your help. <br clear="all"> <u></u><u></u></p> <div> <p class="MsoNormal"> <u></u><u></u></p> </div> <p class="MsoNormal">-- <u></u><u></u></p> <div> <div> <div> <div> <div> <div> <div> <div> <p class="MsoNormal"><span style="color:rgb(7,55,99)">Thank you,</span><u></u><u></u></p> </div> <div> <p class="MsoNormal"> <u></u><u></u></p> </div> <div> <p class="MsoNormal"><span style="color:rgb(7,55,99)">Best Regards,</span><u></u><u></u></p> </div> <div> <p class="MsoNormal"> <u></u><u></u></p> </div> <div> <p class="MsoNormal"><span style="color:rgb(7,55,99)">Nimali</span><u></u><u></u></p> </div> <div> <p class="MsoNormal"> <u></u><u></u></p> <div> <p class="MsoNormal"> <u></u><u></u></p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <p class="MsoNormal">-- <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:cp...@googlegroups.com" target="_blank">cp...@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 href="https://groups.google.com/d/msgid/cp2k/CANmcfQ8wv0ks50wSzUVwzfE4qvFN31QPW_ESfX_P4LxaL34muw%40mail.gmail.com?utm_medium=email&utm_source=footer" target="_blank"> https://groups.google.com/d/msgid/cp2k/CANmcfQ8wv0ks50wSzUVwzfE4qvFN31QPW_ESfX_P4LxaL34muw%40mail.gmail.com</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank"> https://groups.google.com/d/optout</a>.<u></u><u></u></p> </div> </div> <p class="MsoNormal">-- <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:cp...@googlegroups.com" target="_blank">cp...@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 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>.<u></u><u></u></p> </blockquote> </div> <p class="MsoNormal"><br clear="all"> <u></u><u></u></p> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <p class="MsoNormal">-- <u></u><u></u></p> <div> <div> <div> <div> <div> <div> <div> <div> <p class="MsoNormal"><span style="color:rgb(7,55,99)">Thank you,</span><u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal"><span style="color:rgb(7,55,99)">Best Regards,</span><u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal"><span style="color:rgb(7,55,99)">Nimali</span><u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> </div> </div> </div> </div> </div> </div> </div> </div> <p class="MsoNormal">-- <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:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> To post to this group, send email to <a 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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 href="https://groups.google.com/d/msgid/cp2k/FCDF8CAC6EF2504E85F16873A7DF161A4916B5BB%40MBX114.d.ethz.ch?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/FCDF8CAC6EF2504E85F16873A7DF161A4916B5BB%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>.<br> </blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font color="#073763">Thank you,</font></div><div dir="ltr"><font color="#073763"><br></font></div><div><font color="#073763">Best Regards,</font></div><div><font color="#073763"><br></font></div><div><font color="#073763">Nimali</font></div><div dir="ltr"><font color="#073763"><br></font><div><span style="background-color:rgb(255,255,255)"><font color="#674ea7"><br></font></span></div></div></div></div></div></div></div></div></div>