<div dir="ltr">Dear Somananda,<div><br></div><div>Thanks in advance for your explanation. Also, I submitted a job to cp2k and follow I have attached the INPUT, OUTPUT AND .XYZ file. My problem is once I visualize the structure using VMD it appeared as follows. Can you explain me the reason for this unusual structure of graphite?</div><div><br></div><div>I am grateful for your help.</div><div><br></div><div>Regards,</div><div><br></div><div>Nimali</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Apr 30, 2019 at 9:05 PM Somananda Sanyal <<a href="mailto:somanan...@gmail.com" target="_blank">somanan...@gmail.com</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 dir="ltr"><div dir="ltr"><div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">Dear Nimali, </div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"> The best way is to number the C atoms in a series in your .xyz file and put in the .inp as for example: <br><div class="gmail_default"> &CONSTRAINT</div><div class="gmail_default"> &FIXED_ATOMS</div><div class="gmail_default"> COMPONENTS_TO_FIX XYZ</div><div class="gmail_default"> LIST 1..300</div><div class="gmail_default"> &END FIXED_ATOMS</div><div class="gmail_default"> &END CONSTRAINT</div><div class="gmail_default"><br></div><div class="gmail_default">Warm regards,</div><div class="gmail_default">Somananda</div><div><br></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Apr 30, 2019 at 12:14 PM Nimali Rathnayake <<a href="mailto:nimalira...@gmail.com" target="_blank">nimalira...@gmail.com</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 dir="ltr">Dear all,<div><br></div><div>I am working on geometry optimization on graphite intercalated materials. To run the geometry optimization calculations I need to fix all the carbon atoms.</div><div><br></div><div>Can anyone explain me how to list all the carbon atoms under the <span style="background-color:rgb(251,250,249);color:rgb(51,51,51);font-family:Consolas,"Andale Mono WT","Andale Mono","Bitstream Vera Sans Mono","Nimbus Mono L",Monaco,"Courier New",monospace;font-size:14px">CONSTRAINT</span> part? I have 300 carbon atoms in my graphite structure.</div><div><br></div><div>I am new to cp2k and really appreciate your help.</div><div><br></div><div>Regards,</div><div><br></div><div>Nimali</div><div><div><br></div><div dir="ltr" class="gmail-m_-7236706212654836711gmail-m_-6101717862088733696gmail-m_-1264428073626673539gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><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></div></div> <p></p> -- <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> 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-m_-7236706212654836711gmail-m_-6101717862088733696gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><font face="garamond, serif"><b style="color:rgb(102,102,102)">Somananda Sanyal, PhD</b><br></font></div><div><font color="#666666"><b><font face="garamond, serif">Post Doctoral Research Fellow<br>Department of Chemistry and Polymer Sciences<br>Room No. 1002, De Beers Building,<br>Stellenbosch University<br>Private Bag X1, Matieland, 7602<br>Stellenbosch, South Africa.<br>Email (work):</font></b> </font><a href="mailto:san...@sun.ac.za" target="_blank">san...@sun.ac.za</a><br><br></div></div></div></div></div> <p></p> -- <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> 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-m_-7236706212654836711gmail_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>