<div dir="ltr">The formulas are at the end of the linked Nature article from the previous reply in the Methods section. Plug in the energies from your CP2K calculations.<div><br><br>On Thursday, May 23, 2019 at 7:29:27 PM UTC-4, Nimali Rathnayake wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi Travis,<div><br></div><div>Thank you very much for your suggestions. I have already used the above codes to run energy calculations. My problem is using total energy in the output file we can calculate the cohesive energy and the binding energy for LiC6 system. Do you have an idea how to do these calculations?</div><div><br></div><div>Please let me know.I am so grateful for your help.</div><div><br></div><div>Kind regards,</div><div><br></div><div>Nimali</div></div><br><div class="gmail_quote"><div dir="ltr">On Fri, May 24, 2019 at 2:25 AM Travis <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="1X8BXjT7BAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">po...@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>See methods, <a href="https://www.nature.com/articles/s41467-018-07942-z" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.nature.com%2Farticles%2Fs41467-018-07942-z\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNENWruK7bq_W16qA58M2U_Svbhn7g';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.nature.com%2Farticles%2Fs41467-018-07942-z\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNENWruK7bq_W16qA58M2U_Svbhn7g';return true;">https://www.nature.com/<wbr>articles/s41467-018-07942-z</a></div><div><br></div><div>E(Li) is energy of Li atom (not ion) in gas phase. It's rather confusingly worded in this article. You can unambiguously compute this with the same input file as you have for graphite but with the modification,</div><div><br></div><div><div style="background-color:rgb(250,250,250);border-color:rgb(187,187,187);border-style:solid;border-width:1px"><code><div><span style="color:rgb(102,102,0)">...</span><span style="color:rgb(0,0,0)"><br> </span><span style="color:rgb(102,102,0)">&</span><span style="color:rgb(0,0,0)">POISSON<br> POISSON_SOLVER WAVELET<br> PERIODIC NONE<br> </span><span style="color:rgb(102,102,0)">&</span><span style="color:rgb(0,0,136)">END</span><span style="color:rgb(0,0,0)"> POISSON<br> </span><span style="color:rgb(102,102,0)">&</span><span style="color:rgb(0,0,136)">END</span><span style="color:rgb(0,0,0)"> DFT<br> </span><span style="color:rgb(102,102,0)">&</span><span style="color:rgb(0,0,0)">SUBSYS<br> </span><span style="color:rgb(102,102,0)">&</span><span style="color:rgb(0,0,0)">CELL<br> ABC </span><span style="color:rgb(0,102,102)">16</span><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(0,102,102)">16</span><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(0,102,102)">16</span><span style="color:rgb(0,0,0)"><br> ALPHA_BETA_GAMMA </span><span style="color:rgb(0,102,102)">90</span><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(0,102,102)">90</span><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(0,102,102)">90</span><span style="color:rgb(0,0,0)"><br> PERIODIC NONE<br> SYMMETRY CUBIC<br> </span><span style="color:rgb(102,102,0)">&</span><span style="color:rgb(0,0,136)">END</span><span style="color:rgb(0,0,0)"> CELL<br></span></div></code></div><br>This is what I've used previously for (LiPF6)_2. You probably only need a 10 10 10 Angstrom box for Li. Importantly, center the coordinates in the box. Refer to the bolded bit below to have CP2K do that for you.<br></div><div><br></div><div><div style="background-color:rgb(250,250,250);border-color:rgb(187,187,187);border-style:solid;border-width:1px"><code><div><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(102,102,0)">&</span><span style="color:rgb(0,0,0)">TOPOLOGY<br> COORD_FILE_FORMAT XYZ<br> COORD_FILE_NAME foo</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">xyz<br> CONN_FILE_FORMAT off<br></span><b><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(102,102,0)">&</span><span style="color:rgb(0,0,0)">CENTER_COORDINATES<br> </span><span style="color:rgb(102,102,0)">&</span><span style="color:rgb(0,0,136)">END</span><span style="color:rgb(0,0,0)"> CENTER_COORDINATES</span></b><span style="color:rgb(0,0,0)"><br> </span><span style="color:rgb(102,102,0)">&</span><span style="color:rgb(0,0,136)">END</span><span style="color:rgb(0,0,0)"> TOPOLOGY<br></span></div></code></div></div><div><br></div>On Wednesday, May 22, 2019 at 9:57:20 PM UTC-3, Nimali Rathnayake wrote:<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">Hello everyone,<div><br clear="all"><div>Can you explain me how to calculate the cohesive and binding energy of graphite using energy calculations in cp2k?</div><div><br></div><div>For my system I am considering on Li and graphite.</div><div><br></div><div>Please explain me how to do the calculation properly using the data in .OUT in energy calculations.</div><div><br></div>-- <br><div dir="ltr"><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></div></div> </blockquote></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="javascript:" target="_blank" gdf-obfuscated-mailto="1X8BXjT7BAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.<wbr>com</a>.<br> To post to this group, send email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="1X8BXjT7BAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">c...@googlegroups.com</a>.<br> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/group/cp2k';return true;" onclick="this.href='https://groups.google.com/group/cp2k';return true;">https://groups.google.com/<wbr>group/cp2k</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/44ce2980-8378-4c3c-8ceb-9cfaffdbec7d%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/d/msgid/cp2k/44ce2980-8378-4c3c-8ceb-9cfaffdbec7d%40googlegroups.com?utm_medium\x3demail\x26utm_source\x3dfooter';return true;" onclick="this.href='https://groups.google.com/d/msgid/cp2k/44ce2980-8378-4c3c-8ceb-9cfaffdbec7d%40googlegroups.com?utm_medium\x3demail\x26utm_source\x3dfooter';return true;">https://groups.google.com/d/<wbr>msgid/cp2k/44ce2980-8378-4c3c-<wbr>8ceb-9cfaffdbec7d%<wbr>40googlegroups.com</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/d/optout';return true;" onclick="this.href='https://groups.google.com/d/optout';return true;">https://groups.google.com/d/<wbr>optout</a>.<br> </blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><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> </blockquote></div></div>