<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 style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Dev<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">a stress tensor is available with SCCS only in the current development version of CP2K and not in any earlier version including the release version 7.1. Note, that the stress tensor is only needed for MD ensembles with a barostat like NpT, i.e. NVT or NVE should work also with earlier versions.<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">HTH<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Matthias<o:p></o:p></span></p> <p class="MsoNormal"><span 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>Dev Rana<br> <b>Sent:</b> Donnerstag, 4. Juni 2020 18:26<br> <b>To:</b> cp2k <...@googlegroups.com><br> <b>Subject:</b> Re: [CP2K:13461] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics?<o:p></o:p></span></p> <p class="MsoNormal"><o:p> </o:p></p> <div> <p class="MsoNormal">Hi Matthias,<o:p></o:p></p> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">Thank you for your input. I understand that as the distance from C1 (carbon #1) to C2 (carbon #2) increases, the band gap decreases until only the valence electrons remains. When the distance between atoms becomes short, the electrons converge into the conduction band which allows a bond to form with overlapping electrons. Therefore, since my electrons were so far apart, they had no band gap to overcome. I understand your rationale for using a spin polarized run or smearing, and I have tried this using a 6 membered carbon ring, instead. i.e. all 6 atoms are close. Using SCCS & MD, it tells me that I need a stress tensor enabled. So I turn it on, then it says that SCCS is not configured for using the stress tensor. Therefore, I can't really run SCCS with MD, unless I use a SCF OT method. <o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">I guess I just don't understand how to run SCCS and MD with my system in which I'd like to see a reaction occurring between the 6 carbon atoms as they react into a ring or chain. <o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">I apologize for the many questions, I'm a complete newbie with this stuff, with very little guidance as I am self-teaching these topics. <o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">Best Regards,<o:p></o:p></p> </div> <div> <p class="MsoNormal">Dev<br> <br> On Thursday, June 4, 2020 at 4:54:09 AM UTC-4, Matthias Krack wrote:<o:p></o:p></p> <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 style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dev,</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span 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 style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">your setup of a system of six separated carbon atoms does not have a band gap and the addition of an implicit solvent won’t change that most likely. The problem should show up already for a single isolated carbon atom which you can converge either as a triplet within a spin polarized run (LSD and MULTIP 3) or with smearing, i.e. with a fractional occupation of 2/3 for the three degenerated C 2p orbitals. The latter approach works only with diagonalization (try broyden_mixing).</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span 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 style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Matthias</span><span style="font-size:10.0pt;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 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="javascript:" target="_blank">c...@googlegroups.com</a> <<a href="javascript:" target="_blank">c...@googlegroups.com</a>> <b>On Behalf Of </b>Dev Rana<br> <b>Sent:</b> Mittwoch, 3. Juni 2020 20:49<br> <b>To:</b> cp2k <<a href="javascript:" target="_blank">c...@googlegroups.com</a>><br> <b>Subject:</b> Re: [CP2K:13447] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics?</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">Thank you for the confirmation Matthias! Would you be able to look at my input file? I'm having trouble with SCF convergence and my Andreussi model set up. <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'm trying to simulate 6 carbon atoms randomly placed as they migrate through a molten Al system, using MD. Using the solvation model, I've set up my 6 C atoms and have a dieletric constant of 80. I'm also attaching my latest output file. <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 was originally using Diagonalization method for the SCF, but the convergence column was migrating over 1. <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I then tried using OT with minimizer DIIS, Full_ALL preconditioner and 0.001 energy_gap, as recommended for OT, and it stays below 1, however it never converges. <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'm also running this simulation without a solvation model using a full system of 256 Al atom and 6 carbon atoms randomly placed in the system for comparison, with no issues of convergence, i.e. each SCF converges within 24-30 steps with each step taking about 22 seconds. <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">Thank you so much for all your help thus far! I really appreciate it!<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">Best Regards,<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Dev<br> <br> On Wednesday, June 3, 2020 at 12:42:32 PM UTC-4, Matthias Krack wrote:<o:p></o:p></p> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Yes.</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span 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:c...@googlegroups.com">c...@googlegroups.com</a> <<a href="mailto:c...@googlegroups.com">c...@googlegroups.com</a>> <b>On Behalf Of </b>Dev Rana<br> <b>Sent:</b> Mittwoch, 3. Juni 2020 18:19<br> <b>To:</b> cp2k <<a href="mailto:c...@googlegroups.com">c...@googlegroups.com</a>><br> <b>Subject:</b> [CP2K:13443] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics?</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">As the question in the subject suggests, is it possible to run a solvation model with MD?<o:p></o:p></p> </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:c...@googlegroups.com">c...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank"> https://groups.google.com/d/msgid/cp2k/6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e%40googlegroups.com</a>.<o:p></o:p></p> </div> </div> </blockquote> </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="javascript:" target="_blank">c...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/206d8b04-4fb7-4076-8ad6-d7f609f50bf6%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank"> https://groups.google.com/d/msgid/cp2k/206d8b04-4fb7-4076-8ad6-d7f609f50bf6%40googlegroups.com</a>.<o:p></o:p></p> </div> </div> </blockquote> </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:cp2k+unsu...@googlegroups.com">cp2k+unsu...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/461f1bb0-1c1e-4841-94c4-99731983785d%40googlegroups.com?utm_medium=email&utm_source=footer"> https://groups.google.com/d/msgid/cp2k/461f1bb0-1c1e-4841-94c4-99731983785d%40googlegroups.com</a>.<o:p></o:p></p> </div> </body> </html>