<div dir="ltr">Constraint atoms lead to nonphysical velocity assignment. It has been fixed in I-PI but not in CP2K as Thomas mentioned.<div><br>On Monday, 12 August 2019 16:23:42 UTC+2, Yun An wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">Dear Thomas,<br><br></div><div>Thank you very much for the kind reply. I tried with PINT module in cp2k, the weird thing is, I want to fix some atoms during the calculations, but it seems that the "CONSTRAINT" section didn't work, because the atoms which are supposed to be fixed moves a lot according to the structures it gives out. Do you know what is the problem and how to fix it?<br><br></div><div>I attached the input file, thanks a lot in advance.<br><br></div><div>Best regards,<br></div><div>Yun <br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr">Thomas Kühne <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="U2xIikVEDAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">t...@gmail.com</a>> 于2019年8月1日周四下午10:55写道：<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>Dear Yun, <div><br></div><div>yes the trajectories of the individual beads are in H2O-pos-*-<a href="http://1.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2F1.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH7Iopg33wy6-CUZSLr3wQXvVUl3Q';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2F1.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH7Iopg33wy6-CUZSLr3wQXvVUl3Q';return true;">1.xyz</a>, whereas the </div><div>centroid, which corresponds to the center of mass of the closed ring-polymer made </div><div>up of the imaginary-time replica, is in <a href="http://centroid-pos-1.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF1oEWKAIAvleQHRftz0GLXyNINOg';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF1oEWKAIAvleQHRftz0GLXyNINOg';return true;">centroid-pos-1.xyz</a>. </div><div>Conceptually, conducting PIMD-based metadynamics should be rather straightforward, </div><div>however, since there is some bookkeeping is necessary to apply the bias potential </div><div>to the individual beads I suspect it not to directly work as is. Yet, via i-Pi v2 in conjunction </div><div>with PLUMED it is advertised to work: <a href="http://ipi-code.org/assets/pdf/manual.pdf" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fipi-code.org%2Fassets%2Fpdf%2Fmanual.pdf\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEfet3vKzAWolHboEkEMQO6MDMqAQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fipi-code.org%2Fassets%2Fpdf%2Fmanual.pdf\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEfet3vKzAWolHboEkEMQO6MDMqAQ';return true;">http://ipi-code.org/assets/<wbr>pdf/manual.pdf</a></div><div><br></div><div>Best, </div><div>Thomas</div><div><br></div><div><div><blockquote type="cite"><div>Am 01.08.2019 um 19:19 schrieb Yun An <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="U2xIikVEDAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">an...@gmail.com</a>>:</div><br><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">Dear Thomas,<br><br></div><div>Thank you for the kind reply, it helps a lot. I still have some questions:<br><br></div><div>I use 4 beads to test h2o molecule, is it means the trajectory is represented by the average replica positions of each atom, in the current case, is the all the atom positions of these four H2O-pos-?-<a href="http://1.xyz/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2F1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF_AKG0RsGCsWBXQSvp-qAWPGjCnw';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2F1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF_AKG0RsGCsWBXQSvp-qAWPGjCnw';return true;">1.xyz</a> file?<br><br></div><div>Anther question is if I want to run MD simulations to see the quantum effects, for example, H2 and D2 diffusion in the metal surface, is it possible that cp2k combines PINT and metadynamics? Because the RUN_TYPE section to me is like either one can choose MD to perform normal MD or PINT to run PIMD, but not both at one calculations. So in such case, how should I consider quantum effects?<br><br></div><div>Thank you again for your help.<br><br></div><div>Best regards,<br></div><div>Yun <br> </div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr">Thomas Kühne <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="U2xIikVEDAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">t...@gmail.com</a>> 于2019年7月31日周三下午4:16写道：<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>Dear Yun, <div><br></div><div>you can indeed conduct PIMD using the CP2K built-in PINT module, or using the driver mode </div><div>via the i-Pi program. The latter more functionality for more sophisticated PIMD simulations, </div><div>though the former already permits to conduct all sort of conventional PIMD simulations and has </div><div>the advantage of having everything in one package. </div><div>The <a href="http://centroid-pos-1.xyz/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEEyNduLTrAkyavz1obCwXLSQAm1A';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEEyNduLTrAkyavz1obCwXLSQAm1A';return true;">centroid-pos-1.xyz</a> contains not the coordinates of every bead, but only the ones of the centroid, </div><div>i.e. the center of mass of the closed ring-polymer. The <a href="http://centroid-vel-1.xyz/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-vel-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF77jX1jiyUQnL_UjXdkM5ca0X8Sg';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-vel-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF77jX1jiyUQnL_UjXdkM5ca0X8Sg';return true;">centroid-vel-1.xyz</a> contains the corresponding </div><div>velocities, but be aware that except the when centroid molecular dynamics is used, the dynamics of </div><div>the ring-polymer is unphysical, only static ensemble averages are. </div><div><br></div><div>Best, </div><div>Thomas</div><div><br><div><blockquote type="cite"><div>Am 30.07.2019 um 18:39 schrieb Yun An <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="U2xIikVEDAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">an...@gmail.com</a>>:</div><br><div><div dir="ltr"><p>Dear all,</p><p><br></p><p>I want to perform PIMD with cp2k, according to the manual, one can add a PINT session to run path integral simulations; also, can use i-PI mode DRIVER. What is the difference between those two, is that in principle they both can do PIMD? I tried a H2O molecule with run_type of PINT, then I got <a href="http://centroid-pos-1.xyz/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEEyNduLTrAkyavz1obCwXLSQAm1A';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEEyNduLTrAkyavz1obCwXLSQAm1A';return true;">centroid-pos-1.xyz</a> and <a href="http://centroid-vel.xyz/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-vel.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEytbVMLQoRMgQm3WosB_jYALjD5g';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-vel.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEytbVMLQoRMgQm3WosB_jYALjD5g';return true;">centroid-vel.xyz</a>, I thought the <a href="http://centroid-pos-1.xyz/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEEyNduLTrAkyavz1obCwXLSQAm1A';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEEyNduLTrAkyavz1obCwXLSQAm1A';return true;">centroid-pos-1.xyz</a> is the atom positions of each replica, but what is the meaning of <a href="http://centroid-vel.xyz/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-vel.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEytbVMLQoRMgQm3WosB_jYALjD5g';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-vel.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEytbVMLQoRMgQm3WosB_jYALjD5g';return true;">centroid-vel.xyz</a>? Also, I want to see the trajectories, is this directly given in <a href="http://centroid-pos-1.xyz/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEEyNduLTrAkyavz1obCwXLSQAm1A';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEEyNduLTrAkyavz1obCwXLSQAm1A';return true;">centroid-pos-1.xyz</a> or one need to use some script to transform, because from current <a href="http://centroid-pos-1.xyz/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEEyNduLTrAkyavz1obCwXLSQAm1A';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fcentroid-pos-1.xyz%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEEyNduLTrAkyavz1obCwXLSQAm1A';return true;">centroid-pos-1.xyz</a> , the atoms are not quantum at all.</p><p><br></p><p>Thank you all in advance for any help.</p><p><br></p><p>Best regards,</p><p>Yun</p></div><div><br></div> -- <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="U2xIikVEDAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.<wbr>com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/3aa5af5d-4b37-471b-ae2b-18dc83d0b3b5%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/d/msgid/cp2k/3aa5af5d-4b37-471b-ae2b-18dc83d0b3b5%40googlegroups.com?utm_medium\x3demail\x26utm_source\x3dfooter';return true;" onclick="this.href='https://groups.google.com/d/msgid/cp2k/3aa5af5d-4b37-471b-ae2b-18dc83d0b3b5%40googlegroups.com?utm_medium\x3demail\x26utm_source\x3dfooter';return true;">https://groups.google.com/d/<wbr>msgid/cp2k/3aa5af5d-4b37-471b-<wbr>ae2b-18dc83d0b3b5%<wbr>40googlegroups.com</a>.<br> <span><H2O-centroid-pos-1.xyz></span><span><H2O-<wbr>centroid-vel-1.xyz></span></div></blockquote></div><br></div><br><br><div> <div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">==============================</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Thomas D. Kühne</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Dynamics of Condensed Matter</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Chair of Theoretical Chemistry</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">University of Paderborn</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Warburger Str. 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