Dear Matthias,<div><br /></div><div>Thanks for the confirmation! </div><div><br /></div><div>Kind regards,</div><div>Léon</div><div><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday 18 January 2024 at 14:14:57 UTC+1 Krack Matthias wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"> <div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt">Dear Léon<u></u><u></u></span></p> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">That’s correct, the values in the .stress file have already been divided by the cell volume and thus the total pressure in bar can be calculated as (p(xx) + p(yy) + p(zz))/3.<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Best<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Matthias<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p> <div> <div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a> <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>> on behalf of Léon Luntadila Lufungula <<a href data-email-masked rel="nofollow">Leon.luntad...@uantwerpen.be</a>><br> <b>Date: </b>Thursday, 18 January 2024 at 11:41<br> <b>To: </b>cp2k <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>><br> <b>Subject: </b>Re: [CP2K:19774] Printing stress tensor from an existing trajectory<u></u><u></u></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Dear Matthias,<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><u></u> <u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">I've done some checking myself, by comparing my calculated value with that reported in the MD section of the output and the reported value in the output does seem to coincide with just the average of the diagonal elements of the stress tensor as outputted by MOTION/PRINT/STRESS, without dividing by the cell volume... The elements of the stress tensor are already given in bar so dividing by the cell volume would give units of bar/Å^3 and not bar. So is it correct that the pressure is just equal to the average of the diagonal elements or does one need to take into account the cell volume as you suggested?<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><u></u> <u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Kind regards,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Léon<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><u></u> <u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <span style="font-size:11.0pt">P.S. Thanks to all of you from CP2K (Matthias, Jürg, Matt, ...) for being so responsive this last week, it has really helped me in getting my calculations and analysis of the results up and running in a short time!<u></u><u></u></span></p> </div> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">On Thursday 18 January 2024 at 09:59:27 UTC+1 Krack Matthias wrote:<u></u><u></u></span></p> </div> <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="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Dear Léon</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">yes, the pressure is calculated from the average of the three diagonal elements divided by the cell volume.</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> </div> <div> <div> <div> <div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:72.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span> <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>> on behalf of Léon Luntadila Lufungula <<span><a href data-email-masked rel="nofollow">Leon.luntad...@uantwerpen.be</a></span>><br> <b>Date: </b>Wednesday, 17 January 2024 at 13:47<br> <b>To: </b>cp2k <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>><br> <b>Subject: </b>Re: [CP2K:19768] Printing stress tensor from an existing trajectory</span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Dear Matthias,<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Perhaps this is a stupid question, but I want to calculate the pressure from the stress tensor to see if my NPT trajectory is keeping the pressure constant along its trajectory and I'm a bit unsure about how to do this. Is this just taking the average of the diagonal elements of the stress tensor or is it more complex than this?<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Kind regards,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:72.0pt"> <span style="font-size:11.0pt">Léon<u></u><u></u></span></p> </div> <div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">On Friday 12 January 2024 at 12:25:29 UTC+1 Léon Luntadila Lufungula wrote:<u></u><u></u></span></p> </div> <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"> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Dear Matthias,<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Thanks for the quick reply, it wasn't a very expensive calculation so it doesn't matter if I'll have to re-do it. I'll keep this in mind for the future so that I don't forget this again.<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Kind regards,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:72.0pt"> <span style="font-size:11.0pt">Léon<u></u><u></u></span></p> </div> <div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">On Friday 12 January 2024 at 11:22:39 UTC+1 Krack Matthias wrote:<u></u><u></u></span></p> </div> <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="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">Dear Léon</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">I am afraid, it is not possible to recover the stresses a posteriori from a NpT run. The stresses obtained with REFTRAJ would miss the kinetic energy contribution to the total stress tensor.</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">HTH</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> </div> <div> <div> <div> <div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:108.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span> <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>> on behalf of Léon Luntadila Lufungula <<span><a href data-email-masked rel="nofollow">Leon.luntad...@uantwerpen.be</a></span>><br> <b>Date: </b>Friday, 12 January 2024 at 10:16<br> <b>To: </b>cp2k <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>><br> <b>Subject: </b>[CP2K:19730] Printing stress tensor from an existing trajectory</span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">Dear all,<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">I calculated an NPT trajectory and wanted to see how the pressure fluctuated during the MD run, however, I forgot to add the MOTION/PRINT/STRESS keyword so I don't have my stresses. Is there a way to create the file with the stresses after the fact without re-doing the whole trajectory? Perhaps with the REFTRAJ keyword? I don't have any experience with it, but I think it might pose a solution if I read the documentation...<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">Kind regards,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">Léon<u></u><u></u></span></p> </div> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">-- <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 <span><a href data-email-masked rel="nofollow">cp2k+uns...@googlegroups.com</a></span>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/fa512d0f-ede4-4ed7-ad14-92b512851a8fn%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en-GB&q=https://groups.google.com/d/msgid/cp2k/fa512d0f-ede4-4ed7-ad14-92b512851a8fn%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1705670832400000&usg=AOvVaw3JyHEJv01ZxXKox2M_0-um"> https://groups.google.com/d/msgid/cp2k/fa512d0f-ede4-4ed7-ad14-92b512851a8fn%40googlegroups.com</a>.<u></u><u></u></span></p> </div> </div> </div> </div> </blockquote> </div> </blockquote> </div> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">-- <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 <span><a href data-email-masked rel="nofollow">cp2k+uns...@googlegroups.com</a></span><u></u><u></u></span></p> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/8f700419-9d4d-48da-a051-f46ea0ecc86cn%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en-GB&q=https://groups.google.com/d/msgid/cp2k/8f700419-9d4d-48da-a051-f46ea0ecc86cn%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1705670832400000&usg=AOvVaw3RuV2qUX7FnZrGF1WHQxGe"> https://groups.google.com/d/msgid/cp2k/8f700419-9d4d-48da-a051-f46ea0ecc86cn%40googlegroups.com</a>.<u></u><u></u></span></p> </div> </div> </div> </div> </blockquote> </div> </div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">-- <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 data-email-masked rel="nofollow">cp2k+uns...@googlegroups.com</a>.<br></span></p></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/41909f1d-e212-482e-a407-5fdb8536d824n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en-GB&q=https://groups.google.com/d/msgid/cp2k/41909f1d-e212-482e-a407-5fdb8536d824n%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1705670832400000&usg=AOvVaw0VtowSOrZ-WyG7Eb6-k0PL"> https://groups.google.com/d/msgid/cp2k/41909f1d-e212-482e-a407-5fdb8536d824n%40googlegroups.com</a>.<u></u><u></u></span></p> </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="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br /> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/ef623622-6ba7-4bed-8f31-ec6ee3c703d8n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/ef623622-6ba7-4bed-8f31-ec6ee3c703d8n%40googlegroups.com</a>.<br />