<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=iso-8859-1"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div class="WordSection1"> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US">Dear Léon<o:p></o:p></span></p> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">the constant of motion mentioned in the lecture should correspond to the conserved quantity (6<sup>th</sup>) column in the .ener file. Its value will change when you change simulation parameters including those for the thermostat and/or barostat. While the temperature fluctuations of the system might be equilibrated after 10 ps in an acceptable manner, the cell fluctuations will most likely need much longer equilibration times of at least 30 ps or more. Given the computational costs for AIMD, one usually tends to cut corners which results in a significant deterioration of the sampling quality.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Best<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <div id="mail-editor-reference-message-container"> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:0cm;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">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Léon Luntadila Lufungula <Leon.luntadilalufungula@uantwerpen.be><br> <b>Date: </b>Monday, 29 January 2024 at 10:38<br> <b>To: </b>cp2k <cp2k@googlegroups.com><br> <b>Subject: </b>Re: [CP2K:19838] Cons. Qty for different ensembles + Pressure fluctuation<o:p></o:p></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Dear Matthias,<o:p></o:p></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">I've also tried to equilibrate a box of 216 water molecules with DFT and while the temperature and pressure seem to equilibrate quite easily, the constant of motion shows large jumps despite the potential and kinetic energy also being quite constant... If I'm not mistaken, the constant of motion in the NPT ensemble is the energy of the system + the energy of the thermostat + energy of barostat, as shown in this <a href="https://www.cp2k.org/_media/events:2016_summer_school:cp2k_moving_atoms.pdf"> lecture</a> from 2016, so this would suggest that the fluctuations are due to the thermostat or barostat, right? Like the TIP3P NPT run, I used a thermostat timecon of 100 fs and a barostat timecon of 1000 fs and after 21 125 fs (blue vertical line in figures), I restarted the calculation and increased the thermostat timecon to 500 fs. I accidentaly set RESTART_BAROSTAT and RESTART_BAROSTAT_THERMOSTAT to FALSE upon restarting, but I'm unsure if this might have lead to the large jumps in the constant of motion later at t > 28 000 fs... <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><img border="0" width="1487" height="1790" style="width:15.4895in;height:18.6458in" id="_x0000_i1027" src="cid:f98aea52-50fd-4b8b-9572-c67618f26125"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Same goes for the NPT_F calculation of my solvated TiO2 slab. I did a 10 ps simulation with thermostat timecon 50 and barostat timecon 100 and everything seems to equilibrate except for the constant of motion which seems to steadily rise. After 10 ps of simulation I restarted the calculation and again accidentaly messed up my input and set RESTART_BAROSTAT and RESTART_BAROSTAT_THERMOSTAT to FALSE but this time I didn't even change the timecons of the thermostat and barostat, but this time I immediately see a significant jump in the constant of motion after which it continues to increase... Any idea how I can fix this so that the constant of motion stays...well...constant?<br> <img border="0" width="1489" height="1790" style="width:15.5104in;height:18.6458in" id="_x0000_i1026" src="cid:8e496bdf-1e13-4725-a4c5-7626ee3d1be1"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Kind regards,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Léon<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">On Tuesday 23 January 2024 at 14:41:46 UTC+1 Léon Luntadila Lufungula wrote:<o:p></o:p></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"> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Dear Matthias,<o:p></o:p></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">My AIMD calculations are on a slab wherein I keep my bottom layer fixed, but apparently REGION MASSIVE is not compatible with constraints, so I'll have to use REGION GLOBAL. Either way, thanks a lot for the detailed answer! For a novice MD practicioner as myself this is already enough information to get started! I'll try the values you suggested during my production run while keeping an eye on the temperature and pressure during the simulation; I guess when I've chosen my TIMECON too large, this will result in the system drifting away from the equilibrium values.<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">As always, thanks a lot for all the help!<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Kind regards,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <span style="font-size:11.0pt">Léon<o:p></o:p></span></p> </div> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">On Tuesday 23 January 2024 at 14:21:05 UTC+1 Krack Matthias wrote:<o:p></o:p></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="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt">Dear Léon</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Using a MASSIVE CSVR thermostat with a small TIMECON of about 50 is appropriate and efficient for equilibration. Thereafter, the TIMECON for the thermostat can be increased to 500-1000 for the sampling (production) runs and also a GLOBAL instead of a MASSIVE thermostat can be used, if possible, to reduce the impact of the thermostat on the dynamics. You will find different opinions about the absolute and relative values for the TIMECONs of thermostat and barostat in the web or literature. I suggest to use a two to five times larger TIMECON for the barostat compared to the thermostat. You have, however, to keep in mind that the appropriate (best) parameters for baro- and thermostat depend on the type of system and the selected conditions eventually.</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">HTH</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></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="mso-margin-top-alt:auto;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">cp...@googlegroups.com <cp...@googlegroups.com> on behalf of Léon Luntadila Lufungula <Leon.luntad...@uantwerpen.be><br> <b>Date: </b>Tuesday, 23 January 2024 at 11:47<br> <b>To: </b>cp2k <cp...@googlegroups.com><br> <b>Subject: </b>Re: [CP2K:19801] Cons. Qty for different ensembles + Pressure fluctuation</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt">Hi Matthias,<o:p></o:p></span></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt">So I started an NpT directly from the inputs you gave me with a box containing 216 water molecules. After a 300ps equilibration (plots thus starrt at 0.3 ns), the pressure fluctuations are again in the 10kbar range which is okay as you pointed out, while the average pressure is around -14 bar, so tha'ts also within the 20 bar range you mentioned. The energy drift per atom is also below 1K so everything seems to work reasonably. <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt"><img border="0" width="1490" height="1789" style="width:15.5208in;height:18.6354in" id="_x0000_i1025" src="https://groups.google.com/group/cp2k/attach/7718930ba853e/H2O-TIP3P_FLEXIBLE-6x6x6.mp-NPT-plots.png?part=0.1&view=1"><o:p></o:p></span></p> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt"><br> I'm starting my AIMD simulations as we speak, so hopefully all goes well there too. I read that it is best to do a short equilibration with a strong coupling to the thermostat (e.g. CSVR, TIMECON 20 and REGION MASSIVE), before going to a weaker coupling (e.g. CSVR, TIMECON 200 and REGION GLOBAL), but is there also a rule of thumb w.r.t. the barostat TIMECON? I regularly see TIMECON 1000, but is it useful to set it to TIMECON 100 in this early equilibration?<o:p></o:p></span></p> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt">Thanks for all the help already, it really helps me a lot given the fact that I don't have a senior researcher with a lot of hands-on CP2K experience around!<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt">Kind regards,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt">Léon<o:p></o:p></span></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> </div> </div> </div> </blockquote> </div> </blockquote> </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="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/df0cb86d-d2ad-45e0-a054-1fc7d7e0f789n%40googlegroups.com?utm_medium=email&utm_source=footer"> https://groups.google.com/d/msgid/cp2k/df0cb86d-d2ad-45e0-a054-1fc7d7e0f789n%40googlegroups.com</a>.<o:p></o:p></span></p> </div> </div> </div> </body> </html> <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/ZRAP278MB0827BC336DC0022BFD3AD123F47E2%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827BC336DC0022BFD3AD123F47E2%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM</a>.<br />