Dear Marcella,<br><br>your suggestions were so useful! I was able to reduce to 3-4 iterations per MD step. Sorry for my late reply but I played a lot with GAMMA and NOISE_GAMMA to equilibrate the MD run by monitoring the temperature per each kind. However, I have gathered some unusual behaviour (following attached files represent <i>Temp per kind vs MD steps</i>):<div><br>1. I first assumed GAMMA 0.001 fs^-1 (value typically used in other works) and gave different NOISE_GAMMA values for each &DEFINE_REGION (region1: Cu slab ; region2: one toluene molecule). In all cases, for the first 100 MD steps the temperature rapidly drops to very lower values (see attached<b> gamma0.001.png</b> file as an example), though it partially riequilibrates to the target T (900 K) only for sufficiently larger NOISE_GAMMA. Must be the initial temperature drop avoided or is it sufficient only adjusting the NOISE_GAMMA to larger values for T compensation (thus fixing GAMMA to 0.001)?</div><div><br>2. To avoid initial temperature drops, I have tried to directly increase GAMMA. For 0.1 fs^-1 it seems to work well (attached <b>gamma0.1.png</b> file), but it acts like an 'aggressive' thermostat producing large T fluctuations, especially for the toluene region (similar situations for GAMMA = 0.01 fs^-1, attached <b>gamma0.01.png</b> file). I'm aware of the few degrees of freedom of the single toluene molecule causing large temperature fluctuations; therefore it is better to assume GAMMA 0.001, is it?</div><div><br></div><div>3. Most important: the number of iterations per MD step costantly increase from 3-4 to 13-16 iterations during MD runs as it can be seen in the attached output file taken as an example (<b>Cu_toluene.out</b>) with</div><div> <i>grep 'SCF run' Cu_toluene.out</i><br>To restore the convergence with 3-4 iterations per MD step I sometimes did external EXIT and then restart the run with .RESTART.wfn. It initially works, but then the number of iterations increases again.<br>Is it a normal behaviour or is it due to a bad instability of the Langevin dynamics? How to eventually avoid it?</div><div><br></div><div>Many thanks!</div><div><br></div><div>N.B.: <u>No</u> external thermostat and no velocity rescaling (TEMP_TOL) were used during simulations.</div><div><br></div><div>Onofrio<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">Il giorno giovedì 16 giugno 2022 alle 12:23:19 UTC+2 Marcella Iannuzzi ha scritto:<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><br></div><div><br></div>As you may have read in previous works, to run SGCPMD a preliminary study is needed to set the proper GAMMA and NOISY_GAMMA parameters, which allow for the conservation of energy, for a Gaussian distribution of the error in the forces, and for a correct equipartition of the kinetic energy among the degrees of freedom. <div>Moreover the parameters to tune the convergence of the electronic structure at each MD step need also to be properly adjusted to the system. </div><div>This means that a series of preliminary simulations are needed, before the production runs are started. </div><div><br></div><div>This said, my suggestions are the following:</div><div>- Always start sgcpmd from a well converged wfn obtained along a standard BOMD run with diagonalisation and smearing</div><div>- Let the first steps run on many scf iterations if needed, i.e., set MAX_SCF large enough</div><div>- But use a relative large eps_scf. The wfn is not going to be optimised as in the BOMD, energy convergence around 10^-5 is desirable</div><div>- Use FULL_ALL preconditioner + ASPC</div><div>- Use a small time step</div><div>- Tune properly GAMMA and NOISY_GAMMA</div><div>- Monitor the conservation of energy and the temperature per kind or per region : TEMP_KIND<br><br></div><div>Regards</div><div>Marcella</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, June 16, 2022 at 10:53:53 AM UTC+2 <a href data-email-masked rel="nofollow">onofr...@gmail.com</a> 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">Hi Sam,<div>yes, of course. I set up more standard BOMD with ENSEMBLE NVT and DIAGONALIZATION with smear (look at my input file) and worked fine: it took more or less <b>30 steps to reach convergence</b> every AIMD step.</div><div><br></div><div>Then, I tried with ENSEMBLE NVT and OT (without smear obviously) and I got (MAX_SCF 200):</div><div><br></div><div><b> *** WARNING in qs_scf.F:598 :: SCF run NOT converged ***<br> *** WARNING in qs_scf.F:598 :: SCF run NOT converged ***<br> *** SCF run converged in 79 steps ***<br> *** SCF run converged in 72 steps ***<br> *** SCF run converged in 84 steps ***<br> *** SCF run converged in 53 steps ***<br> *** SCF run converged in 49 steps ***<br> *** SCF run converged in 48 steps ***<br> *** SCF run converged in 38 steps ***<br> *** SCF run converged in 40 steps ***<br> *** SCF run converged in 38 steps ***<br> *** SCF run converged in 30 steps ***<br> *** SCF run converged in 23 steps ***<br> *** SCF run converged in 26 steps ***<br> *** SCF run converged in 27 steps ***<br> *** SCF run converged in 26 steps ***<br> *** SCF run converged in 26 steps ***<br> *** SCF run converged in 23 steps ***<br> *** SCF run converged in 16 steps ***<br> *** SCF run converged in 16 steps ***<br> *** SCF run converged in 16 steps ***<br> *** SCF run converged in 18 steps ***</b></div><div><b> ...</b></div><div><br></div><div>Though SCF run not converged for the first two AIMD steps, then it worked sometimes fine (SCF run converged in 16 steps, but not always!). Could be a possible solution.</div><div>N.B.: setting MAX_SCF below 200 (i.e., 50) makes SCF run not converged more than two initial AIMD steps.</div><div><br></div><div>Anyway, I'm looking for correctly set up SGCPMD as that found in the following works:</div><div>- Lan, Jinggang, Jürg Hutter, and Marcella Iannuzzi. "First-principles simulations of an aqueous CO/Pt (111) interface." <i>The Journal of Physical Chemistry C</i> 122.42 (2018): 24068-24076.</div><div>- Musso, Tiziana, et al. "Second generation Car-Parrinello MD: application to the h-BN/Rh (111) nanomesh." <i>The European Physical Journal B</i> 91.7 (2018): 1-8.</div><div><br></div><div>However, I'm struggling with and I kindly need your help.</div><div>Kind regards.</div><div><br></div><div>Onofrio</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">Il giorno giovedì 16 giugno 2022 alle 09:58:41 UTC+2 <a rel="nofollow">wave...@gmail.com</a> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Onofrio<div><br></div><div>Question: have you set this up and run a more standard simulation to work out the convergence first?</div><div><br></div><div>If I guess, it's probably Cu as a transition metal with d-orbitals that is difficult (I am suffering with Au).<br><br></div><div><div>Kind Regards</div><div><br></div><div>Sam </div></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, June 15, 2022 at 3:20:20 PM UTC+2 <a rel="nofollow">onofr...@gmail.com</a> 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">Dear CP2K community,<br><br>I'm new to CP2K and I'm trying to set up a second-generation Car-Parrinello (SGCP) MD simulation. I have started with a geometrically optimized system of toluene adsorbed on a 3-layer Cu slab (8x6). I would to know what sections/keywords in the input file must be used to correctly set up a SGCPMD simulation and, possibly, the best settings to improve the speed of such simulations since I have not found any related tutorial (but only few things in the cp2k google group). <br>If I well understood, it has to be turn on the Langevin dynamics section in combination with the OT method. For example:<br><br>&FORCE_EVAL<br> ...<br> &DFT<br> ...<br> &QS<br> METHOD GPW<br> EXTRAPOLATION ASPC<br> EXTRAPOLATION_ORDER 3<br> EPS_DEFAULT 1.0E-10<br> &END QS<br> ...<br> &SCF<br> ...<br> &OT<br> PRECONDITIONER FULL_SINGLE_INVERSE ! or FULL_KINETIC<br> MINIMIZER DIIS<br> N_DIIS 7<br> &END OT<br> &OUTER_SCF<br> MAX_SCF 3<br> EPS_SCF 1.0E-05<br> &END OUTER_SCF <br> ...<br> &END SCF<br> ...<br> &END DFT<br> ...<br>&END FORCE_EVAL<br><br>&MOTION<br> &MD<br> ENSEMBLE LANGEVIN<br> ...<br> &LANGEVIN<br> GAMMA 0.001<br> &END LANGEVIN<br> ...<br> &END MD<br> ...<br>&END MOTION<br><br>Is it correct? To follow what I just mentioned, I prepared an input file (attached below) based on sections/keywords defined just above and I got from the output file (attached below) only <br> <b><i>"Leaving inner SCF loop after reaching 200 steps" </i></b><div>(200 steps because I set MAX_SCF 200)<br>resulting in a very bad convergence. <br>As a result, it seems that I have not been running any SGCPMD simulation but a simple bad BOMD. Am I missing something?<br>How can I correctly set up my input file for SGCPMD?<br><br>Any help would be greatly appreciated.</div><div>Thanks.<br><br>Onofrio<br></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div>
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