<div dir="ltr">Dear Nam,<div><br></div><div>Thanks for your suggestion. I use the 2018 version, the memory usage is still increasing.</div><div>I gauss the problem is from some of libs. But I don't know which the libs cause the problem. </div><div><br></div><div>Best,</div><div>Ke </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Nam Tran <<a href="mailto:trann...@gmail.com">trann...@gmail.com</a>> 于2019年10月28日周一下午3:44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 dir="ltr"><div>Hi, </div><div><br></div>I am not sure about your case but I have a similar problem when I updated to intel compiler and mkl 2019. Maybe I made something wrong during the installation but downgrade to 2018 version solved my problem.<div><br></div><div>Nam<br><br>On Monday, 28 October 2019 18:35:15 UTC+11, Ke Zhou wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear Developers,<div><br></div><div><div style="font-size:small">Now I am running <span>cp2k</span> 6.1 on our new cluster. </div><div style="font-size:small">The <b>memory usage for <span>cp2k</span> is increased with time </b>during running. Finally, it stops when the usage reach the upper bound. I also tried <span>cp2k</span> 5.1 and had same problem. </div><div style="font-size:small"><b>But I run it in our old cluster which is 2.5.1 version, it works well.</b></div><div style="font-size:small"><br></div><div style="font-size:small">However, I run one of the example in CP2K package, H2O-64.inp (path: ./test/QS/benchmark, bulk water), using both 6.1 and 5.1, it runs well.</div><div style="font-size:small"><br></div><div style="font-size:small">Can you help me?</div><div style="font-size:small">Is the problem from compile or the input file?</div><div style="font-size:small"><br></div><div style="font-size:small"><div>Best,</div><div>Ke </div><div><br></div><div><br></div></div><div style="font-size:small"><br></div><div style="font-size:small">Input file:</div><div style="font-size:small">########## H2O-64.inp, from example file ##################</div><div><div><font size="2">&FORCE_EVAL</font></div><div><font size="2"> METHOD QS</font></div><div><font size="2"> &DFT</font></div><div><font size="2"> BASIS_SET_FILE_NAME GTH_BASIS_SETS</font></div><div><font size="2"> POTENTIAL_FILE_NAME POTENTIAL</font></div><div><font size="2"> &MGRID</font></div><div><font size="2"> CUTOFF 280</font></div><div><font size="2"> REL_CUTOFF 30</font></div><div><font size="2"> &END MGRID</font></div><div><font size="2"> &QS</font></div><div><font size="2"> EPS_DEFAULT 1.0E-12</font></div><div><font size="2"> WF_INTERPOLATION PS </font></div><div><font size="2"> EXTRAPOLATION_ORDER 3 </font></div><div><font size="2"> &END QS</font></div><div><font size="2"> &SCF</font></div><div><font size="2"> SCF_GUESS ATOMIC</font></div><div><font size="2"> &OT ON</font></div><div><font size="2"> MINIMIZER DIIS</font></div><div><font size="2"> &END OT</font></div><div><font size="2"><br></font></div><div><font size="2"> &PRINT</font></div><div><font size="2"> &RESTART OFF</font></div><div><font size="2"> &END</font></div><div><font size="2"> &END</font></div><div><font size="2"><br></font></div><div><font size="2"> # SCF_GUESS RESTART</font></div><div><font size="2"> # EPS_SCF 1.0E-7</font></div><div><font size="2"> &END SCF</font></div><div><font size="2"> &XC</font></div><div><font size="2"> &XC_FUNCTIONAL Pade</font></div><div><font size="2"> &END XC_FUNCTIONAL</font></div><div><font size="2"> &END XC</font></div><div><font size="2"> &END DFT</font></div><div><font size="2"> &SUBSYS</font></div><div><font size="2"> &CELL</font></div><div><font size="2"> ABC 12.4138 12.4138 12.4138</font></div><div><font size="2"> &END CELL</font></div><div><font size="2"> # 64 H2O (TIP5P,1bar,300K) a = 12.4138</font></div><div><font size="2"> &COORD</font></div><div><font size="2"> O 12.235322 1.376642 10.869880</font></div><div><font size="2"> O 6.445390 3.706940 8.650794</font></div><div><font size="2"> O 0.085977 2.181322 8.276663</font></div><div><font size="2"> O 12.052554 2.671366 2.147199</font></div><div><font size="2"> O 12.250036 4.190930 12.092014</font></div><div><font size="2"> O 7.187422 0.959062 4.733469</font></div><div><font size="2"> O 8.346457 7.210040 4.667644</font></div><div><font size="2"> O 12.361546 11.527875 8.106887</font></div><div><font size="2"> O 3.299984 4.440816 9.193275</font></div><div><font size="2"> O 2.855829 3.759909 6.552815</font></div><div><font size="2"> O 1.392494 6.362753 0.586172</font></div><div><font size="2"> O 1.858645 8.694013 2.068738</font></div><div><font size="2"> O 3.770231 12.094519 8.652183</font></div><div><font size="2"> O 6.432508 3.669828 2.772418</font></div><div><font size="2"> O 1.998724 1.820217 4.876440</font></div><div><font size="2"> O 8.248581 2.404730 6.931303</font></div><div><font size="2"> O 5.753814 3.360029 12.461534</font></div><div><font size="2"> O 11.322212 5.649239 2.236798</font></div><div><font size="2"> O 4.277318 2.113956 10.590808</font></div><div><font size="2"> O 5.405015 3.349247 5.484702</font></div><div><font size="2"> O 6.493278 11.869958 0.684912</font></div><div><font size="2"> O 3.275250 2.346576 2.425241</font></div><div><font size="2"> O 7.981003 6.352512 7.507970</font></div><div><font size="2"> O 5.985990 6.512854 12.194648</font></div><div><font size="2"> O 10.636714 11.856872 12.209540</font></div><div><font size="2"> O 9.312283 3.670384 3.508594</font></div><div><font size="2"> O 1.106885 5.830301 6.638695</font></div><div><font size="2"> O 8.008007 3.326363 10.869818</font></div><div><font size="2"> O 12.403000 9.687405 11.761901</font></div><div><font size="2"> O 4.219782 7.085315 8.153470</font></div><div><font size="2"> O 3.781557 8.203821 11.563272</font></div><div><font size="2"> O 11.088898 4.532081 7.809475</font></div><div><font size="2"> O 10.387548 8.408890 1.017882</font></div><div><font size="2"> O 1.979016 6.418091 10.374159</font></div><div><font size="2"> O 4.660547 0.549666 5.617403</font></div><div><font size="2"> O 8.745880 12.256257 8.089383</font></div><div><font size="2"> O 2.662041 10.489890 0.092980</font></div><div><font size="2"> O 7.241661 10.471815 4.226946</font></div><div><font size="2"> O 2.276827 0.276647 10.810417</font></div><div><font size="2"> O 8.887733 0.946877 1.333885</font></div><div><font size="2"> O 1.943554 8.088552 7.567650</font></div><div><font size="2"> O 9.667942 8.056759 9.868847</font></div><div><font size="2"> O 10.905491 8.339638 6.484782</font></div><div><font size="2"> O 3.507733 4.862402 1.557439</font></div><div><font size="2"> O 8.010457 8.642846 12.055969</font></div><div><font size="2"> O 8.374446 10.035932 6.690309</font></div><div><font size="2"> O 5.635247 6.076875 5.563993</font></div><div><font size="2"> O 11.728434 1.601906 5.079475</font></div><div><font size="2"> O 9.771134 9.814114 3.548703</font></div><div><font size="2"> O 3.944355 10.563450 4.687536</font></div><div><font size="2"> O 0.890357 6.382287 4.065806</font></div><div><font size="2"> O 6.862447 6.425182 2.488202</font></div><div><font size="2"> O 3.813963 6.595122 3.762649</font></div><div><font size="2"> O 6.562448 8.295463 8.807182</font></div><div><font size="2"> O 9.809455 0.143325 3.886553</font></div><div><font size="2"> O 4.117074 11.661225 2.221679</font></div><div><font size="2"> O 5.295317 8.735561 2.763183</font></div><div><font size="2"> O 9.971999 5.379339 5.340378</font></div><div><font size="2"> O 12.254708 8.643874 3.957116</font></div><div><font size="2"> O 2.344274 10.761274 6.829162</font></div><div><font size="2"> O 7.013416 0.643488 10.518797</font></div><div><font size="2"> O 5.152349 10.233624 10.359388</font></div><div><font size="2"> O 11.184278 5.884064 10.298279</font></div><div><font size="2"> O 12.252335 8.974142 9.070831</font></div><div><font size="2"> H 12.415139 2.233125 11.257611</font></div><div><font size="2"> H 11.922476 1.573799 9.986994</font></div><div><font size="2"> H 5.608192 3.371543 8.971482</font></div><div><font size="2"> H 6.731226 3.060851 8.004962</font></div><div><font size="2"> H -0.169205 1.565594 7.589645</font></div><div><font size="2"> H -0.455440 2.954771 8.118939</font></div><div><font size="2"> H 12.125168 2.826463 1.205443</font></div><div><font size="2"> H 12.888828 2.969761 2.504745</font></div><div><font size="2"> H 11.553255 4.386613 11.465566</font></div><div><font size="2"> H 12.818281 4.960808 12.067151</font></div><div><font size="2"> H 7.049495 1.772344 4.247898</font></div><div><font size="2"> H 6.353019 0.798145 5.174047</font></div><div><font size="2"> H 7.781850 7.384852 5.420566</font></div><div><font size="2"> H 9.103203 6.754017 5.035898</font></div><div><font size="2"> H 12.771232 11.788645 8.931744</font></div><div><font size="2"> H 12.018035 10.650652 8.276334</font></div><div><font size="2"> H 3.557245 3.792529 9.848846</font></div><div><font size="2"> H 2.543844 4.884102 9.577958</font></div><div><font size="2"> H 2.320235 4.521250 6.329813</font></div><div><font size="2"> H 2.872128 3.749963 7.509824</font></div><div><font size="2"> H 1.209685 7.121391 1.140501</font></div><div><font size="2"> H 2.238885 6.038801 0.894245</font></div><div><font size="2"> H 2.763109 8.856353 2.336735</font></div><div><font size="2"> H 1.329379 9.047369 2.783755</font></div><div><font size="2"> H 4.315639 11.533388 9.203449</font></div><div><font size="2"> H 3.098742 12.433043 9.244412</font></div><div><font size="2"> H 5.987369 3.448974 3.590530</font></div><div><font size="2"> H 5.813096 3.419344 2.086985</font></div><div><font size="2"> H 1.057126 1.675344 4.969379</font></div><div><font size="2"> H 2.248496 2.292119 5.670892</font></div><div><font size="2"> H 8.508264 1.653337 7.464411</font></div><div><font size="2"> H 8.066015 2.034597 6.067646</font></div><div><font size="2"> H 5.197835 2.915542 11.821572</font></div><div><font size="2"> H 6.630900 3.329981 12.079371</font></div><div><font size="2"> H 10.788986 6.436672 2.127933</font></div><div><font size="2"> H 11.657923 5.463602 1.359832</font></div><div><font size="2"> H 3.544476 1.634958 10.977765</font></div><div><font size="2"> H 4.755770 1.455054 10.087655</font></div><div><font size="2"> H 4.465371 3.375459 5.665294</font></div><div><font size="2"> H 5.682663 4.264430 5.524498</font></div><div><font size="2"> H 6.174815 11.778676 1.582954</font></div><div><font size="2"> H 5.713640 12.089924 0.174999</font></div><div><font size="2"> H 3.476076 1.498708 2.028983</font></div><div><font size="2"> H 2.730229 2.134295 3.182949</font></div><div><font size="2"> H 7.119624 5.936450 7.474030</font></div><div><font size="2"> H 8.536492 5.799405 6.958665</font></div><div><font size="2"> H 5.909499 5.717477 11.667621</font></div><div><font size="2"> H 6.125402 6.196758 13.087330</font></div><div><font size="2"> H 11.203499 12.513536 11.804844</font></div><div><font size="2"> H 10.260930 12.300153 12.970145</font></div><div><font size="2"> H 9.985036 3.927685 2.878172</font></div><div><font size="2"> H 8.545584 3.468329 2.972331</font></div><div><font size="2"> H 1.399882 6.620092 7.093246</font></div><div><font size="2"> H 0.963561 6.112523 5.735345</font></div><div><font size="2"> H 8.067363 3.674002 9.979955</font></div><div><font size="2"> H 8.000737 2.375959 10.756190</font></div><div><font size="2"> H 11.821629 10.402510 12.020482</font></div><div><font size="2"> H 12.206854 8.983242 12.379892</font></div><div><font size="2"> H 3.461473 7.606485 7.889688</font></div><div><font size="2"> H 3.844478 6.304711 8.560946</font></div><div><font size="2"> H 3.179884 7.585614 11.148494</font></div><div><font size="2"> H 4.401957 7.652030 12.039573</font></div><div><font size="2"> H 11.573777 5.053211 7.169515</font></div><div><font size="2"> H 10.342076 4.186083 7.320831</font></div><div><font size="2"> H 10.065640 8.919194 1.760981</font></div><div><font size="2"> H 9.629585 8.322499 0.439729</font></div><div><font size="2"> H 1.396302 6.546079 9.625630</font></div><div><font size="2"> H 1.405516 6.479759 11.138049</font></div><div><font size="2"> H 4.024008 1.232518 5.405828</font></div><div><font size="2"> H 4.736858 0.579881 6.571077</font></div><div><font size="2"> H 9.452293 12.313381 8.732772</font></div><div><font size="2"> H 8.976559 11.502788 7.545965</font></div><div><font size="2"> H 1.834701 10.012311 0.153462</font></div><div><font size="2"> H 3.295197 9.836403 -0.204175</font></div><div><font size="2"> H 7.056724 11.401702 4.095264</font></div><div><font size="2"> H 6.499038 10.020287 3.825865</font></div><div><font size="2"> H 1.365541 0.487338 11.013887</font></div><div><font size="2"> H 2.501591 -0.428131 11.417871</font></div><div><font size="2"> H 8.644279 1.812362 1.005409</font></div><div><font size="2"> H 8.142674 0.388030 1.112955</font></div><div><font size="2"> H 1.272659 8.365063 8.191888</font></div><div><font size="2"> H 2.142485 8.877768 7.063867</font></div><div><font size="2"> H 8.961493 7.826192 9.265523</font></div><div><font size="2"> H 9.227102 8.487654 10.601118</font></div><div><font size="2"> H 10.150144 7.758934 6.392768</font></div><div><font size="2"> H 10.596082 9.187988 6.167290</font></div><div><font size="2"> H 3.463106 4.096188 2.129414</font></div><div><font size="2"> H 3.919461 4.539801 0.755791</font></div><div><font size="2"> H 7.418998 9.394959 12.028876</font></div><div><font size="2"> H 7.430413 7.883095 12.106546</font></div><div><font size="2"> H 7.972905 10.220334 5.841196</font></div><div><font size="2"> H 7.675111 9.631498 7.203725</font></div><div><font size="2"> H 5.332446 6.381336 6.419473</font></div><div><font size="2"> H 5.000025 6.434186 4.943466</font></div><div><font size="2"> H 11.575078 2.271167 4.412540</font></div><div><font size="2"> H 11.219802 0.847030 4.783357</font></div><div><font size="2"> H 8.865342 9.721516 3.843998</font></div><div><font size="2"> H 10.000732 10.719285 3.758898</font></div><div><font size="2"> H 3.186196 10.476397 5.265333</font></div><div><font size="2"> H 4.407331 11.335128 5.013723</font></div><div><font size="2"> H 0.558187 7.255936 3.859331</font></div><div><font size="2"> H 0.341672 5.789383 3.552346</font></div><div><font size="2"> H 7.459933 6.526049 3.229193</font></div><div><font size="2"> H 6.696228 5.483739 2.440372</font></div><div><font size="2"> H 3.864872 6.313007 2.849385</font></div><div><font size="2"> H 2.876419 6.621201 3.953862</font></div><div><font size="2"> H 5.631529 8.079145 8.753997</font></div><div><font size="2"> H 7.003296 7.568245 8.367822</font></div><div><font size="2"> H 9.615413 0.527902 3.031755</font></div><div><font size="2"> H 8.962985 0.109366 4.332162</font></div><div><font size="2"> H 3.825854 11.139182 1.474087</font></div><div><font size="2"> H 4.063988 11.063232 2.967211</font></div><div><font size="2"> H 5.784391 7.914558 2.708486</font></div><div><font size="2"> H 4.780461 8.655167 3.566110</font></div><div><font size="2"> H 10.880659 5.444664 5.046607</font></div><div><font size="2"> H 9.593331 4.687991 4.797350</font></div><div><font size="2"> H 11.562317 8.960134 3.376765</font></div><div><font size="2"> H 11.926084 8.816948 4.839320</font></div><div><font size="2"> H 2.856874 11.297981 7.433660</font></div><div><font size="2"> H 1.492332 11.195517 6.786033</font></div><div><font size="2"> H 7.145820 0.090200 9.749009</font></div><div><font size="2"> H 7.227275 0.077690 11.260665</font></div><div><font size="2"> H 4.662021 9.538430 10.798155</font></div><div><font size="2"> H 5.994537 9.833472 10.142985</font></div><div><font size="2"> H 10.544299 6.595857 10.301445</font></div><div><font size="2"> H 11.281750 5.653082 9.374494</font></div><div><font size="2"> H 12.103020 8.841164 10.006916</font></div><div><font size="2"> H 11.491592 8.576221 8.647557</font></div><div><font size="2"> &END COORD</font></div><div><font size="2"> &KIND H</font></div><div><font size="2"> BASIS_SET TZV2P-GTH</font></div><div><font size="2"> POTENTIAL GTH-PADE-q1</font></div><div><font size="2"> &END KIND</font></div><div><font size="2"> &KIND O</font></div><div><font size="2"> BASIS_SET TZV2P-GTH</font></div><div><font size="2"> POTENTIAL GTH-PADE-q6</font></div><div><font size="2"> &END KIND</font></div><div><font size="2"> &END SUBSYS</font></div><div><font size="2">&END FORCE_EVAL</font></div><div><font size="2">&GLOBAL</font></div><div><font size="2"> PROJECT H2O-64</font></div><div><font size="2"> RUN_TYPE MD</font></div><div><font size="2"> PRINT_LEVEL LOW</font></div><div><font size="2"><br></font></div><div><font size="2"> &TIMINGS</font></div><div><font size="2"> THRESHOLD 0.000001</font></div><div><font size="2"> &END</font></div><div><font size="2"><br></font></div><div><font size="2">&END GLOBAL</font></div><div><font size="2">&MOTION</font></div><div><font size="2"> &MD</font></div><div><font size="2"> ENSEMBLE NVE</font></div><div><font size="2"> STEPS 10000000</font></div><div><font size="2"> TIMESTEP 0.5</font></div><div><font size="2"> TEMPERATURE 300.0</font></div><div><font size="2"> &END MD</font></div><div><font size="2">&END MOTION</font></div></div><div style="font-size:small"><div>########## H2O-64.inp, from example file ##################</div><div style="font-size:13px"></div></div><div style="font-size:small"><br></div><div style="font-size:small"><br></div><div style="font-size:small"><div>########## my input file, the memory usage for <span>cp2k</span> is increased with time<b> </b>##################</div><div><div>########## the system is bulk water + one Cl ion ##################</div><div><br></div></div><div style="font-size:13px"></div></div><div style="font-size:small"><br></div><div><div><font size="2">@SET SYSTEM Bulk</font></div><div><font size="2"><br></font></div><div><font size="2">&GLOBAL</font></div><div><font size="2"> PROJECT ${SYSTEM}</font></div><div><font size="2"> RUN_TYPE MD </font></div><div><font size="2"> PRINT_LEVEL low</font></div><div><font size="2"> EXTENDED_FFT_LENGTHS T</font></div><div><font size="2">&END GLOBAL</font></div><div><font size="2"><br></font></div><div><font size="2">&FORCE_EVAL</font></div><div><font size="2"> ! the electronic structure part of CP2K is named Quickstep</font></div><div><font size="2"> METHOD Quickstep</font></div><div><font size="2"> STRESS_TENSOR ANALYTICAL</font></div><div><font size="2"> &DFT</font></div><div><font size="2"> ! basis sets and pseudopotential files can be found in cp2k/data</font></div><div><font size="2"> BASIS_SET_FILE_NAME ./GTH_BASIS_SETS </font></div><div><font size="2"> POTENTIAL_FILE_NAME ./POTENTIAL </font></div><div><font size="2"> WFN_RESTART_FILE_NAME ./${SYSTEM}-RESTART.wfn</font></div><div><font size="2"><br></font></div><div><font size="2"> ! Charge and multiplicity</font></div><div><font size="2"> CHARGE -1</font></div><div><font size="2"># LSD </font></div><div><font size="2"># MULTIPLICITY 1</font></div><div><font size="2"># <span style="white-space:pre-wrap"> </span>Two times the total spin plus one. Specify 3 for a triplet, 4 for a quartet, and so on. </font></div><div><font size="2">#<span style="white-space:pre-wrap"> </span>Default is 1 (singlet) for an even number and 2 (doublet) for an odd number of electrons.</font></div><div><font size="2">#</font></div><div><font size="2"><br></font></div><div><font size="2"> &MGRID</font></div><div><font size="2"> ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect.</font></div><div><font size="2"> ! certain calculations (e.g. geometry optimization, vibrational frequencies,</font></div><div><font size="2"> ! NPT and cell optimizations, need higher cutoffs)</font></div><div><font size="2"> CUTOFF [Ry] 500 </font></div><div><font size="2"> ##REL_CUTOFF [Ry] 50</font></div><div><font size="2"> &END</font></div><div><font size="2"><br></font></div><div><font size="2"> &QS</font></div><div><font size="2"> ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme).</font></div><div><font size="2"> METHOD GPW </font></div><div><font size="2"> ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron,</font></div><div><font size="2"> ! sets reasonable values for all other thresholds.</font></div><div><font size="2"> EPS_DEFAULT 1.0E-10 </font></div><div><font size="2"> ! used for MD, the method used to generate the initial guess.</font></div><div><font size="2"> MAP_CONSISTENT TRUE</font></div><div><font size="2"> EXTRAPOLATION ASPC </font></div><div><font size="2"> EXTRAPOLATION_ORDER 4</font></div><div><font size="2"> &END</font></div><div><font size="2"><br></font></div><div><font size="2"> &POISSON</font></div><div><font size="2"> PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver</font></div><div><font size="2"> &END</font></div><div><font size="2"><br></font></div><div><font size="2"> &PRINT</font></div><div><font size="2"> ! output atomic charge</font></div><div><font size="2"> &MULLIKEN </font></div><div><font size="2"> FILENAME ${SYSTEM}</font></div><div><font size="2"> &EACH</font></div><div><font size="2"> <span style="white-space:pre-wrap"> </span> MD 10</font></div><div><font size="2"> &END EACH</font></div><div><font size="2"> &END MULLIKEN</font></div><div><font size="2"> ! output others </font></div><div><font size="2"> &END</font></div><div><font size="2"><br></font></div><div><font size="2"> ! use the OT METHOD for robust and efficient SCF, suitable for all non-metallic systems.</font></div><div><font size="2"> &SCF </font></div><div><font size="2"> SCF_GUESS RESTART #ATOMIC ! can be used to RESTART an interrupted calculation</font></div><div><font size="2"> MAX_SCF 1000</font></div><div><font size="2"> EPS_SCF 1.0E-7 #1.0E-7 ! accuracy of the SCF procedure typically 1.0E-6 - 1.0E-7</font></div><div><font size="2"> &OUTER_SCF ! repeat the inner SCF cycle 10 times</font></div><div><font size="2"> MAX_SCF 10</font></div><div><font size="2"> EPS_SCF 1.0E-7 #1.0E-7 ! must match the above</font></div><div><font size="2"> &END</font></div><div><font size="2">####### for OT #######</font></div><div><font size="2"> CHOLESKY OFF</font></div><div><font size="2"> &OT</font></div><div><font size="2"> #CHOLESKY OFF</font></div><div><font size="2"> ! an accurate preconditioner suitable also for larger systems</font></div><div><font size="2"> PRECONDITIONER FULL_ALL</font></div><div><font size="2"> ! the most robust choice (DIIS might sometimes be faster, but not as stable).</font></div><div><font size="2"> MINIMIZER DIIS ## CG</font></div><div><font size="2"> N_DIIS 5</font></div><div><font size="2"><span style="white-space:pre-wrap"> </span>ENERGY_GAP 1.0E-5</font></div><div><font size="2"> &END OT</font></div><div><font size="2"><br></font></div><div><font size="2">###### for diagonalization #######</font></div><div><font size="2"># ADDED_MOS 100</font></div><div><font size="2"># CHOLESKY OFF #INVERSE</font></div><div><font size="2"># &SMEAR ON</font></div><div><font size="2"># METHOD FERMI_DIRAC</font></div><div><font size="2"># ELECTRONIC_TEMPERATURE [K] 300</font></div><div><font size="2"># &END SMEAR</font></div><div><font size="2"># &DIAGONALIZATION</font></div><div><font size="2"># ALGORITHM STANDARD</font></div><div><font size="2"># EPS_ADAPT 0.01</font></div><div><font size="2"># &END DIAGONALIZATION</font></div><div><font size="2"><br></font></div><div><font size="2"> &MIXING</font></div><div><font size="2"> METHOD BROYDEN_MIXING</font></div><div><font size="2"> ALPHA 0.2</font></div><div><font size="2"> BETA 1.5</font></div><div><font size="2"> NBROYDEN 8</font></div><div><font size="2"> &END MIXING</font></div><div><font size="2"><br></font></div><div><font size="2"> &END SCF</font></div><div><font size="2"><br></font></div><div><font size="2"> ! specify the exchange and correlation treatment</font></div><div><font size="2"> &XC</font></div><div><font size="2"> ! use a PBE functional </font></div><div><font size="2"> &XC_FUNCTIONAL PBE </font></div><div><font size="2"> &PBE</font></div><div><font size="2"> PARAMETRIZATION revPBE</font></div><div><font size="2"> #SCALE_C 0.0</font></div><div><font size="2"> &END PBE</font></div><div><font size="2"> &VWN</font></div><div><font size="2"> &END VWN</font></div><div><font size="2"> &END XC_FUNCTIONAL</font></div><div><font size="2"> ! adding Grimme's D3 correction (by default without C9 terms) </font></div><div><font size="2"> &VDW_POTENTIAL</font></div><div><font size="2"> POTENTIAL_TYPE PAIR_POTENTIAL </font></div><div><font size="2"> &PAIR_POTENTIAL</font></div><div><font size="2"> TYPE DFTD3</font></div><div><font size="2"> #CALCULATE_C9_TERM T</font></div><div><font size="2"> #REFEREBCE_C9_TERM T</font></div><div><font size="2"> #LONG_RANGE_CORRECTION T</font></div><div><font size="2"><span style="white-space:pre-wrap"> </span> PARAMETER_FILE_NAME dftd3.dat</font></div><div><font size="2"> REFERENCE_FUNCTIONAL revPBE</font></div><div><font size="2"> R_CUTOFF [angstrom] 11</font></div><div><font size="2"> &END</font></div><div><font size="2"> &END VDW_POTENTIAL</font></div><div><font size="2"> &END XC</font></div><div><font size="2"> &END DFT</font></div><div><font size="2"> </font></div><div><font size="2"> ! description of the system</font></div><div><font size="2"> &SUBSYS</font></div><div><font size="2"> &CELL </font></div><div><font size="2"> ! unit cells that are orthorhombic are more efficient with CP2K</font></div><div><font size="2"> ABC [angstrom] 12.42 12.42 12.42</font></div><div><font size="2"> &END CELL</font></div><div><font size="2"><br></font></div><div><font size="2"> ! atom coordinates can be in the &COORD section,</font></div><div><font size="2"> ! or provided as an external file.</font></div><div><font size="2"># &TOPOLOGY</font></div><div><font size="2"># COORD_FILE_NAME Na.xyz</font></div><div><font size="2"># COORD_FILE_FORMAT XYZ</font></div><div><font size="2"># &END</font></div><div><font size="2"><br></font></div><div><font size="2"> ! MOLOPT basis sets are fairly costly,</font></div><div><font size="2"> ! but in the 'DZVP-MOLOPT-SR-GTH' available for all elements</font></div><div><font size="2"> ! their contracted nature makes them suitable</font></div><div><font size="2"> ! for condensed and gas phase systems alike.</font></div><div><font size="2"><br></font></div><div><font size="2"> &KIND C</font></div><div><font size="2"> BASIS_SET DZVP-MOLOPT-SR-GTH ## TZV2P-GTH </font></div><div><font size="2"> POTENTIAL GTH-PBE</font></div><div><font size="2"> &END KIND</font></div><div><font size="2"> &KIND O</font></div><div><font size="2"> BASIS_SET DZVP-MOLOPT-SR-GTH ## TZV2P-GTH ###DZVP-GTH-PBE</font></div><div><font size="2"> POTENTIAL GTH-PBE-q6</font></div><div><font size="2"> &END KIND</font></div><div><font size="2"> &KIND H</font></div><div><font size="2"> BASIS_SET DZVP-MOLOPT-SR-GTH ## TZV2P-GTH ##DZVP-GTH-PBE</font></div><div><font size="2"> POTENTIAL GTH-PBE-q1</font></div><div><font size="2"> &END KIND</font></div><div><font size="2"> &KIND Cl</font></div><div><font size="2"> BASIS_SET DZVP-MOLOPT-SR-GTH ## TZV2P-GTH ##DZVP-GTH-PBE</font></div><div><font size="2"> POTENTIAL GTH-PBE-q7</font></div><div><font size="2"> &END KIND</font></div><div><font size="2"><br></font></div><div><font size="2"> &END SUBSYS</font></div><div><font size="2">&END FORCE_EVAL</font></div><div><font size="2"><br></font></div><div><font size="2">! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section</font></div><div><font size="2">&MOTION</font></div><div><font size="2"> &MD</font></div><div><font size="2"> ENSEMBLE NVT ! sampling the canonical ensemble, accurate properties might need NVE</font></div><div><font size="2"> TEMPERATURE [K] 330</font></div><div><font size="2"> TIMESTEP [fs] 0.5</font></div><div><font size="2"> STEPS 40000 # 20 ps </font></div><div><font size="2"># COMVEL_TOL 0.00001</font></div><div><font size="2"><br></font></div><div><font size="2"> &THERMOSTAT</font></div><div><font size="2"> # REGION MOLECULE</font></div><div><font size="2"> # REGION GLOBAL</font></div><div><font size="2"> # REGION MASSIVE</font></div><div><font size="2"> TYPE NOSE</font></div><div><font size="2"> &NOSE</font></div><div><font size="2"> LENGTH 4 # CPMD</font></div><div><font size="2"> YOSHIDA 9 # 3 5 7 9 15 25 125#</font></div><div><font size="2"> TIMECON 100</font></div><div><font size="2"> MTS 2</font></div><div><font size="2"> &END NOSE</font></div><div><font size="2"> &END THERMOSTAT</font></div><div><font size="2"><br></font></div><div><font size="2"> &END MD</font></div><div><font size="2"># &CONSTRAINT</font></div><div><font size="2"># &FIXED_ATOMS</font></div><div><font size="2"># COMPONENTS_TO_FIX XYZ</font></div><div><font size="2"># LIST 1..120</font></div><div><font size="2"># &END FIXED_ATOMS</font></div><div><font size="2"># &END CONSTRAINT</font></div><div><font size="2"><br></font></div><div><font size="2"><br></font></div><div><font size="2"> &PRINT</font></div><div><font size="2"> &TRAJECTORY</font></div><div><font size="2"> &EACH</font></div><div><font size="2"> MD 1</font></div><div><font size="2"> &END EACH</font></div><div><font size="2"> FORMAT XYZ</font></div><div><font size="2"> &END TRAJECTORY</font></div><div><font size="2"> &VELOCITIES</font></div><div><font size="2"> &EACH</font></div><div><font size="2"> MD 1</font></div><div><font size="2"> &END EACH</font></div><div><font size="2"> FORMAT XYZ</font></div><div><font size="2"> &END VELOCITIES</font></div><div><font size="2"> &FORCES</font></div><div><font size="2"> &EACH</font></div><div><font size="2"> MD 5</font></div><div><font size="2"> &END EACH</font></div><div><font size="2"> &END FORCES</font></div><div><font size="2"> &RESTART</font></div><div><font size="2"> &EACH</font></div><div><font size="2"> MD 20</font></div><div><font size="2"> &END</font></div><div><font size="2"> &END</font></div><div><font size="2"><br></font></div><div><font size="2"><br></font></div><div><font size="2"> &MIXED_ENERGIES</font></div><div><font size="2"> &EACH</font></div><div><font size="2"> MD 5</font></div><div><font size="2"> &END EACH</font></div><div><font size="2"> &END MIXED_ENERGIES</font></div><div><font size="2"><br></font></div><div><font size="2"><br></font></div><div><font size="2"> </font></div><div><font size="2"> &CELL</font></div><div><font size="2"> &EACH</font></div><div><font size="2"> MD 1</font></div><div><font size="2"> &END EACH</font></div><div><font size="2"> &END CELL</font></div><div><font size="2"><br></font></div><div><font size="2"> &STRESS</font></div><div><font size="2"> &EACH </font></div><div><font size="2"> MD 10</font></div><div><font size="2"> &END EACH</font></div><div><font size="2"> &END STRESS</font></div><div><font size="2"><br></font></div><div><font size="2"> &RESTART_HISTORY</font></div><div><font size="2"> &EACH</font></div><div><font size="2"> MD 50</font></div><div><font size="2"> &END EACH</font></div><div><font size="2"> &END RESTART_HISTORY</font></div><div><font size="2"><br></font></div><div><font size="2"> &END PRINT</font></div><div><font size="2">&END MOTION</font></div><div><font size="2"><br></font></div><div><font size="2">&EXT_RESTART</font></div><div><font size="2"> RESTART_FILE_NAME ./Bulk-1.restart</font></div><div><font size="2"> RESTART_POS</font></div><div><font size="2"> RESTART_VEL</font></div><div><font size="2"> RESTART_CELL</font></div><div><font size="2"> RESTART_CONSTRAINT F</font></div><div><font size="2">&END EXT_RESTART</font></div></div><div style="font-size:small"><div><div>########## my input file, the memory usage for <span>cp2k</span> is increased with time<b> </b>##################</div><div style="font-size:13px"></div></div><div><br></div></div><div style="font-size:small"><br></div></div></div></blockquote></div></div> <p></p> -- <br> You received this message because you are subscribed to a topic in the Google Groups "cp2k" group.<br> To unsubscribe from this topic, visit <a href="https://groups.google.com/d/topic/cp2k/UqBT61dIsi8/unsubscribe" target="_blank">https://groups.google.com/d/topic/cp2k/UqBT61dIsi8/unsubscribe</a>.<br> To unsubscribe from this group and all its topics, send an email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/c496f4ee-8767-44f2-9c01-c0e3b1b92d7e%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/c496f4ee-8767-44f2-9c01-c0e3b1b92d7e%40googlegroups.com</a>.<br> </blockquote></div>