<div dir="ltr">Dear Wu,<div><br></div><div>it would help if you sent you output, clarified the code version and the environment you used for you job. I does not look like a bug.</div><div><br></div><div>Yours,</div><div><br></div><div>Vladimir<br><br>среда, 17 июля 2019 г., 15:34:08 UTC+2 пользователь Peiyao Wu написал:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">







<p><span><font face="trebuchet ms, sans-serif">I'm trying to run a first principle MD for a box with nitrogen and zeolite (structure with xyz coordinate). The job started running with no error message and terminate in about five minutes with "OT -----killed-----". What are some things that might be wrong in my input file? </font></span></p><p><span><br></span></p><p><span>&GLOBAL</span></p>
<p><span><span>  </span>PROJECT MOF</span></p>
<p><span><span>  </span>RUN_TYPE MD</span></p>
<p><span><span>  </span>! limit the runs to 5min</span></p>
<p><span><span>  </span>WALLTIME</span></p>
<p><span><span>  </span>! reduce the amount of IO</span></p>
<p><span><span>  </span>IOLEVEL<span>  </span>LOW</span></p>
<p><span>&END GLOBAL</span></p>
<p><span></span><br></p>
<p><span>&FORCE_EVAL</span></p>
<p><span><span> </span>METHOD QS</span></p>
<p><span><span> </span>!STRESS_TENSOR DIAGONAL_NUMERICAL</span></p>
<p><span><span> </span>&DFT</span></p>
<p><span><span>  </span>BASIS_SET_FILE_NAME ~/cp2k/data/BASIS_MOLOPT</span></p>
<p><span><span>  </span>POTENTIAL_FILE_NAME ~/cp2k/data/GTH_POTENTIALS</span></p>
<p><span><span>  </span>&MGRID</span></p>
<p><span><span>   </span>CUTOFF 300</span></p>
<p><span><span>   </span>NGRIDS 5</span></p>
<p><span><span>  </span>&END</span></p>
<p><span><span>  </span>&QS</span></p>
<p><span><span>   </span>METHOD GPW</span></p>
<p><span><span>   </span>EPS_DEFAULT 1.0E-10</span></p>
<p><span><span>   </span>EXTRAPOLATION ASPC</span></p>
<p><span><span>  </span>&END QS</span></p>
<p><span><span>  </span>&POISSON</span></p>
<p><span><span>   </span>PERIODIC XYZ</span></p>
<p><span><span>  </span>&END</span></p>
<p><span></span><br></p>
<p><span><span>  </span>&SCF</span></p>
<p><span><span>   </span>EPS_SCF 1.0E-6</span></p>
<p><span><span>   </span>SCF_GUESS ATOMIC</span></p>
<p><span><span>   </span>MAX_SCF 20</span></p>
<p><span><span>   </span>&OT</span></p>
<p><span><span>    </span>MINIMIZER DIIS</span></p>
<p><span><span>    </span>PRECONDITIONER FULL_KINETIC</span></p>
<p><span><span>   </span>&END OT</span></p>
<p><span><span>   </span>&OUTER_SCF</span></p>
<p><span><span>    </span>EPS_SCF 1.0E-6</span></p>
<p><span><span>    </span>MAX_SCF 10</span></p>
<p><span><span>   </span>&END OUTER_SCF</span></p>
<p><span><span>  </span>&END SCF</span></p>
<p><span><span>  </span>&XC</span></p>
<p><span><span>   </span>&XC_FUNCTIONAL PBE</span></p><p><span><span>   </span>&END</span></p><p><span><span>   </span>&VDW_POTENTIAL</span></p><p><span><span>    </span>POTENTIAL_TYPE PAIR_POTENTIAL</span></p><p><span><span>    </span>&PAIR_POTENTIAL</span></p><p><span><span>     </span>TYPE DFTD3</span></p><p><span><span>     </span>REFERENCE_C9_TERM .TRUE.</span></p><p><span><span>     </span>LONG_RANGE_CORRECTION .TRUE.</span></p><p><span><span>     </span>PARAMETER_FILE_NAME dftd3.dat</span></p><p><span><span>     </span>REFERENCE_FUNCTIONAL PBE</span></p><p><span><span>     </span>R_CUTOFF [angstrom] 10.0</span></p><p><span><span>     </span>EPS_CN 1.0E-6</span></p><p><span><span>    </span>&END PAIR_POTENTIAL</span></p><p><span><span>   </span>&END VDW_POTENTIAL</span></p><p><span><span>  </span>&END XC</span></p><p><span><span> </span>&END DFT</span></p><p><span><span> </span>&SUBSYS</span></p><p><span><span>  </span>&CELL</span></p><p><span><span>   </span>ABC 24.188 24.188 24.188</span></p><p><span><span>   </span>ALPHA_BETA_GAMMA 90.0 90.0 90.0</span></p><p><span><span>  </span>&END CELL</span></p><p><span><span>  </span>&COORD</span></p><p><span><span>   </span>@INCLUDE <a href="http://box1config.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fbox1config.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHLZt6ODgU62pX4Vp8-j2CWm-6AdQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fbox1config.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHLZt6ODgU62pX4Vp8-j2CWm-6AdQ';return true;">box1config.xyz</a></span></p><p><span><span>  </span>&END COORD</span></p><p><span><span>  </span>&KIND Si</span></p><p><span><span>   </span>BASIS_SET DZVP-MOLOPT-SR-GTH</span></p><p><span><span>   </span>POTENTIAL GTH-PBE-q4</span></p><p><span><span>  </span>&END KIND</span></p><p><span><span>  </span>&KIND Al</span></p><p><span><span>   </span>BASIS_SET DZVP-MOLOPT-SR-GTH</span></p><p><span><span>   </span>POTENTIAL GTH-PBE-q3</span></p><p><span><span>  </span>&END KIND</span></p><p><span><span>  </span>&KIND O</span></p><p><span><span>   </span>BASIS_SET DZVP-MOLOPT-SR-GTH</span></p><p><span><span>   </span>POTENTIAL GTH-PBE-q6</span></p><p><span><span>   </span>ELEMENT O</span></p><p><span><span>  </span>&END KIND</span></p><p><span><span>  </span>&KIND Ca</span></p><p><span><span>   </span>BASIS_SET DZVP-MOLOPT-SR-GTH</span></p><p><span><span>   </span>POTENTIAL GTH-PBE-q10</span></p><p><span><span>  </span>&END KIND</span></p><p><span><span>  </span>&KIND N</span></p><p><span><span>   </span>BASIS_SET DZVP-MOLOPT-SR-GTH</span></p><p><span>

















































</span></p><p><span><span>   </span>POTENTIAL GTH-PBE-q5</span></p><p><span><span>  </span>&END KIND</span></p><p><span><span> </span>&END SUBSYS</span></p><p><span>&END FORCE_EVAL</span></p><p><span></span><br></p><p><span>&MOTION</span></p><p><span><span> </span>&GEO_OPT</span></p><p><span><span>   </span>OPTIMIZER LBFGS ! Good choice for 'small' systems (use LBFGS for large systems)</span></p><p><span><span>   </span>MAX_ITER<span>  </span>100</span></p><p><span><span>   </span>MAX_DR<span>    </span>[bohr] 0.003 ! adjust target as needed</span></p><p><span><span>   </span>&LBFGS</span></p><p><span><span>   </span>&END</span></p><p><span><span> </span>&END</span></p><p><span><span> </span>&MD</span></p><p><span><span>   </span>ENSEMBLE NVT<span>  </span>! sampling the canonical ensemble, accurate properties might need NVE</span></p><p><span><span>   </span>TEMPERATURE [K] 77.0</span></p><p><span><span>   </span>TIMESTEP [fs] 0.5</span></p><p><span><span>   </span>STEPS 100</span></p><p><span><span>   </span># GLE thermostat as generated at <a href="http://epfl-cosmo.github.io/gle4md" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fepfl-cosmo.github.io%2Fgle4md\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFTPPvBlKuANngeLG-fs7SSHzZUtQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fepfl-cosmo.github.io%2Fgle4md\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFTPPvBlKuANngeLG-fs7SSHzZUtQ';return true;">http://epfl-cosmo.github.io/<wbr>gle4md</a></span></p><p><span><span>   </span># GLE provides an effective NVT sampling.</span></p><p><span><span>   </span>&THERMOSTAT</span></p><p><span><span>     </span>TYPE NOSE</span></p><p><span><span>     </span>REGION MASSIVE</span></p><p><span><span>     </span>&NOSE</span></p><p><span><span>       </span>LENGTH 3</span></p><p><span><span>       </span>YOSHIDA 3</span></p><p><span><span>       </span>TIMECON [wavenumber_t] 1000.0</span></p><p><span><span>       </span>MTS 2</span></p><p><span><span>     </span>&END NOSE</span></p><p><span><span>    </span>&END THERMOSTAT</span></p><p><span><span> </span>&END</span></p><p><span><span>  </span>&PRINT</span></p><p><span><span>   </span>&TRAJECTORY</span></p><p><span><span>     </span>&EACH</span></p><p><span><span>       </span>MD 1</span></p><p><span><span>     </span>&END EACH</span></p><p><span><span>   </span>&END TRAJECTORY</span></p><p><span><span>   </span>&VELOCITIES OFF</span></p><p><span><span>   </span>&END VELOCITIES</span></p><p><span>













































</span></p><p><span><span>   </span>&FORCES OFF</span></p><p><span><span>   </span>&END FORCES</span></p><p><span><span>   </span>&</span><span>RESTART</span><span>_HISTORY</span></p><p><span><span>     </span>&EACH</span></p><p><span><span>       </span>MD 500</span></p><p><span><span>     </span>&END EACH</span></p><p><span><span>   </span>&END </span><span>RESTART</span><span>_HISTORY</span></p><p><span><span>   </span>&</span><span>RESTART</span></p><p><span><span>     </span>BACKUP_COPIES 3</span></p><p><span><span>     </span>&EACH</span></p><p><span><span>       </span>MD 1</span></p><p><span><span>     </span>&END EACH</span></p><p><span><span>   </span>&END </span><span>RESTART</span></p><p><span><span>  </span>&END PRINT</span></p><p><span>




















</span></p><p><span>&END MOTION</span></p><p><span><br></span></p><p><span><br></span></p><p><span><br></span></p><p><span><br></span></p></div></blockquote></div></div>