<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">WIthout entering in the details of the input and looking only at the plots you sent, all is normal.. <div>I wonder what you consider strange..<div><br><div><div>On Sep 26, 2013, at 7:01 AM, Bonakala Satyanarayana <<a href="mailto:satyanaray...@gmail.com">satyanaray...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Dear <span style="font-family:arial,sans-serif;font-size:13px;font-weight:bold;white-space:nowrap">Marcella Iannuzzi,</span><div><span style="font-family:arial,sans-serif;font-size:13px;font-weight:bold;white-space:nowrap"> </span><font face="arial, sans-serif"><span style="white-space:nowrap">I performed NVT simulations to the same input what I have prescribed for previous post ( NPT simulation). I ran 80 fs, however I found some of strange behaviors in temperature, Stress tensor determinant and total energy. I enclosed corresponding plots and input file. </span></font><span style="white-space:nowrap;font-family:arial,sans-serif"> Could you please suggest me where I made mistake. </span></div>
<div><span style="white-space:nowrap;font-family:arial,sans-serif"><br></span></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &FORCE_EVAL</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> METHOD Quickstep</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"><br></span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &DFT</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> BASIS_SET_FILE_NAME /home1/bala/cp2k/tests/QS/BASIS_MOLOPT</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> POTENTIAL_FILE_NAME /home1/bala/cp2k/tests/QS/GTH_POTENTIALS</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> CHARGE = 0</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &MGRID</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> CUTOFF 350</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> NGRIDS 5</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> REL_CUTOFF 50 </span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END MGRID</span></font></div><div>
<font face="arial, sans-serif"><span style="white-space:nowrap"> &QS</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> METHOD GPW</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> EPS_DEFAULT 1.0E-11</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END QS</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &SCF</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> SCF_GUESS RESTART </span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> EPS_SCF 1.0E-7</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> MAX_SCF 50 </span></font></div><div>
<font face="arial, sans-serif"><span style="white-space:nowrap"> CHOLESKY OFF</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &OT </span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> MINIMIZER DIIS </span></font></div><div>
<font face="arial, sans-serif"><span style="white-space:nowrap"> PRECONDITIONER FULL_ALL</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> ENERGY_GAP 0.001</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"># STEPSIZE 0.05</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END OT</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &OUTER_SCF</span></font></div><div>
<font face="arial, sans-serif"><span style="white-space:nowrap"> EPS_SCF 1E-7</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> MAX_SCF 150</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END OUTER_SCF </span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END SCF</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &XC</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &XC_FUNCTIONAL PBE</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END XC_FUNCTIONAL</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &vDW_POTENTIAL</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> POTENTIAL_TYPE PAIR_POTENTIAL</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &PAIR_POTENTIAL</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> TYPE DFTD3</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> PARAMETER_FILE_NAME /home1/bala/cp2k/tests/QS/dftd3.dat</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> REFERENCE_FUNCTIONAL PBE</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> REFERENCE_C9_TERM .TRUE.</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> CALCULATE_C9_TERM .TRUE. </span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> R_CUTOFF 25.0</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END PAIR_POTENTIAL</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END vDW_POTENTIAL</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &XC_GRID</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> XC_DERIV SPLINE2</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> XC_SMOOTH_RHO NN50</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END XC_GRID</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END XC</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END DFT</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"><br>
</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &SUBSYS</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &CELL</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> ABC 21.8620 16.2099 43.6020</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> ALPHA_BETA_GAMMA 90.0 92.7540 90.0</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &CELL_REF</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> ABC 22.8620 17.2099 44.6020</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> ALPHA_BETA_GAMMA 90.0 126.0 90.0</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END CELL_REF</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> </span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END CELL</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"><br>
</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &COORD</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> @INCLUDE coor.xyz </span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END COORD</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"><br></span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &KIND H</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> BASIS_SET DZVP-MOLOPT-SR-GTH</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> POTENTIAL GTH-PBE-q1</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END KIND</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"><br></span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &KIND C</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> BASIS_SET DZVP-MOLOPT-SR-GTH</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> POTENTIAL GTH-PBE-q4</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END KIND</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"><br></span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &KIND N</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> BASIS_SET DZVP-MOLOPT-SR-GTH</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> POTENTIAL GTH-PBE-q5</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END KIND</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &KIND O</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> BASIS_SET DZVP-MOLOPT-SR-GTH</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> POTENTIAL GTH-PBE-q6</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END KIND</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"><br></span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &KIND Fe</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> BASIS_SET DZVP-MOLOPT-SR-GTH</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> POTENTIAL GTH-PBE-q16</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END KIND</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &KIND Zn</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> BASIS_SET DZVP-MOLOPT-SR-GTH</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> POTENTIAL GTH-PBE-q12</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END KIND</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"><br></span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &KIND Cd</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> BASIS_SET DZVP-MOLOPT-SR-GTH</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> POTENTIAL GTH-PBE-q12</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END KIND</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END SUBSYS</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> STRESS_TENSOR ANALYTICAL</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap">&END FORCE_EVAL</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"><br></span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap">&GLOBAL</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> PROJECT OUT-GEO-OPT</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> RUN_TYPE MD</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> PRINT_LEVEL MEDIUM</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap">&END GLOBAL</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"><br></span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap">&MOTION</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &MD</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> ENSEMBLE NVT</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> STEPS 10000</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> TIMESTEP 0.5</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> TEMPERATURE 195.0</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &BAROSTAT</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> PRESSURE 1.0</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> TIMECON [wavenumber_t] 4000.</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &THERMOSTAT</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> TYPE CSVR</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END THERMOSTAT</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END BAROSTAT</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &THERMOSTAT</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> TYPE NOSE</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> REGION GLOBAL</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &NOSE</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> TIMECON [wavenumber_t] 4000.0</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> LENGTH 3</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> YOSHIDA 3</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> MTS 2</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END NOSE</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END THERMOSTAT</span></font></div>
<div>
<font face="arial, sans-serif"><span style="white-space:nowrap"> &END MD</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &PRINT</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &RESTART</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> LOG_PRINT_KEY T</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &EACH</span></font></div><div>
<font face="arial, sans-serif"><span style="white-space:nowrap"> MD 50 </span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END EACH</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> ADD_LAST NUMERIC</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END RESTART</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &TRAJECTORY</span></font></div><div>
<font face="arial, sans-serif"><span style="white-space:nowrap"> LOG_PRINT_KEY T</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &EACH</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> MD 1 </span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END EACH</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> ADD_LAST NUMERIC</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END TRAJECTORY</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &VELOCITIES</span></font></div>
<div>
<font face="arial, sans-serif"><span style="white-space:nowrap"> LOG_PRINT_KEY T</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &EACH</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> MD 1 </span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END EACH</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> ADD_LAST NUMERIC</span></font></div>
<div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END VELOCITIES</span></font></div><div><font face="arial, sans-serif"><span style="white-space:nowrap"> &END PRINT</span></font></div><div>
<font face="arial, sans-serif"><span style="white-space:nowrap">&END MOTION</span></font></div><div><br></div><div>Thank you..</div></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr">Thank you<br><br>
B.Satyanarayana, Ph. D<br>
Molecular modeling lab<div>JNCASR<br>Bangalore</div></div></div>
<br><br><div class="gmail_quote">On Mon, Sep 23, 2013 at 5:21 PM, Marcella Iannuzzi <span dir="ltr"><<a href="mailto:marc...@pci.uzh.ch" target="_blank">marc...@pci.uzh.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi<div><br></div><div>As already posted before, you should run a NVT equilibration (more than a few step) and monitor also the stress tensor along the NVT</div><div>Then you should be able to understand better what is going wrong in your system.</div>
<div><br></div><div><br></div><div>regards</div><div>Marcella</div><div><br></div><div><br><div>
<span style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word">
<div>--------------------------------------------------------------<br>Marcella Iannuzzi Phone : ++41 44 635 4479<br>Physical Chemistry Institute FAX : ++41 44 635 6838<br>University of Zurich E-mail: <font color="#103ffb"><u>marcella<a href="mailto:hut...@pci.uzh.ch" target="_blank">@pci.uzh.ch</a></u></font><br>
Winterthurerstrasse 190<br>CH-8057 Zurich, Switzerland<br>---------------------------------------------------------------</div><div style="font-style:normal;font-size:medium;font-family:Helvetica;font-weight:normal"><br>
</div>
</div></span><br></span><br>
</div>
<br><div><div><div class="h5"><div>On Sep 23, 2013, at 12:44 PM, satya wrote:</div><br></div></div><blockquote type="cite"><div><div class="h5"><div dir="ltr">Hi,<div> I am performing NPT simulations for periodic system. Calculations had terminated after 5 MD runs. It displayed error as follows: </div>
<div> </div><div> *** 15:51:55 ERRORL3 in thermostat_utils:communication_thermo_low1 ***</div><div> *** processor 0 :: err=-300 condition FAILED at line 1877 ***</div><div> </div><div>System energies are:</div><div>
</div><div><div>ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -7813.110428731847605</div><div> ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -7813.095863475370606</div><div> ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -7813.041441177719207</div>
<div> ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -7812.690468241983581</div><div> ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -7805.323597671352218</div><div> ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -7660.983699391561458</div>
<div> ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -8324.938935873122318</div></div><div>I found barostat temperature going on increasing:</div><div><br></div><div><div> BAROSTAT TEMP[K] = 0.214256751812E+03 0.214256751812E+03</div>
<div> BAROSTAT TEMP[K] = 0.858960883736E+03 0.536608817774E+03</div><div> BAROSTAT TEMP[K] = 0.201349929027E+05 0.706940351276E+04</div><div> BAROSTAT TEMP[K] = 0.240108654447E+06 0.653292162464E+05</div>
<div> BAROSTAT TEMP[K] = 0.218578079197E+08 0.442382495693E+07</div></div><div><br></div><div>I enclosed corresponding input file also. Could you please explain, reasons for this error.</div><div>
<br>
</div><div>Thank you..</div><div><br></div><div><br></div></div><div><br></div>
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<span><det_Stree.pdf></span><span><energy.pdf></span><span><temp.pdf></span></blockquote></div><br></div></div></body></html>