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Hi John<div><br></div><div>first, your input file is setup for GEO_OPT which will never show up an error in the thermostat (are you really sure about the</div><div>input you sent ?)</div><div><br></div><div>Second, I tried to run your input file with RUN_TYPE set to MD and run it. and I could not see any problem.</div><div><br></div><div>So I would definitely suggest you to double check your help request (specifically the input file you attached!) and in case provide definitely more data like:</div><div>architecture, compiler, serial/parallel, number of procs in case of parallel runs.</div><div><br></div><div>The information provided are definitely not sufficient and possibly even wrong.</div><div>Best,</div><div>Teo</div><div><br></div><div><br><div><div>On 5 Apr 2009, at 18:12, John wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br>Hi <br><br> I am sorry. That's true. I tried iron, it didn't work also. I pasted wrong xyz coordinate. It could be like this.<br><br>> Ru -2.8799089789 4.4833993160 -0.9253798435<br> > O -4.5590653502 4.9284583342 -0.0621601829<br> > H -4.9705923716 4.3640441785 0.6893891668<br> > H -5.3164182399 5.5362415756 -0.2538566219<br> ......<br>.....<br>......<br><br>that's error report:<br><br>------------------------------------------------<br><br> ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): 441.893460017026825<br><br> *<br> *<br> *** 20:50:57 ERRORL3 in thermostat_utils:communication_thermo_low1 ***<br> *** processor 0 err=-300 condition FAILED at line 1485 ***<br> *<br> *<br><br> ===== Routine Calling Stack ===== <br><br> 2 qs_mol_dyn_low<br> 1 CP2K<br> CP2K| condition FAILED at line 1485<br> CP2K| Abnormal program termination, stopped by process number 0<br><br><br>--------------------------------------------------------<br><br>regards<br><br><br> <br><br><br><br><div class="gmail_quote">On Sun, Apr 5, 2009 at 1:42 PM, Juerg Hutter <span dir="ltr"><<a href="mailto:hut...@pci.uzh.ch" target="_blank">hut...@pci.uzh.ch</a>></span> wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi<br> <div><br> &COORD<br> Fe -2.8799089789 4.4833993160 -0.9253798435<br> <br> </div>I thought you wanted to calculate Ru?<br> <br> regards<br> <br> Juerg<br> <br> ----------------------------------------------------------<br> <font color="#888888">Juerg Hutter Phone : ++41 44 635 4491<br> Physical Chemistry Institute FAX : ++41 44 635 6838<br> University of Zurich E-mail: <a href="mailto:hut...@pci.uzh.ch" target="_blank">hut...@pci.uzh.ch</a><br> Winterthurerstrasse 190<br> CH-8057 Zurich, Switzerland<br> ----------------------------------------------------------<br> </font><div><div></div><div><br> <br> On Sat, 4 Apr 2009, John wrote:<br> <br> > Dear all,<br> ><br> > I'm trying to reproduce Blumberger & Sprik?s article. ?Quantum versus<br> > classical electron transfer energy as reaction coordinate for aqueous<br> > Ru2+/Ru3+ redox reaction? I want to calculate Ru2+ and Ru3+ separately. I<br> > am stuck in this file.<br> ><br> ><br> ><br> > -------------------------------------------------------------------------<br> ><br> > &FORCE_EVAL<br> > METHOD QS<br> > &DFT<br> > LSD<br> > CHARGE +2<br> > BASIS_SET_FILE_NAME ~/bin/GTH_BASIS1<br> > POTENTIAL_FILE_NAME ~/bin/GTH_POTENTIALS<br> > &SCF<br> > SCF_GUESS ATOMIC<br> > &END SCF<br> > &XC<br> > &XC_FUNCTIONAL<br> > &LYP<br> > &END<br> > &BECKE88<br> > &END<br> > &END XC_FUNCTIONAL<br> > &END XC<br> > &END DFT<br> > &SUBSYS<br> > &CELL<br> > ABC 9.860 9.860 9.860<br> > UNIT ANGSTROM<br> > &END CELL<br> > &TOPOLOGY<br> > CONNECTIVITY GENERATE<br> > &GENERATE<br> > CREATE_MOLECULES<br> > &END GENERATE<br> > COORD_FILE_FORMAT OFF<br> > &END TOPOLOGY<br> > &COORD<br> > Fe -2.8799089789 4.4833993160 -0.9253798435<br> > O -4.5590653502 4.9284583342 -0.0621601829<br> > H -4.9705923716 4.3640441785 0.6893891668<br> > H -5.3164182399 5.5362415756 -0.2538566219<br> > O -6.3299935050 4.6501002553 -3.2165611248<br> > H -6.2549146971 3.6508586162 -3.3792673655<br> > H -6.9156034477 4.8348081172 -3.9501089172<br> > O -2.2309178755 1.9923408769 2.7645911766<br> > H -2.1565313777 1.2884476066 3.3749391873<br> > H -2.9197925757 2.4899670577 3.2035338211<br> > O -6.0770832172 -2.7231315785 -9.5448709624<br> > H -6.6824231738 -1.9822385218 -9.4211280474<br> > H -5.9382474726 -3.0338301873 -8.6189155739<br> > O -1.5590539933 8.4581237145 2.8351416768<br> > H -0.7014554610 8.2291741700 2.4524975037<br> > H -2.0130061115 8.5474909348 1.9935461408<br> > O 9.2452622342 -5.2016109500 5.4580407027<br> > H 9.0803631056 -5.7141148150 4.6416799086<br> > H 9.9239068093 -4.6374143187 5.0948223542<br> > O -2.2747965553 -3.6412773460 -0.5034106904<br> > H -1.3309475835 -3.3368322136 -0.4927701592<br> > H -2.6785712553 -2.7337453156 -0.3003969352<br> > O -5.0150050737 -6.7585442027 1.9265699321<br> > H -5.1775069842 -7.7010260951 1.7351149107<br> > H -5.8697740333 -6.3925551219 2.1581907946<br> > O 0.8447530721 6.9676594900 11.9177287714<br> > H 1.7073334916 7.3677191845 11.6947056467<br> > H 0.6518913920 6.5141851347 11.1177738640<br> > O 6.0591575870 2.6714044751 -1.4726489030<br> > H 5.3474665764 2.0757487291 -1.1127385014<br> > H 6.4466468961 2.0834641415 -2.1735884409<br> > O 3.4899901096 -1.6971208479 -4.9827700523<br> > H 3.7505437278 -2.0037236132 -5.8540717308<br> > H 4.1006777437 -2.1268748806 -4.4328135502<br> > O -1.9498492896 3.8218715791 0.7845270001<br> > H -1.5328361779 4.4385739266 1.4442998839<br> > H -2.0488871006 2.9605980239 1.2847914463<br> > O 0.9321859840 -7.8126933636 -7.4250105857<br> > H 0.0329414295 -8.0583782013 -7.5266562638<br> > H 1.1486171832 -8.1200037817 -6.5120872061<br> > O -1.2177439540 3.9800638489 -1.8131933683<br> > H -0.6840991767 3.1313826129 -1.5906664292<br> > H -0.9145330384 4.0982865398 -2.7613003118<br> > O -3.3284227931 -1.8974729757 7.2635935278<br> > H -2.4263964010 -1.6247806670 6.8788457601<br> > H -3.8045549804 -1.0362892279 7.1060434158<br> > O 3.1479370099 -0.6458937922 -2.5276483725<br> > H 3.3884480789 -0.8514820589 -3.4557508136<br> > H 3.6344722272 -1.3774434262 -2.0751013265<br> > O 7.1879953337 -8.9239121082 -13.3442298597<br> > H 6.8446671365 -8.5711562075 -14.1613048318<br> > H 7.7254300021 -9.6624243506 -13.7044807394<br> > O -8.6023482493 -3.3193550929 -5.1537580676<br> > H -8.7819195227 -3.1689491809 -6.1212676794<br> > H -7.8410327266 -2.7039484048 -4.9109258801<br> > O -1.6312805667 5.5167292375 -6.9923342866<br> > H -0.8056792472 5.7540718563 -6.5608867815<br> > H -2.1505132312 6.3409324352 -7.1702717642<br> > O -1.1599325173 -1.2492174249 5.5835548423<br> > H -0.5586672445 -2.0053137874 5.5852786019<br> > H -1.2162000273 -1.1965002980 4.5769153998<br> > O 0.4507584677 1.9022651399 8.0400381780<br> > H 0.3803588966 1.5946413528 7.1350748078<br> > H 0.7456410323 1.1634439653 8.5439230412<br> > O 2.3267512174 -0.6727042425 1.1854652355<br> > H 2.5458646034 0.0652573671 1.7955595250<br> > H 1.4034743190 -0.7956305233 1.3884420398<br> > O 6.5672661690 -1.0984518909 0.4890215160<br> > H 6.6148451731 -0.1508625403 0.5933987343<br> > H 5.6183713508 -1.1822689592 0.6206551821<br> > O 13.8241697211 1.1652120167 -0.1672218219<br> > H 13.2121429387 1.9116181141 -0.2940170580<br> > H 13.1950907565 0.4365600472 -0.0399679561<br> > O -7.4988319221 -5.5555520991 1.8185232839<br> > H -7.3837127821 -5.7699475363 0.8563643360<br> > H -8.1964989733 -6.1053099532 2.1088034849<br> > O 3.2659641904 1.9791770773 6.1150563807<br> > H 3.4940757601 1.1736027719 6.5963750850<br> > H 2.3515019134 1.7588235846 5.7327525956<br> > O 10.6859668444 0.9023905651 5.3551106427<br> > H 9.8594127269 0.4030003706 5.2356781202<br> > H 11.1491058894 0.1555256165 5.7681348240<br> > O 0.3760363101 -3.1586261422 -0.8543017938<br> > H 0.5403724685 -2.2421497891 -0.9851024800<br> > H 1.2122330106 -3.5814031598 -1.0268333285<br> > O 5.5807230240 -7.1801081002 -5.1191205524<br> > H 5.3360212979 -6.4482539508 -5.7290439438<br> > H 4.6785146465 -7.5446958824 -4.8933286755<br> > O 2.6572577924 3.6535389336 -0.8327578995<br> > H 2.9537750589 4.1567130338 -1.6386441686<br> > H 1.8520090260 3.2252090800 -1.1268435488<br> > O -5.8148422292 -3.3672919847 2.9400281976<br> > H -6.4576770992 -4.0665517099 3.0231423099<br> > H -5.0407848682 -3.8319856458 3.2242012598<br> > O 6.1901471261 5.2539472758 -2.5686945148<br> > H 5.3182543979 5.0205417149 -2.9790688482<br> > H 6.2705281827 6.1021482659 -3.1176707935<br> > &END COORD<br> > &KIND RU<br> > BASIS_SET DZV-GTH<br> > POTENTIAL GTH-PADE-q8<br> > &END KIND<br> > &KIND H<br> > BASIS_SET DZV-GTH<br> > POTENTIAL GTH-BP-q1<br> > &END KIND<br> > &KIND O<br> > BASIS_SET DZVP-GTH<br> > POTENTIAL GTH-BP-q6<br> > &END KIND<br> > &END SUBSYS<br> > &END FORCE_EVAL<br> > &GLOBAL<br> > PREFERRED_FFT_LIBRARY FFTSG<br> > EXTENDED_FFT_LENGTHS T<br> > PROJECT test<br> > RUN_TYPE GEO_OPT<br> > &END GLOBAL<br> > &MOTION<br> > &MD<br> > ENSEMBLE NVT<br> > STEPS 10000<br> > TIMESTEP 1.0<br> > TEMPERATURE 300.0<br> > &THERMOSTAT<br> > REGION GLOBAL<br> > &NOSE<br> > LENGTH 3<br> > YOSHIDA 3<br> > TIMECON 1000<br> > MTS 2<br> > &END NOSE<br> > &END<br> > &PRINT<br> > &ENERGY<br> > &EACH<br> > MD 10<br> > &END EACH<br> > &END ENERGY<br> > &END PRINT<br> > &END MD<br> > &PRINT<br> > &TRAJECTORY<br> > &EACH<br> > MD 10<br> > &END EACH<br> > &END TRAJECTORY<br> > &END PRINT<br> > &END MOTION<br> ><br> ><br> > -------------------------------------<br> ><br> ><br> ><br> ><br> ><br> > Thanks in advance<br> > John<br> ><br> > ><br> ><br> </div></div><div><div></div><div><br> </div></div></blockquote></div><br> <br> <br> <br></blockquote></div><br></div></body></html>