[CP2K:1957] Re: bond problem
John
johnb... at gmail.com
Sun Apr 5 16:12:40 UTC 2009
Hi
I am sorry. That's true. I tried iron, it didn't work also. I pasted wrong
xyz coordinate. It could be like this.
> Ru -2.8799089789 4.4833993160 -0.9253798435
> O -4.5590653502 4.9284583342 -0.0621601829
> H -4.9705923716 4.3640441785 0.6893891668
> H -5.3164182399 5.5362415756 -0.2538566219
......
.....
......
that's error report:
------------------------------------------------
ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):
441.893460017026825
*
*
*** 20:50:57 ERRORL3 in thermostat_utils:communication_thermo_low1 ***
*** processor 0 err=-300 condition FAILED at line 1485 ***
*
*
===== Routine Calling Stack =====
2 qs_mol_dyn_low
1 CP2K
CP2K| condition FAILED at line 1485
CP2K| Abnormal program termination, stopped by process number 0
--------------------------------------------------------
regards
On Sun, Apr 5, 2009 at 1:42 PM, Juerg Hutter <hut... at pci.uzh.ch> wrote:
> Hi
>
> &COORD
> Fe -2.8799089789 4.4833993160 -0.9253798435
>
> I thought you wanted to calculate Ru?
>
> regards
>
> Juerg
>
> ----------------------------------------------------------
> Juerg Hutter Phone : ++41 44 635 4491
> Physical Chemistry Institute FAX : ++41 44 635 6838
> University of Zurich E-mail: hut... at pci.uzh.ch
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> ----------------------------------------------------------
>
>
> On Sat, 4 Apr 2009, John wrote:
>
> > Dear all,
> >
> > I'm trying to reproduce Blumberger & Sprik?s article. ?Quantum versus
> > classical electron transfer energy as reaction coordinate for aqueous
> > Ru2+/Ru3+ redox reaction? I want to calculate Ru2+ and Ru3+ separately.
> I
> > am stuck in this file.
> >
> >
> >
> > -------------------------------------------------------------------------
> >
> > &FORCE_EVAL
> > METHOD QS
> > &DFT
> > LSD
> > CHARGE +2
> > BASIS_SET_FILE_NAME ~/bin/GTH_BASIS1
> > POTENTIAL_FILE_NAME ~/bin/GTH_POTENTIALS
> > &SCF
> > SCF_GUESS ATOMIC
> > &END SCF
> > &XC
> > &XC_FUNCTIONAL
> > &LYP
> > &END
> > &BECKE88
> > &END
> > &END XC_FUNCTIONAL
> > &END XC
> > &END DFT
> > &SUBSYS
> > &CELL
> > ABC 9.860 9.860 9.860
> > UNIT ANGSTROM
> > &END CELL
> > &TOPOLOGY
> > CONNECTIVITY GENERATE
> > &GENERATE
> > CREATE_MOLECULES
> > &END GENERATE
> > COORD_FILE_FORMAT OFF
> > &END TOPOLOGY
> > &COORD
> > Fe -2.8799089789 4.4833993160 -0.9253798435
> > O -4.5590653502 4.9284583342 -0.0621601829
> > H -4.9705923716 4.3640441785 0.6893891668
> > H -5.3164182399 5.5362415756 -0.2538566219
> > O -6.3299935050 4.6501002553 -3.2165611248
> > H -6.2549146971 3.6508586162 -3.3792673655
> > H -6.9156034477 4.8348081172 -3.9501089172
> > O -2.2309178755 1.9923408769 2.7645911766
> > H -2.1565313777 1.2884476066 3.3749391873
> > H -2.9197925757 2.4899670577 3.2035338211
> > O -6.0770832172 -2.7231315785 -9.5448709624
> > H -6.6824231738 -1.9822385218 -9.4211280474
> > H -5.9382474726 -3.0338301873 -8.6189155739
> > O -1.5590539933 8.4581237145 2.8351416768
> > H -0.7014554610 8.2291741700 2.4524975037
> > H -2.0130061115 8.5474909348 1.9935461408
> > O 9.2452622342 -5.2016109500 5.4580407027
> > H 9.0803631056 -5.7141148150 4.6416799086
> > H 9.9239068093 -4.6374143187 5.0948223542
> > O -2.2747965553 -3.6412773460 -0.5034106904
> > H -1.3309475835 -3.3368322136 -0.4927701592
> > H -2.6785712553 -2.7337453156 -0.3003969352
> > O -5.0150050737 -6.7585442027 1.9265699321
> > H -5.1775069842 -7.7010260951 1.7351149107
> > H -5.8697740333 -6.3925551219 2.1581907946
> > O 0.8447530721 6.9676594900 11.9177287714
> > H 1.7073334916 7.3677191845 11.6947056467
> > H 0.6518913920 6.5141851347 11.1177738640
> > O 6.0591575870 2.6714044751 -1.4726489030
> > H 5.3474665764 2.0757487291 -1.1127385014
> > H 6.4466468961 2.0834641415 -2.1735884409
> > O 3.4899901096 -1.6971208479 -4.9827700523
> > H 3.7505437278 -2.0037236132 -5.8540717308
> > H 4.1006777437 -2.1268748806 -4.4328135502
> > O -1.9498492896 3.8218715791 0.7845270001
> > H -1.5328361779 4.4385739266 1.4442998839
> > H -2.0488871006 2.9605980239 1.2847914463
> > O 0.9321859840 -7.8126933636 -7.4250105857
> > H 0.0329414295 -8.0583782013 -7.5266562638
> > H 1.1486171832 -8.1200037817 -6.5120872061
> > O -1.2177439540 3.9800638489 -1.8131933683
> > H -0.6840991767 3.1313826129 -1.5906664292
> > H -0.9145330384 4.0982865398 -2.7613003118
> > O -3.3284227931 -1.8974729757 7.2635935278
> > H -2.4263964010 -1.6247806670 6.8788457601
> > H -3.8045549804 -1.0362892279 7.1060434158
> > O 3.1479370099 -0.6458937922 -2.5276483725
> > H 3.3884480789 -0.8514820589 -3.4557508136
> > H 3.6344722272 -1.3774434262 -2.0751013265
> > O 7.1879953337 -8.9239121082 -13.3442298597
> > H 6.8446671365 -8.5711562075 -14.1613048318
> > H 7.7254300021 -9.6624243506 -13.7044807394
> > O -8.6023482493 -3.3193550929 -5.1537580676
> > H -8.7819195227 -3.1689491809 -6.1212676794
> > H -7.8410327266 -2.7039484048 -4.9109258801
> > O -1.6312805667 5.5167292375 -6.9923342866
> > H -0.8056792472 5.7540718563 -6.5608867815
> > H -2.1505132312 6.3409324352 -7.1702717642
> > O -1.1599325173 -1.2492174249 5.5835548423
> > H -0.5586672445 -2.0053137874 5.5852786019
> > H -1.2162000273 -1.1965002980 4.5769153998
> > O 0.4507584677 1.9022651399 8.0400381780
> > H 0.3803588966 1.5946413528 7.1350748078
> > H 0.7456410323 1.1634439653 8.5439230412
> > O 2.3267512174 -0.6727042425 1.1854652355
> > H 2.5458646034 0.0652573671 1.7955595250
> > H 1.4034743190 -0.7956305233 1.3884420398
> > O 6.5672661690 -1.0984518909 0.4890215160
> > H 6.6148451731 -0.1508625403 0.5933987343
> > H 5.6183713508 -1.1822689592 0.6206551821
> > O 13.8241697211 1.1652120167 -0.1672218219
> > H 13.2121429387 1.9116181141 -0.2940170580
> > H 13.1950907565 0.4365600472 -0.0399679561
> > O -7.4988319221 -5.5555520991 1.8185232839
> > H -7.3837127821 -5.7699475363 0.8563643360
> > H -8.1964989733 -6.1053099532 2.1088034849
> > O 3.2659641904 1.9791770773 6.1150563807
> > H 3.4940757601 1.1736027719 6.5963750850
> > H 2.3515019134 1.7588235846 5.7327525956
> > O 10.6859668444 0.9023905651 5.3551106427
> > H 9.8594127269 0.4030003706 5.2356781202
> > H 11.1491058894 0.1555256165 5.7681348240
> > O 0.3760363101 -3.1586261422 -0.8543017938
> > H 0.5403724685 -2.2421497891 -0.9851024800
> > H 1.2122330106 -3.5814031598 -1.0268333285
> > O 5.5807230240 -7.1801081002 -5.1191205524
> > H 5.3360212979 -6.4482539508 -5.7290439438
> > H 4.6785146465 -7.5446958824 -4.8933286755
> > O 2.6572577924 3.6535389336 -0.8327578995
> > H 2.9537750589 4.1567130338 -1.6386441686
> > H 1.8520090260 3.2252090800 -1.1268435488
> > O -5.8148422292 -3.3672919847 2.9400281976
> > H -6.4576770992 -4.0665517099 3.0231423099
> > H -5.0407848682 -3.8319856458 3.2242012598
> > O 6.1901471261 5.2539472758 -2.5686945148
> > H 5.3182543979 5.0205417149 -2.9790688482
> > H 6.2705281827 6.1021482659 -3.1176707935
> > &END COORD
> > &KIND RU
> > BASIS_SET DZV-GTH
> > POTENTIAL GTH-PADE-q8
> > &END KIND
> > &KIND H
> > BASIS_SET DZV-GTH
> > POTENTIAL GTH-BP-q1
> > &END KIND
> > &KIND O
> > BASIS_SET DZVP-GTH
> > POTENTIAL GTH-BP-q6
> > &END KIND
> > &END SUBSYS
> > &END FORCE_EVAL
> > &GLOBAL
> > PREFERRED_FFT_LIBRARY FFTSG
> > EXTENDED_FFT_LENGTHS T
> > PROJECT test
> > RUN_TYPE GEO_OPT
> > &END GLOBAL
> > &MOTION
> > &MD
> > ENSEMBLE NVT
> > STEPS 10000
> > TIMESTEP 1.0
> > TEMPERATURE 300.0
> > &THERMOSTAT
> > REGION GLOBAL
> > &NOSE
> > LENGTH 3
> > YOSHIDA 3
> > TIMECON 1000
> > MTS 2
> > &END NOSE
> > &END
> > &PRINT
> > &ENERGY
> > &EACH
> > MD 10
> > &END EACH
> > &END ENERGY
> > &END PRINT
> > &END MD
> > &PRINT
> > &TRAJECTORY
> > &EACH
> > MD 10
> > &END EACH
> > &END TRAJECTORY
> > &END PRINT
> > &END MOTION
> >
> >
> > -------------------------------------
> >
> >
> >
> >
> >
> > Thanks in advance
> > John
> >
> > >
> >
> >
>
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