[CPMD-list] NAN trajectory for 32 water simulation
Axel Kohlmeyer
akohlmey at cmm.chem.upenn.edu
Mon Dec 10 19:17:57 UTC 2007
On Sun, 9 Dec 2007, Chang Y. Won wrote:
CW> Dear CPMD users,
CW>
CW> I'm running CPMD with 32 water for a test case.
CW> I get NAN in TRAJEC.xyz for my water simulation. I found some
CW> posting about NAN problem in the CPMD mailing-list. My case is
you are getting NaNs because your electronic structure
is diverging. this usually happens when you have too large
a time step or not the right balance between fictitious mass
and time step.
since there seem to be a lot of posts recently where people
consider the thermostats to be a source of problems. whatever
you do, _first_ make sure that your CP dynamics works _without_
_any_ thermostat (TEMPCONTROL is _not_ a thermostat but merely
a tool to removed or add kinetic energy to your system), particularly
without a thermostat on the electrons. putting a thermostat on
the electrons can hide a lot of problems and more importantly
if the parameters are not well tuned, this will render your
trajectory unusable for anything else than equilibration.
CW> little different. Now I'm trying to follow published work: JCP 120,
CW> 300 (2004). Since the paper didn't specify temperature coupling, I
CW> took Nose-hoover parameters from JPCB 108, 12990 (2004).
no, you are _not_ following published work!
the paper uses a 0.075fs time step which translates
into (much more reasonable) 3 a.u. and a fictitious mass
of 340 a.u.; 760 a.u. was _only_ used for D2O (which you
are not using). please check the CPMD manual for details.
CW> I don't know why I'm getting NAN.
you were asking for them. ;-)
as the paper you refer to states, CP dynamics are
not simple to get right.
cheers,
axel.
CW>
CW> Please help me if anyone knows. Thanks a lot in advance!
CW>
CW> Chang
CW> Here is my input file.
CW>
CW> &CPMD
CW> MOLECULAR DYNAMICS CP
CW> RESTART WAVEFUNCTION COORDINATES LATEST
CW> TRAJECTORY XYZ
CW> TEMPERATURE
CW> 300
CW> TIMESTEP
CW> 7.0
CW> MAXSTEP
CW> 100
CW> EMASS
CW> 760
CW> NOSE IONS
CW> 298 2000
CW> NOSE ELECTRONS
CW> 0.04 10000
CW> &END
CW>
CW> &DFT
CW> FUNCTIONAL BLYP
CW> &END
CW>
CW> &SYSTEM
CW> SYMMETRY
CW> 1
CW> CELL
CW> 18.6251 1.0 1.0 0 0 0
CW> CUTOFF
CW> 80.0
CW> &END
CW>
CW> &ATOMS
CW> *O_GO_BLYP.psp KLEINMAN-BYLANDER
CW> LMAX=P
CW> 32
CW> 0.3590 6.9542 12.2265
CW> 2.8157 13.2848 13.5493
CW> 12.9446 0.4913 12.5667
CW> 11.4517 18.2170 2.3244
CW> 11.3006 13.7761 5.1023
CW> 0.0945 7.7479 4.8377
CW> 1.0393 13.2470 8.1069
CW> 10.3935 3.7039 16.7241
CW> 7.2188 13.2281 9.0707
CW> 17.4233 9.5053 16.9886
CW> 10.1856 1.2094 9.6754
CW> 10.6014 4.1952 3.0425
CW> 13.3226 1.2094 6.9542
CW> 10.6958 10.1478 16.3461
CW> 4.2141 9.9211 5.1967
CW> 13.8328 11.9809 1.4740
CW> 5.8015 1.1905 11.6785
CW> 0.6992 14.4753 18.2548
CW> 6.0282 15.3068 17.9335
CW> 6.4062 9.6187 0.3779
CW> 15.4013 10.8092 6.1416
CW> 8.9384 9.4486 3.6094
CW> 5.9715 16.1572 5.8393
CW> 1.5685 5.1401 0.6803
CW> 17.0642 1.6252 2.5133
CW> 4.9700 6.1605 13.6060
CW> 17.3099 17.1965 5.4991
CW> 1.3606 3.1369 6.0093
CW> 4.5164 6.1416 8.4849
CW> 11.2250 14.0785 12.3210
CW> 16.2327 18.0658 16.2705
CW> 8.0880 8.0124 9.8266
CW> *H_MT_BLYP.psp
CW> LMAX=S
CW> 64
CW> -1.1905 7.7668 12.9635
CW> -0.1701 5.5747 11.0360
CW> 3.8928 14.7588 13.0769
CW> 1.6819 13.7761 14.9855
CW> 14.2485 0.1890 13.8895
CW> 11.5651 1.5685 13.2848
CW> 11.5840 19.8043 1.3039
CW> 12.3210 18.4626 3.9873
CW> 11.7541 15.0800 3.8172
CW> 9.8266 14.3997 6.1227
CW> -1.3606 8.3904 5.8582
CW> -0.5480 6.7841 3.3448
CW> 1.5307 13.1714 9.9211
CW> -0.5669 12.2832 7.8424
CW> 10.2990 3.6094 18.6138
CW> 10.4313 5.5180 16.1761
CW> 8.0691 11.5273 9.0140
CW> 5.4424 13.0202 9.6943
CW> 16.9508 9.3352 15.1745
CW> 18.3303 7.9557 17.5745
CW> 8.6549 1.2283 10.7714
CW> 10.2423 2.7779 8.6360
CW> 11.3195 2.6078 3.7417
CW> 8.9384 4.5542 3.8739
CW> 13.0580 1.3417 8.8250
CW> 14.9099 0.2457 6.6140
CW> 10.9226 11.3950 14.9477
CW> 11.5651 10.7903 17.9146
CW> 4.4598 8.3337 6.2172
CW> 3.6661 11.3195 6.3306
CW> 14.9477 11.4895 0.0378
CW> 13.3037 13.7950 1.2661
CW> 5.5936 2.9669 12.3021
CW> 5.7070 0.0000 13.1336
CW> 0.9827 14.8721 20.0689
CW> 0.1323 12.6801 18.0847
CW> 7.7857 15.9871 18.0280
CW> 5.9148 13.7005 18.9162
CW> 5.4235 8.0502 0.0567
CW> 7.8613 9.7132 -0.8315
CW> 15.5335 9.1274 5.2723
CW> 13.6249 11.4517 5.9904
CW> 10.0911 10.9604 3.6850
CW> 7.1432 10.0344 3.7417
CW> 4.3464 15.5713 6.6329
CW> 5.8959 15.8926 3.9684
CW> 1.4740 5.1212 2.5700
CW> 0.0000 4.3653 -0.0378
CW> 18.0280 1.6441 0.8882
CW> 18.1225 0.8315 3.8550
CW> 3.4771 7.1243 12.9635
CW> 4.7999 5.8770 15.4580
CW> 18.5004 17.9146 4.2141
CW> 18.0658 15.6280 6.2361
CW> 1.0393 4.7054 4.9889
CW> 3.0614 2.4377 5.5936
CW> 5.7448 4.7432 8.2770
CW> 4.8944 7.0865 10.0722
CW> 12.1698 15.6847 11.9620
CW> 9.5620 14.1163 11.4139
CW> 17.2532 16.7619 17.1776
CW> 15.6280 19.3697 17.5178
CW> 8.6549 6.6518 8.6549
CW> 7.3510 7.2565 11.3950
CW> &END
CW>
CW>
CW> Chang Yeon Won
CW> -------------------------------------------------------------------------
CW> Grad. Res. Asst. (Ph.D Candidate)
CW> Computational MEMS/Nano Lab
CW> 3213 Beckman Institute
CW> University of Illinois at Urbana-Champaign
CW> 405 N. Mathews Avenue
CW> Urbana, IL 61801 Office (217)244-1964
CW> -------------------------------------------------------------------------
CW> _______________________________________________
CW> CPMD-list mailing list
CW> CPMD-list at cpmd.org
CW> http://cpmd.org/mailman/listinfo/cpmd-list
CW>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
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