[CPMD-list] NAN trajectory for 32 water simulation
Alexandr Isayev
alex at ccmsi.us
Mon Dec 10 20:02:35 UTC 2007
Dear Chang,
Just couple of remarks:
1. Your time step (7 au) is too high, even if you replace hydrogen by
deuterium. BTW, did you replace hydrogens at all? I do not see this
section in your input. Time step around 5 au will be more realistic.
2. If you following cpmd list, please always pay attention to the
Axel's remarks :) For instance, restating his last reply:
do you really need thermostat on electrons? Where did you get value
0.04. On my memory, this value is for 64 water molecules. You can not
just just take it.
3. The other possible source of NANs can be improper restarting and/or
corrupted restart file, poor geometry, etc. Without looking to results
is hard to say more.
Sincerely,
Alexandr
Sunday, December 9, 2007, 10:11:30 PM, you wrote:
CYW> Dear CPMD users,
CYW> I'm running CPMD with 32 water for a test case.
CYW> I get NAN in TRAJEC.xyz for my water simulation. I found some
CYW> posting about NAN problem in the CPMD mailing-list. My case is little different. Now I'm
CYW> trying to follow published work: JCP 120, 300 (2004). Since the
CYW> paper didn't specify temperature coupling, I took Nose-hoover parameters from JPCB 108,
CYW> 12990 (2004).
CYW> I don't know why I'm getting NAN.
CYW> Please help me if anyone knows. Thanks a lot in advance!
CYW> Chang
CYW> Here is my input file.
CYW> &CPMD
CYW> MOLECULAR DYNAMICS CP
CYW> RESTART WAVEFUNCTION COORDINATES LATEST
CYW> TRAJECTORY XYZ
CYW> TEMPERATURE
CYW> 300
CYW> TIMESTEP
CYW> 7.0
CYW> MAXSTEP
CYW> 100
CYW> EMASS
CYW> 760
CYW> NOSE IONS
CYW> 298 2000
CYW> NOSE ELECTRONS
CYW> 0.04 10000
CYW> &END
CYW> &DFT
CYW> FUNCTIONAL BLYP
CYW> &END
CYW> &SYSTEM
CYW> SYMMETRY
CYW> 1
CYW> CELL
CYW> 18.6251 1.0 1.0 0 0 0
CYW> CUTOFF
CYW> 80.0
CYW> &END
CYW> &ATOMS
CYW> *O_GO_BLYP.psp KLEINMAN-BYLANDER
CYW> LMAX=P
CYW> 32
CYW> 0.3590 6.9542 12.2265
CYW> 2.8157 13.2848 13.5493
CYW> 12.9446 0.4913 12.5667
CYW> 11.4517 18.2170 2.3244
CYW> 11.3006 13.7761 5.1023
CYW> 0.0945 7.7479 4.8377
CYW> 1.0393 13.2470 8.1069
CYW> 10.3935 3.7039 16.7241
CYW> 7.2188 13.2281 9.0707
CYW> 17.4233 9.5053 16.9886
CYW> 10.1856 1.2094 9.6754
CYW> 10.6014 4.1952 3.0425
CYW> 13.3226 1.2094 6.9542
CYW> 10.6958 10.1478 16.3461
CYW> 4.2141 9.9211 5.1967
CYW> 13.8328 11.9809 1.4740
CYW> 5.8015 1.1905 11.6785
CYW> 0.6992 14.4753 18.2548
CYW> 6.0282 15.3068 17.9335
CYW> 6.4062 9.6187 0.3779
CYW> 15.4013 10.8092 6.1416
CYW> 8.9384 9.4486 3.6094
CYW> 5.9715 16.1572 5.8393
CYW> 1.5685 5.1401 0.6803
CYW> 17.0642 1.6252 2.5133
CYW> 4.9700 6.1605 13.6060
CYW> 17.3099 17.1965 5.4991
CYW> 1.3606 3.1369 6.0093
CYW> 4.5164 6.1416 8.4849
CYW> 11.2250 14.0785 12.3210
CYW> 16.2327 18.0658 16.2705
CYW> 8.0880 8.0124 9.8266
CYW> *H_MT_BLYP.psp
CYW> LMAX=S
CYW> 64
CYW> -1.1905 7.7668 12.9635
CYW> -0.1701 5.5747 11.0360
CYW> 3.8928 14.7588 13.0769
CYW> 1.6819 13.7761 14.9855
CYW> 14.2485 0.1890 13.8895
CYW> 11.5651 1.5685 13.2848
CYW> 11.5840 19.8043 1.3039
CYW> 12.3210 18.4626 3.9873
CYW> 11.7541 15.0800 3.8172
CYW> 9.8266 14.3997 6.1227
CYW> -1.3606 8.3904 5.8582
CYW> -0.5480 6.7841 3.3448
CYW> 1.5307 13.1714 9.9211
CYW> -0.5669 12.2832 7.8424
CYW> 10.2990 3.6094 18.6138
CYW> 10.4313 5.5180 16.1761
CYW> 8.0691 11.5273 9.0140
CYW> 5.4424 13.0202 9.6943
CYW> 16.9508 9.3352 15.1745
CYW> 18.3303 7.9557 17.5745
CYW> 8.6549 1.2283 10.7714
CYW> 10.2423 2.7779 8.6360
CYW> 11.3195 2.6078 3.7417
CYW> 8.9384 4.5542 3.8739
CYW> 13.0580 1.3417 8.8250
CYW> 14.9099 0.2457 6.6140
CYW> 10.9226 11.3950 14.9477
CYW> 11.5651 10.7903 17.9146
CYW> 4.4598 8.3337 6.2172
CYW> 3.6661 11.3195 6.3306
CYW> 14.9477 11.4895 0.0378
CYW> 13.3037 13.7950 1.2661
CYW> 5.5936 2.9669 12.3021
CYW> 5.7070 0.0000 13.1336
CYW> 0.9827 14.8721 20.0689
CYW> 0.1323 12.6801 18.0847
CYW> 7.7857 15.9871 18.0280
CYW> 5.9148 13.7005 18.9162
CYW> 5.4235 8.0502 0.0567
CYW> 7.8613 9.7132 -0.8315
CYW> 15.5335 9.1274 5.2723
CYW> 13.6249 11.4517 5.9904
CYW> 10.0911 10.9604 3.6850
CYW> 7.1432 10.0344 3.7417
CYW> 4.3464 15.5713 6.6329
CYW> 5.8959 15.8926 3.9684
CYW> 1.4740 5.1212 2.5700
CYW> 0.0000 4.3653 -0.0378
CYW> 18.0280 1.6441 0.8882
CYW> 18.1225 0.8315 3.8550
CYW> 3.4771 7.1243 12.9635
CYW> 4.7999 5.8770 15.4580
CYW> 18.5004 17.9146 4.2141
CYW> 18.0658 15.6280 6.2361
CYW> 1.0393 4.7054 4.9889
CYW> 3.0614 2.4377 5.5936
CYW> 5.7448 4.7432 8.2770
CYW> 4.8944 7.0865 10.0722
CYW> 12.1698 15.6847 11.9620
CYW> 9.5620 14.1163 11.4139
CYW> 17.2532 16.7619 17.1776
CYW> 15.6280 19.3697 17.5178
CYW> 8.6549 6.6518 8.6549
CYW> 7.3510 7.2565 11.3950
CYW> &END
CYW> Chang Yeon Won
CYW> -------------------------------------------------------------------------
CYW> Grad. Res. Asst. (Ph.D Candidate)
CYW> Computational MEMS/Nano Lab
CYW> 3213 Beckman Institute
CYW> University of Illinois at Urbana-Champaign
CYW> 405 N. Mathews Avenue
CYW> Urbana, IL 61801 Office (217)244-1964
CYW> -------------------------------------------------------------------------
CYW> _______________________________________________
CYW> CPMD-list mailing list
CYW> CPMD-list at cpmd.org
CYW> http://cpmd.org/mailman/listinfo/cpmd-list
-------------------------------------------------------
Alexandr Isayev,
Graduate Research Assistant, and System Administrator
@ Computational Center for Molecular Structure
and Interactions (CCMSI),
Jackson State University,
Jackson, MS USA
Tel: +(601) 979-1134
e-mail: alex(at)ccmsi.us
Web: http://www.ccmsi.us
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