[CPMD-list] Segmentation fault for a molecular dynamics run
Juerg Hutter
hutter at pci.unizh.ch
Fri Apr 9 17:13:12 CEST 2004
Hi
In order to get reasonable Car-Parrinello dynamics
you have to start close to the Born-Oppenheimer surface.
1) Optimize the wavefunction
2) Restart the calculation for MD from the optimized
wavefunctions
----------------------------------------------------------
Juerg Hutter Phone : ++41 1 635 4491
Physical Chemistry Institute FAX : ++41 1 635 6838
University of Zurich E-mail: hutter at pci.unizh.ch
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
----------------------------------------------------------
On Fri, 9 Apr 2004, Dai Ling wrote:
> Dear Axel:
>
> Thanks for your kind suggestions. I have tried the program with smaller timestep but it results the same problem, here is my input file. Is there any improvements to be made?
>
> Thanks & Best Regards!
> Scott
>
> &CPMD
> MOLECULAR DYNAMICS
> SPLINE POINTS
> 500
> TEMPERATURE
> 300
> TIMESTEP
> 1
> &END
> &SYSTEM
> ANGSTROM
> CELL ABSOLUTE DEGREE
> 10.3651 10.3651 33.6851 90.0000 90.0000 90.0000
> SYMMETRY
> 1
> CUTOFF
> 29.4009555
> 400eV
> &END
> &DFT
> FUNCTIONAL BLYP
> &END
> &ATOMS
> Carbon
> *C_SG_BLYP
> LMAX=P
> 64
> -7.388012732 -1.642168534 25.01440235
> -6.382609051 -0.978175454 24.63538093
> -5.323723058 -0.089043005 24.05093371
> -4.854726663 1.088428581 24.69780765
> -4.719722672 -0.45536938 22.77058871
> -3.853670574 1.878791233 24.05481075
> -3.727203589 0.322337745 22.12793105
> -3.285603018 1.529112936 22.75270539
> -2.31179763 2.370312667 22.06837233
> -1.657811935 3.083353134 21.29678098
> -0.969260023 3.919725664 20.31394199
> -1.245222179 5.332024449 20.32965785
> -0.794927554 6.149140856 19.26327506
> -0.133808243 3.346577987 19.2650768
> 0.066483028 5.554478915 18.21924126
> 0.358692971 4.168632108 18.25181672
> 0.760322484 6.096840284 17.0399977
> 1.330943039 5.969193527 15.93724099
> 2.064764037 4.551925203 13.40019082
> 2.110723841 5.519109311 14.75412533
> 2.844470922 2.580936109 9.150681578
> 3.206511944 4.244947858 12.30471085
> 3.721941516 6.077936036 14.60025391
> 3.480826739 3.50950027 8.637025095
> 4.333974732 5.834360573 9.068761058
> 4.201365474 4.691822097 8.207886525
> 4.6564382 4.794709024 12.38031206
> 4.84559896 5.741309672 13.58730304
> 5.217790181 6.854258569 8.696382427
> 4.86446849 4.668075611 6.964101537
> 5.69689119 4.469174387 11.4296495
> 5.6736301 5.740027018 6.581398159
> 5.87675123 6.862179387 7.443676852
> 6.498456315 4.162042335 10.54699918
> 6.911204616 7.838693848 7.08030164
> 7.133496501 2.42842985 8.798213476
> 7.161538395 3.753563367 9.319849702
> 7.820688397 8.377438701 6.438704627
> 7.783175783 4.742433501 8.539547392
> 7.73090042 2.056853041 7.570379483
> 8.252167403 7.725651567 4.102205182
> 8.344226381 4.402685273 7.304779751
> 8.617559259 8.549669206 5.227281327
> 8.391879435 3.069415265 6.803032604
> 8.859026526 7.896469794 2.855611781
> 9.705998505 9.45431933 4.991295902
> 9.22919318 2.972069614 5.601124026
> 9.918410068 8.839326375 2.643068958
> 10.37954295 9.617247186 3.776823625
> 10.06424046 3.441634566 4.792302618
> 10.35035758 5.416632762 2.945596858
> 10.53537128 9.082036274 1.318533568
> 10.86952412 4.345838673 3.966050179
> 11.09091158 9.230083247 0.217174145
> 11.19845421 6.349572904 2.050379437
> 11.37106703 9.383173339 -2.273832771
> 11.90967153 9.455959601 -0.974837543
> 12.15396279 9.686972916 -3.387359715
> 12.38778786 4.206898028 4.217927143
> 12.75866426 6.191201085 2.410354645
> 13.28457026 9.743101186 -0.78930858
> 13.30994919 5.261226317 3.528976273
> 13.51585246 9.97209375 -3.1888067
> 14.09264366 9.965891298 -1.895177182
> Hydrogen
> *H_SG_BLYP
> LMAX=S
> 36
> -8.28627065 -2.221067521 25.32458106
> -5.314762155 1.404516996 25.69734891
> -5.037422356 -1.408474281 22.27937223
> -3.542887875 2.826165676 24.5564517
> -3.267304898 0.013662949 21.13173595
> -1.936650946 5.76726208 21.12205615
> -1.079491558 7.223681278 19.25296379
> -0.002696172 2.250159556 19.16440929
> 1.318563979 3.936515068 12.7808767
> 0.979181639 3.704700398 17.416767
> 2.20623476 1.82672308 9.624491821
> 2.932778866 3.53733391 11.50000647
> 3.833335676 5.913336627 10.06093243
> 4.150794282 6.838793694 15.3040995
> 5.370120666 7.642366536 9.468855023
> 4.773184306 3.763289962 6.320925188
> 5.813356723 6.260950236 13.76031594
> 6.222505306 5.670580942 5.624376089
> 6.625950492 1.635336454 9.391389515
> 7.480756175 6.93225646 4.291961097
> 7.82778424 5.790369108 8.898001536
> 7.62979369 0.942071996 7.390266623
> 8.829068316 5.215307381 6.730866222
> 8.523895065 7.234066969 2.019013533
> 10.09118356 10.1193112 5.810743664
> 9.257100872 5.391549447 2.984442268
> 11.21018477 10.35863759 3.71808614
> 10.29944541 9.165648173 -2.407440086
> 11.06682354 7.128203412 1.154317173
> 11.70110255 9.732722955 -4.399371766
> 12.95767729 3.414805613 4.779787108
> 13.2792451 6.833931151 1.628962234
> 13.45640309 9.701370504 0.330786893
> 14.14605727 10.1441285 -4.080386464
> 14.41749211 5.126797661 4.075302533
> 15.18151391 10.09264052 -1.760186938
> &END
> &CONSTRAINTS
> FIX COORDINATES
> 2
> 98 0 0 0
> 99 0 0 0
>
> &END CONSTRAINTS
>
>
> -----Original Message-----
> From: Axel Kohlmeyer [mailto:axel.kohlmeyer at theochem.ruhr-uni-bochum.de]
> Sent: Wed 4/7/2004 12:48 PM
> To: cpmd-list at cpmd.org; Dai Ling
> Cc:
> Subject: Re: [CPMD-list] Segmentation fault for a molecular dynamics run
>
>
>
>
> On Wed, 7 Apr 2004, Dai Ling wrote:
>
> DL> I met a problem when runing a molecular dynamics (CP) run with some benzene ring structures. There is some odd marks as "NaNQ" in the output file as shown below. Then the running failed with "Segmentation fault". Who can help me to point out what goes wrong?
> DL>
> DL> Thanks in advance!
> DL>
> DL> Scott
> DL>
> DL> Outpupt:
> DL>
> DL> ....
> DL> ....
> DL> TOTAL INTEGRATED ELECTRONIC DENSITY
> DL> IN G-SPACE = 292.000000
> DL> IN R-SPACE = 292.000000
> DL> (K+E1+L+N+X) TOTAL ENERGY = -370.10939613 A.U.
> DL> (K) KINETIC ENERGY = 247.71353333 A.U.
> DL> (E1=A-S+R) ELECTROSTATIC ENERGY = -328.45005481 A.U.
> DL> (S) ESELF = 352.39900035 A.U.
> DL> (R) ESR = 17.54351703 A.U.
> DL> (L) LOCAL PSEUDOPOTENTIAL ENERGY = -214.10105210 A.U.
> DL> (N) N-L PSEUDOPOTENTIAL ENERGY = 41.28274138 A.U.
> DL> (X) EXCHANGE-CORRELATION ENERGY = -116.55456393 A.U.
> DL> GRADIENT CORRECTION ENERGY = -5.18331838 A.U.
> DL>
> DL> NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU
> DL> 1 3.11966 309.0 -370.10940 -369.96407 -366.84441 .000 48.41
>
> DL> FILE ./TRAJECTORY EXISTS, NEW DATA WILL BE APPENDED
> DL> FILE ./MOVIE EXISTS, NEW DATA WILL BE APPENDED
> DL> 2 4.88578 320.2 -371.88325 -371.73269 -366.84691 .000 49.49
>
> hmmmm, EKINC seems a bit high, and is fluctaing quite a bit.
> also EHAM ist not the conserved quantity that is should be.
> seems like are not very close to the BO-surface anymore
> (if ever) as you should be.
>
> could you please post your input file, so that we can have
> a better guess at the problem. my guess would be that you
> have a too large timestep or starte from a non-converged
> wavefunction.
>
> DL> 3 3.92472 319.0 -370.49747 -370.34748 -366.42276 .000 48.96
> DL> 4 4.22976 305.3 -371.13380 -370.99025 -366.76049 .000 52.20
> DL> 5 3.52748 288.6 -370.19907 -370.06334 -366.53586 .001 55.75
> DL> 6 3.28840 276.3 -369.96661 -369.83670 -366.54830 .001 54.76
> DL> 7 3.79151 269.8 -370.58147 -370.45460 -366.66309 .001 43.70
> DL> 8 3.77854 268.6 -370.52295 -370.39664 -366.61810 .001 43.22
> DL> 9 3.59004 273.2 -370.32378 -370.19530 -366.60527 .002 44.05
> DL> 10 3.48053 283.8 -370.23346 -370.09998 -366.61946 .002 43.19
> DL> .......................
> DL> .......................
> DL> 248 3.57992 1050.5 -370.66655 -370.17254 -366.59262 .270 42.99
> DL> 249 3.57719 1046.8 -370.66159 -370.16935 -366.59216 .269 41.47
> DL> 250 3.57912 1042.9 -370.66254 -370.17212 -366.59300 .269 38.90
> DL> 251 3.57836 1039.3 -370.65993 -370.17121 -366.59285 .268 43.86
> DL> 252 3.57595 1036.0 -370.65579 -370.16860 -366.59265 .267 42.58
> DL> 253 3.57593 1033.0 -370.65463 -370.16889 -366.59296 .267 40.59
> DL> 254 3.57641 1029.8 -370.65402 -370.16977 -366.59335 .266 44.35
> DL> 255 3.57504 1026.4 -370.65056 -370.16789 -366.59285 .266 44.05
> DL> 256 3.57670 1022.9 -370.65037 -370.16934 -366.59264 .265 43.99
> DL> 257 3.58117 1019.5 -370.65368 -370.17426 -366.59308 .265 44.41
>
> ok, your temperature has risen to >1000K (is that intentional?) and your
> Kohn-Sham energy has dropped. it seems that your starting structure was
> not in equilibrium. OTOH, if you are too far away from the BO-surface,
> it could mean anything or nothing.
>
> DL> 258 -NaNQ 1016.4**************************** -NaNQ .265 42.87
> DL> 259 NaNQ -NaNQ NaNQ -NaNQ -NaNQ .264 43.87
> DL> 260 NaNQ -NaNQ NaNQ -NaNQ -NaNQ NaNQ 42.20
> DL> 261 NaNQ -NaNQ NaNQ -NaNQ -NaNQ NaNQ 37.84
> DL> 262 NaNQ -NaNQ NaNQ -NaNQ -NaNQ NaNQ 38.56
>
> well seems like the fictitious dynamic of the electronic system
> could not keep up with atoms/ions anymore. again, it could be from a too
> large time step.
>
> hope this helps,
> axel kohlmeyer.
>
> DL> _______________________________________________
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> DL>
> DL>
>
> --
>
>
> =======================================================================
> Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
>
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