[CPMD-list] Segmentation fault for a molecular dynamics run

Dai Ling g0306324 at nus.edu.sg
Fri Apr 9 15:50:35 CEST 2004 

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> _______________________________________________
	DL> CPMD-list mailing list
	DL> CPMD-list at cpmd.org
	DL> http://www.cpmd.org/mailman/listinfo/cpmd-list
	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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