[DFTB-Plus-User] Request for Radial distribution function from md output and severe (174): SIGSEGV, segmentation fault occurred
Faruq, Muhammad
MAF2MPO at bolton.ac.uk
Tue Jan 5 13:05:07 CET 2016
Dear Dr Aradi/All
I want to calculate the RDF from the MD output. Could you please let me how can I do it. One more problem is that I am having a segmentation fault. Please suggest me what to do. Thanks in advanced.
Here are output and input file.
Output:..............
Total Energy: 59.7693903136 H
Total Mermin free energy: 59.7599550331 H
Volume: 0.271644E+05 au^3
Pressure: 0.138303E-01 au 0.406902E+12 Pa
MD Temperature:: NaN H NaN K
MD Kinetic Energy: NaN H
Total MD Energy: NaN H
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
dftb.exe 0000000000C41C39 Unknown Unknown Unknown
dftb.exe 0000000000C4050E Unknown Unknown Unknown
dftb.exe 0000000000BE1D52 Unknown Unknown Unknown
dftb.exe 0000000000B8B113 Unknown Unknown Unknown
dftb.exe 0000000000B8FEEB Unknown Unknown Unknown
libpthread.so.0 000000389640E4C0 Unknown Unknown Unknown
dftb.exe 000000000051023E Unknown Unknown Unknown
dftb.exe 00000000005111F3 Unknown Unknown Unknown
dftb.exe 000000000049B33E Unknown Unknown Unknown
dftb.exe 000000000043B8B5 Unknown Unknown Unknown
dftb.exe 000000000043B826 Unknown Unknown Unknown
libc.so.6 0000003895C1D974 Unknown Unknown Unknown
dftb.exe 000000000043B729 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
dftb.exe 0000000000C41C39 Unknown Unknown Unknown
dftb.exe 0000000000C4050E Unknown Unknown Unknown
dftb.exe 0000000000BE1D52 Unknown Unknown Unknown
dftb.exe 0000000000B8B113 Unknown Unknown Unknown
dftb.exe 0000000000B8FEEB Unknown Unknown Unknown
libpthread.so.0 000000389640E4C0 Unknown Unknown Unknown
dftb.exe 000000000051023E Unknown Unknown Unknown
dftb.exe 00000000005111F3 Unknown Unknown Unknown
dftb.exe 000000000049B33E Unknown Unknown Unknown
dftb.exe 000000000043B8B5 Unknown Unknown Unknown
dftb.exe 000000000043B826 Unknown Unknown Unknown
libc.so.6 0000003895C1D974 Unknown Unknown Unknown
dftb.exe 000000000043B729 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
dftb.exe 0000000000C41C39 Unknown Unknown Unknown
dftb.exe 0000000000C4050E Unknown Unknown Unknown
dftb.exe 0000000000BE1D52 Unknown Unknown Unknown
dftb.exe 0000000000B8B113 Unknown Unknown Unknown
dftb.exe 0000000000B8FEEB Unknown Unknown Unknown
libpthread.so.0 000000389640E4C0 Unknown Unknown Unknown
dftb.exe 000000000051023E Unknown Unknown Unknown
dftb.exe 00000000005111F3 Unknown Unknown Unknown
dftb.exe 000000000049B33E Unknown Unknown Unknown
dftb.exe 000000000043B8B5 Unknown Unknown Unknown
dftb.exe 000000000043B826 Unknown Unknown Unknown
libc.so.6 0000003895C1D974 Unknown Unknown Unknown
dftb.exe 000000000043B729 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
dftb.exe 0000000000C41C39 Unknown Unknown Unknown
dftb.exe 0000000000C4050E Unknown Unknown Unknown
dftb.exe 0000000000BE1D52 Unknown Unknown Unknown
dftb.exe 0000000000B8B113 Unknown Unknown Unknown
dftb.exe 0000000000B8FEEB Unknown Unknown Unknown
libpthread.so.0 000000389640E4C0 Unknown Unknown Unknown
dftb.exe 000000000051023E Unknown Unknown Unknown
dftb.exe 00000000005111F3 Unknown Unknown Unknown
dftb.exe 000000000049B33E Unknown Unknown Unknown
dftb.exe 000000000043B8B5 Unknown Unknown Unknown
dftb.exe 000000000043B826 Unknown Unknown Unknown
libc.so.6 0000003895C1D974 Unknown Unknown Unknown
dftb.exe 000000000043B729 Unknown Unknown Unknown
Total time: 91 sec
Here is input details:
Geometry = GenFormat {
<<< Cu5Si.gen
}
Driver = VelocityVerlet {
MovedAtoms = "1:-1"
Steps = 1415
TimeStep[Femtosecond] = 1.0 #Time interval between two MD steps
KeepStationary = No #Remove translational motion from the system
MDRestartFrequency=10
Velocities = {
<<< velocity.txt
}
ConvergentForcesOnly = No
Barostat = {
Pressure = 0
Timescale[ps] =1
}
Thermostat = NoseHoover{
Temperature[Kelvin] = 2000
CouplingStrength[cm^-1]=100
# IntegratorSteps = 1
}
OutputPrefix = "final_geo"
}
Hamiltonian = DFTB {
SCC = Yes
SCCTolerance = 1.0e-5
EwaldParameter = 0.1
MaxSCCIterations = 10000
Mixer = Broyden {
MixingParameter = 0.2
}
MaxAngularMomentum = {
Cu = "d"
Si = "d"
}
Filling = Fermi {
Temperature [Kelvin] = 300
}
SlaterKosterFiles = Type2FileNames {
Prefix = "/home/maf2mpo/FAST_cal_Others/DFTB+/sk/matsci-0-3/"
Separator = "-"
Suffix = ".skf"
}
KPointsAndWeights = {
0.0 0.0 0.0 1.0
}
ReadInitialCharges = Yes
}
Options = {
WriteEigenvectors = No
WriteResultsTag = Yes
WriteDetailedOut = Yes
WriteBandOut = Yes
}
160 F
Cu Si
1 1 0.1278333428E-01 0.2295439435E-01 0.3686574986E-01
2 1 0.2526126908E+00 0.4626727799E+00 0.2968527723E+00
3 1 0.4515813204E+00 0.2602742519E+00 0.2194274709E+00
4 1 0.2528154120E+00 0.2878714232E+00 0.4023040088E+00
5 1 0.3696926801E+00 0.1295438402E+00 0.8896370274E-01
6 2 0.4128157413E+00 0.3781843150E+00 0.3413019257E+00
7 1 0.1168146339E+00 0.1313519344E+00 0.3719349833E+00
8 1 0.1076629045E+00 0.4017313031E+00 0.1736873449E+00
9 1 0.9891989384E+00 0.1173363822E+00 0.2179776112E+00
10 1 0.2144012139E+00 0.4608000093E+00 0.4988322123E+00
11 1 0.4667824332E+00 0.3077896993E+00 0.3083697412E-01
12 1 0.2946229567E+00 0.1480266561E+00 0.2727627958E+00
13 1 0.1711327771E+00 0.2286693339E-01 0.1757141440E+00
14 1 0.4344612622E+00 0.2011977441E+00 0.4084214758E+00
15 1 0.8164011230E-01 0.3854714071E+00 0.3713660934E+00
16 1 0.2726653942E+00 0.2954940707E+00 0.1359959226E+00
17 1 0.1166643904E+00 0.1886990439E+00 0.8099467914E-01
18 1 0.4004296741E+00 0.4444842995E+00 0.1617705795E+00
19 2 0.3585143455E+00 0.3041561713E-01 0.4061282973E+00
20 2 0.1326473827E+00 0.2451169460E+00 0.2543370420E+00
21 1 0.4936515924E+00 -0.1037018618E-03 0.9392303485E-02
22 1 0.7709949774E+00 0.4323900263E+00 0.2803379588E+00
23 1 0.9337418247E+00 0.3079826011E+00 0.2118702993E+00
24 1 0.7415856676E+00 0.2778819725E+00 0.4119938180E+00
25 1 0.8732271409E+00 0.1818148217E+00 0.6865085173E-01
26 2 0.9018136603E+00 0.3608212795E+00 0.3835174887E+00
27 1 0.6164397545E+00 0.1300019477E+00 0.3610904721E+00
28 1 0.5980874233E+00 0.4158858083E+00 0.1381283842E+00
29 1 0.5355908095E+00 0.8452629736E-01 0.1859174660E+00
30 1 0.7178687889E+00 0.4666329826E+00 0.4760847289E+00
31 1 0.9939898303E+00 0.3316404563E+00 0.1795908752E-01
32 1 0.7898586891E+00 0.1676668805E+00 0.2505005470E+00
33 1 0.7292028327E+00 0.4566452510E-01 0.1067221828E+00
34 1 0.9218019914E+00 0.1706461961E+00 0.3990615471E+00
35 1 0.5794420776E+00 0.4358219072E+00 0.3358269307E+00
36 1 0.7859432029E+00 0.3628930245E+00 0.9502776582E-01
37 1 0.6410322874E+00 0.2248680969E+00 0.8824067538E-01
38 1 0.9590601422E+00 0.5004474023E+00 0.2560087267E+00
39 2 0.8119941203E+00 0.2568997462E-01 0.4531452508E+00
40 2 0.6415129044E+00 0.2841101444E+00 0.2626316514E+00
41 1 0.3032126159E-01 0.5261391018E+00 0.4257481883E-01
42 1 0.2172925846E+00 0.8552403719E+00 0.2781458556E+00
43 1 0.5070748160E+00 0.7615472848E+00 0.2528798306E+00
44 1 0.2507852364E+00 0.7733985099E+00 0.4591648537E+00
45 1 0.3988082362E+00 0.6416787568E+00 0.1359857555E+00
46 2 0.3832255064E+00 0.8544057958E+00 0.3635225843E+00
47 1 0.1076338769E+00 0.5811959689E+00 0.3709946786E+00
48 1 0.6366258101E-01 0.8572760206E+00 0.1398367664E+00
49 1 0.8305442058E-01 0.6707687991E+00 0.1985140104E+00
50 1 0.1970331253E+00 0.9640589881E+00 0.4450860484E+00
51 1 0.4218760479E+00 0.8338643959E+00 0.8798633395E-01
52 1 0.2671304825E+00 0.6613162891E+00 0.2799881906E+00
53 1 0.2216527526E+00 0.5551625275E+00 0.1134232846E+00
54 1 0.4205289369E+00 0.6888172093E+00 0.4160140058E+00
55 1 0.4610520564E-01 0.9522136410E+00 0.3125345315E+00
56 1 0.2355455628E+00 0.7600554457E+00 0.1048558382E+00
57 1 0.7198069578E-01 0.7145798221E+00 0.9996309266E+00
58 1 0.3693487479E+00 0.9748844948E+00 0.2157905827E+00
59 2 0.3622319444E+00 0.5297048590E+00 0.4233705221E+00
60 2 0.8721203921E-01 0.7622975246E+00 0.3830044918E+00
61 1 0.4929432959E+00 0.5117262617E+00 0.9972164602E+00
62 1 0.7309363813E+00 0.9816826340E+00 0.2959808608E+00
63 1 0.9381170956E+00 0.7899924393E+00 0.2817582021E+00
64 1 0.7236720631E+00 0.7184840578E+00 0.5021298927E+00
65 1 0.8981990929E+00 0.6451342353E+00 0.1352729178E+00
66 2 0.9381911307E+00 0.8995171961E+00 0.4410626618E+00
67 1 0.6049276375E+00 0.6295862719E+00 0.3704739423E+00
68 1 0.6001659670E+00 0.9000574558E+00 0.1446826275E+00
69 2 0.5359156258E+00 0.5757474159E+00 0.2166118590E+00
70 1 0.6735657632E+00 0.9090351577E+00 0.4696704331E+00
71 1 0.9024392560E+00 0.8124582484E+00 0.3284067435E-01
72 1 0.7980978679E+00 0.6575956884E+00 0.3220129213E+00
73 1 0.7109415299E+00 0.5784233180E+00 0.1586934281E+00
74 1 0.9197771931E+00 0.7186930234E+00 0.4662761852E+00
75 1 0.5371012206E+00 0.9487082385E+00 0.3277888420E+00
76 1 0.7646540823E+00 0.7891297220E+00 0.1746484901E+00
77 1 0.5773610069E+00 0.7075780985E+00 0.7272436213E-01
78 1 0.8884926337E+00 0.9493527844E+00 0.1762137338E+00
79 2 0.8867515413E+00 0.5370559839E+00 0.4223839306E+00
80 2 0.6716808555E+00 0.7991433000E+00 0.3339244491E+00
81 1 0.3619774922E-01 0.4221434959E-01 0.5326019801E+00
82 1 0.2434030826E+00 0.4292678316E+00 0.7987606160E+00
83 2 0.4910027005E+00 0.2863579430E+00 0.7648260274E+00
84 1 0.2882650816E+00 0.2428681672E+00 0.9441510931E+00
85 1 0.4568535327E+00 0.1901615872E+00 0.6077994671E+00
86 2 0.3998494474E+00 0.3894368574E+00 0.8817188368E+00
87 1 0.1497271453E+00 0.1004135326E+00 0.9058915592E+00
88 1 0.1161345367E+00 0.3832370705E+00 0.6543320137E+00
89 1 0.1176021287E+00 0.9228224549E-01 0.7103016952E+00
90 1 0.1810411143E+00 0.4031273621E+00 0.9928360946E+00
91 1 0.3952477498E+00 0.3622742574E+00 0.5178541786E+00
92 1 0.3042297309E+00 0.1167341609E+00 0.7752985405E+00
93 1 0.2918424364E+00 0.7932220966E-01 0.5773027975E+00
94 1 0.4602000122E+00 0.1582170144E+00 0.8916144594E+00
95 1 0.5185633450E-01 0.4134692797E+00 0.8411537125E+00
96 1 0.2909322391E+00 0.2821051823E+00 0.6684427897E+00
97 1 0.1446937835E+00 0.2121395329E+00 0.5520553037E+00
98 1 0.4167775516E+00 0.4361893461E+00 0.7015559364E+00
99 2 0.3201656569E+00 0.3078946895E-01 0.9352349214E+00
100 2 0.1608960511E+00 0.2545803310E+00 0.8029292836E+00
101 1 0.5178812138E+00 0.2883987588E-01 0.5052104789E+00
102 1 0.7710998641E+00 0.4498608404E+00 0.8037564300E+00
103 1 0.9907636939E+00 0.2452199086E+00 0.7220908341E+00
104 1 0.7286106417E+00 0.2823775931E+00 0.9214666820E+00
105 1 0.8765850750E+00 0.1463556669E+00 0.5944779565E+00
106 2 0.8974503002E+00 0.3186980777E+00 0.8525051116E+00
107 1 0.6469655380E+00 0.1009215609E+00 0.9330842701E+00
108 1 0.5781699213E+00 0.3525401722E+00 0.6073892987E+00
109 1 0.5938745445E+00 0.1224063746E+00 0.7396210599E+00
110 1 0.6899455118E+00 0.4935973928E+00 0.9788975112E+00
111 1 0.9708700194E+00 0.3127997700E+00 0.5335784344E+00
112 1 0.7876029593E+00 0.1452114510E+00 0.7822781078E+00
113 1 0.7328897247E+00 0.1086800585E-01 0.6279491742E+00
114 1 0.9590201528E+00 0.1482408600E+00 0.8901416872E+00
115 1 0.5717087409E+00 0.4484409283E+00 0.8250667115E+00
116 1 0.7779653332E+00 0.3206442238E+00 0.6042681614E+00
117 1 0.6469257183E+00 0.1744079579E+00 0.5534260863E+00
118 1 0.9254335963E+00 0.4302174359E+00 0.6876424463E+00
119 2 0.8225665978E+00 0.5315973872E-01 0.9514245599E+00
120 2 0.6700696846E+00 0.2975698627E+00 0.7529288897E+00
121 1 0.2383452768E-01 0.5226888453E+00 0.5414767822E+00
122 1 0.2883735717E+00 0.9165032292E+00 0.7762419514E+00
123 1 0.4582092094E+00 0.7776905360E+00 0.7621240945E+00
124 1 0.2396810254E+00 0.7627253553E+00 0.8970014940E+00
125 1 0.3651205652E+00 0.5944882757E+00 0.5925303737E+00
126 2 0.4030832846E+00 0.8715316974E+00 0.9112208804E+00
127 1 0.1409487752E+00 0.5943393122E+00 0.8581744226E+00
128 1 0.1520849342E+00 0.9114858936E+00 0.6330267102E+00
129 1 -0.5640914845E-02 0.6143424610E+00 0.7172276207E+00
130 1 0.1858690350E+00 0.9273047349E+00 0.9987635195E+00
131 1 0.4129309555E+00 0.8625860014E+00 0.5460171472E+00
132 1 0.3278358859E+00 0.6193954635E+00 0.7871905358E+00
133 1 0.1810747077E+00 0.5707264251E+00 0.6619612245E+00
134 1 0.4199613800E+00 0.6924074200E+00 0.9468169702E+00
135 1 0.9241757404E-01 0.9276312911E+00 0.8230238899E+00
136 1 0.2767447089E+00 0.7599493700E+00 0.6553155916E+00
137 1 0.9035918446E-01 0.7195803069E+00 0.5675303854E+00
138 1 0.4407411414E+00 0.4275061333E-02 0.6859591849E+00
139 2 0.3120670301E+00 0.5346727926E+00 0.9453631162E+00
140 2 0.1129281436E+00 0.7550663120E+00 0.7542974329E+00
141 1 0.5258104171E+00 0.5121355245E+00 0.5091859109E+00
142 1 0.7646658231E+00 0.9442630126E+00 0.8139530272E+00
143 1 0.9306871149E+00 0.7846077715E+00 0.7874488208E+00
144 1 0.7595544349E+00 0.6798411498E+00 0.9928659122E+00
145 1 0.8406311377E+00 0.5846513691E+00 0.5952565188E+00
146 2 0.9340247757E+00 0.9215275962E+00 0.8993962474E+00
147 1 0.5968736966E+00 0.6399477828E+00 0.8790442616E+00
148 1 0.5858818188E+00 0.8779678286E+00 0.6439557382E+00
149 2 0.5043228647E+00 0.6017891543E+00 0.7245170948E+00
150 1 0.6798676653E+00 0.8603412889E+00 0.9720385392E+00
151 1 0.9609005605E+00 0.8630789724E+00 0.6081602595E+00
152 1 0.7694850057E+00 0.6490397320E+00 0.7775888096E+00
153 1 0.6610429347E+00 0.5295796928E+00 0.6578053821E+00
154 1 0.9237233822E+00 0.6221074503E+00 0.9035605705E+00
155 1 0.5621479179E+00 0.9457569645E+00 0.8310900775E+00
156 1 0.7785223067E+00 0.8177853757E+00 0.6618157015E+00
157 1 0.5361640397E+00 0.6998727400E+00 0.5770901123E+00
158 1 0.9364354992E+00 0.1398291167E-01 0.7360353263E+00
159 2 0.8721562888E+00 0.4588113640E+00 0.9628021443E+00
160 2 0.6512059017E+00 0.7927150979E+00 0.7981363320E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.1244971267E+02 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.1244971267E+02 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.1244971267E+02
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