!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! VERIFICATION CHECK: vc-memory-leak !!!!! !!!!! !!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Description: Check that the model has no memory leaks. This is tested using the Valgrind memory debugging tool (http://valgrind.org) by performing a series of energy and force calculations on a randomly distorted face-centered cubic (FCC) cube base structure for both non-periodic and periodic boundary conditions. Separate configurations are tested for each species supported by the model, as well as one containing a random distribution of all species. Configurations used for testing are provided as auxiliary files. Author: Ellad Tadmor and Daniel S. Karls ----------------------------------------------------------------------------------------------------- Results for KIM Model : Tersoff_LAMMPS_Tersoff_1989_SiC__MO_171585019474_004 Supported species : C Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = C (Configuration in file "config-F-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 192.84954524394897 Forces: 1 -6.57564229e+00 -1.28580971e+01 -2.46761753e+01 2 -2.06761098e+01 2.25108520e+01 -3.10950245e+01 3 2.14971248e+01 -2.35107620e+01 -1.66732856e+01 4 -2.67254771e+01 1.25579598e+01 4.67671930e+00 5 -1.25575108e+01 -4.45426067e+01 8.46208327e+00 6 3.68087902e+01 9.37523525e+00 -1.97036872e+01 7 1.64257338e+00 -7.55855071e+01 -7.18144904e+01 8 -1.26008503e+01 -4.93088813e+01 7.07404065e+00 9 -1.52793238e+01 -2.26501476e+01 -5.90702197e+01 10 -1.63243209e+01 4.53126159e+01 -7.39546205e+01 11 -3.13534964e+01 -6.51286333e+01 -1.02253482e+01 12 -3.86832593e+01 3.69785690e+01 1.25200637e+01 13 -1.91086452e+01 -4.90607349e+00 -1.12951539e+02 14 2.43835980e+01 2.15049143e+01 -2.01118883e+01 15 1.00165885e+02 -7.21973294e+00 2.96196580e+00 16 3.26089524e+01 8.16118874e+01 5.35374496e+01 17 -3.82419303e+01 -1.25325194e+01 2.98486813e+00 18 1.72408440e+01 2.85708666e+01 -1.41298773e+01 19 1.51304345e+01 -3.37983210e+01 3.71582183e+01 20 -1.29350472e+01 1.07901880e+01 1.67908680e+01 21 -1.65198853e+01 -2.12157323e+01 1.11440736e+01 22 4.24061832e+01 6.14156948e+01 6.61278845e+01 23 6.07154084e+00 -3.63602886e+00 1.34426506e+01 24 3.96031523e-01 -1.18904422e+01 1.62350253e+01 25 -3.84796809e+01 -1.18777213e+01 5.21536333e+01 26 -1.53071248e+01 3.27911829e+01 -7.34158134e+00 27 3.23967886e+01 -7.33548396e+01 2.00285259e+01 28 -8.97638378e+01 5.96789953e+01 1.11152540e+01 29 -3.99359408e+01 -1.43821176e+01 1.74303544e+01 30 4.72680289e+01 4.53860801e+01 1.15354668e+01 31 4.04074605e+01 -9.79917431e+00 5.85434899e+01 32 3.26438478e+01 2.97122965e+01 3.78251017e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 192.84954524394897 Forces: 1 -6.57564229e+00 -1.28580971e+01 -2.46761753e+01 2 -2.06761098e+01 2.25108520e+01 -3.10950245e+01 3 2.14971248e+01 -2.35107620e+01 -1.66732856e+01 4 -2.67254771e+01 1.25579598e+01 4.67671930e+00 5 -1.25575108e+01 -4.45426067e+01 8.46208327e+00 6 3.68087902e+01 9.37523525e+00 -1.97036872e+01 7 1.64257338e+00 -7.55855071e+01 -7.18144904e+01 8 -1.26008503e+01 -4.93088813e+01 7.07404065e+00 9 -1.52793238e+01 -2.26501476e+01 -5.90702197e+01 10 -1.63243209e+01 4.53126159e+01 -7.39546205e+01 11 -3.13534964e+01 -6.51286333e+01 -1.02253482e+01 12 -3.86832593e+01 3.69785690e+01 1.25200637e+01 13 -1.91086452e+01 -4.90607349e+00 -1.12951539e+02 14 2.43835980e+01 2.15049143e+01 -2.01118883e+01 15 1.00165885e+02 -7.21973294e+00 2.96196580e+00 16 3.26089524e+01 8.16118874e+01 5.35374496e+01 17 -3.82419303e+01 -1.25325194e+01 2.98486813e+00 18 1.72408440e+01 2.85708666e+01 -1.41298773e+01 19 1.51304345e+01 -3.37983210e+01 3.71582183e+01 20 -1.29350472e+01 1.07901880e+01 1.67908680e+01 21 -1.65198853e+01 -2.12157323e+01 1.11440736e+01 22 4.24061832e+01 6.14156948e+01 6.61278845e+01 23 6.07154084e+00 -3.63602886e+00 1.34426506e+01 24 3.96031523e-01 -1.18904422e+01 1.62350253e+01 25 -3.84796809e+01 -1.18777213e+01 5.21536333e+01 26 -1.53071248e+01 3.27911829e+01 -7.34158134e+00 27 3.23967886e+01 -7.33548396e+01 2.00285259e+01 28 -8.97638378e+01 5.96789953e+01 1.11152540e+01 29 -3.99359408e+01 -1.43821176e+01 1.74303544e+01 30 4.72680289e+01 4.53860801e+01 1.15354668e+01 31 4.04074605e+01 -9.79917431e+00 5.85434899e+01 32 3.26438478e+01 2.97122965e+01 3.78251017e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 196.85373897252714 Forces: 1 -7.42957039e+00 -2.23849920e+01 -1.64378414e+01 2 -2.03883380e+01 -2.59842302e+00 -1.87151569e+01 3 -1.19938426e+01 -2.07472091e+01 -7.73907903e+00 4 -1.29891897e+01 7.56680586e+00 1.22448703e+01 5 -7.88067300e+00 -2.98476137e+01 -1.93671877e+01 6 3.80621641e+01 2.68213114e+00 -2.26343252e+01 7 2.92484923e+01 -3.05602687e+01 1.22768808e+00 8 -2.98157785e+01 2.37060037e+01 -5.88933363e+01 9 -1.20445518e+01 2.03556064e+00 -1.29940148e+01 10 1.01838459e+01 1.02629545e+01 -1.92503550e+01 11 -2.68254880e+01 3.81197054e+00 1.20366451e+01 12 -1.06443502e+01 1.46159758e+01 8.06783240e+00 13 -1.08025779e+01 1.10437500e+01 -6.54920264e+01 14 1.92970842e+01 1.12895423e+01 -2.25258306e+01 15 5.96036826e+01 2.01645947e+01 5.57978670e+00 16 -1.95136962e+01 3.58123929e+01 2.35808035e+01 17 -9.49644028e+00 -9.23223585e+00 5.12141010e+00 18 -2.66074424e+01 -1.77876935e+01 -1.58529142e+01 19 -1.72705160e+01 -2.96166230e+01 1.31862100e+01 20 -1.99727435e+01 1.21155709e+00 1.24962482e+01 21 -8.00776953e+00 -9.28417790e+01 3.37127426e+01 22 8.71819925e+01 -7.81740898e+00 1.12999627e+01 23 1.10057459e+01 -9.36938309e+00 7.78725363e+00 24 1.11119372e+01 1.06485762e+01 4.53949604e+01 25 -1.50934965e+01 -4.73857050e+00 3.66078535e-01 26 -1.21585488e+01 3.40092192e+01 -4.97066196e+01 27 -1.68281302e+01 -9.66375960e+00 3.27448259e+01 28 -2.36773509e+01 8.87827994e+00 2.27516684e+01 29 -2.31296576e+01 4.76238732e+01 9.23838184e+00 30 7.67292624e+00 1.45756215e+01 -2.64780250e+00 31 2.15015986e+01 6.27538141e+00 3.74694429e+01 32 4.77006824e+01 2.09917693e+01 3.79496785e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 196.85373897252714 Forces: 1 -7.42957039e+00 -2.23849920e+01 -1.64378414e+01 2 -2.03883380e+01 -2.59842302e+00 -1.87151569e+01 3 -1.19938426e+01 -2.07472091e+01 -7.73907903e+00 4 -1.29891897e+01 7.56680586e+00 1.22448703e+01 5 -7.88067300e+00 -2.98476137e+01 -1.93671877e+01 6 3.80621641e+01 2.68213114e+00 -2.26343252e+01 7 2.92484923e+01 -3.05602687e+01 1.22768808e+00 8 -2.98157785e+01 2.37060037e+01 -5.88933363e+01 9 -1.20445518e+01 2.03556064e+00 -1.29940148e+01 10 1.01838459e+01 1.02629545e+01 -1.92503550e+01 11 -2.68254880e+01 3.81197054e+00 1.20366451e+01 12 -1.06443502e+01 1.46159758e+01 8.06783240e+00 13 -1.08025779e+01 1.10437500e+01 -6.54920264e+01 14 1.92970842e+01 1.12895423e+01 -2.25258306e+01 15 5.96036826e+01 2.01645947e+01 5.57978670e+00 16 -1.95136962e+01 3.58123929e+01 2.35808035e+01 17 -9.49644028e+00 -9.23223585e+00 5.12141010e+00 18 -2.66074424e+01 -1.77876935e+01 -1.58529142e+01 19 -1.72705160e+01 -2.96166230e+01 1.31862100e+01 20 -1.99727435e+01 1.21155709e+00 1.24962482e+01 21 -8.00776953e+00 -9.28417790e+01 3.37127426e+01 22 8.71819925e+01 -7.81740898e+00 1.12999627e+01 23 1.10057459e+01 -9.36938309e+00 7.78725363e+00 24 1.11119372e+01 1.06485762e+01 4.53949604e+01 25 -1.50934965e+01 -4.73857050e+00 3.66078535e-01 26 -1.21585488e+01 3.40092192e+01 -4.97066196e+01 27 -1.68281302e+01 -9.66375960e+00 3.27448259e+01 28 -2.36773509e+01 8.87827994e+00 2.27516684e+01 29 -2.31296576e+01 4.76238732e+01 9.23838184e+00 30 7.67292624e+00 1.45756215e+01 -2.64780250e+00 31 2.15015986e+01 6.27538141e+00 3.74694429e+01 32 4.77006824e+01 2.09917693e+01 3.79496785e+01 MIXED STRUCTURE (pbc=False)-- Species = C Si (Configuration in file "config-F-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 91.27111402804553 Forces: 1 -1.86091224e+01 -1.50958034e+01 -1.68371806e+01 2 4.99268336e+00 1.50199941e+01 -4.65178023e+01 3 2.22944846e+01 -4.99794599e+01 -1.38913931e+01 4 -7.80175714e+01 1.41514190e+01 -3.04644679e+01 5 9.33357720e-01 -1.28387432e+01 -1.42434630e+01 6 1.37565468e+01 -2.66699406e+00 -9.34886791e+00 7 5.97708003e+00 -6.25181636e+00 -2.61737307e+00 8 1.46429265e+01 -1.33209142e+01 3.05473204e+01 9 -1.10270009e+01 -1.14653749e+01 -1.17316549e+01 10 1.77575763e+01 1.57593653e+01 -1.53974071e+01 11 6.99614049e+00 2.86269636e+00 -1.55998377e+00 12 -9.01610972e+00 1.27184821e+01 1.00335384e+01 13 -2.47883436e+01 2.08615880e+01 -3.57628702e+01 14 2.00711114e+01 3.02268439e+01 -1.18761333e+01 15 1.62844064e+01 -1.26148686e+01 1.26114956e+01 16 -9.60778282e+00 5.97569865e+00 9.17104182e+00 17 -3.12592405e+01 -3.74557231e+01 5.84662164e+00 18 7.34560347e+01 -9.88304617e+00 4.77882010e+01 19 6.61604971e+01 -6.64837966e+01 1.80026790e+01 20 -6.09995121e+01 7.02345053e+01 8.65417023e+00 21 5.34130075e+00 -1.44082883e+01 1.70520165e+01 22 1.86606965e+01 3.59356394e+00 -1.10929511e+01 23 9.93925706e+00 -2.74317948e+01 1.14232536e+01 24 -2.54738180e+01 -1.71823220e+01 8.61535068e+00 25 -5.30308212e+01 4.99748808e+01 2.94651222e+01 26 6.00560408e+00 5.35737266e+00 -3.00341735e+00 27 1.54126503e+00 3.96267912e+00 8.88406139e+00 28 -9.72970421e-02 -2.28770303e-01 -4.55809571e-01 29 2.69147256e-02 -1.71743479e+00 -8.66258725e+00 30 -4.99697579e-01 4.59660178e+00 7.02839623e+00 31 1.67169474e+01 3.76457460e+01 5.12366640e+00 32 8.71486379e-01 6.08371346e+00 3.21642736e+00 MIXED STRUCTURE (pbc=True)-- Species = C Si (Configuration in file "config-T-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 139.14531644408444 Forces: 1 -5.25507855e+00 -3.91625904e+01 -7.15768068e+00 2 1.41808269e+01 2.63304990e+01 -4.06496369e+01 3 3.27259590e+01 -3.25408909e+01 -1.81726162e+01 4 -5.22790558e+01 2.56517884e+01 -3.50835995e+01 5 6.18912711e-01 -1.24455768e+01 -1.41556673e+01 6 -2.20200207e+01 1.81834619e+01 -5.70120491e+00 7 2.82762674e+00 -7.68989912e+00 -2.03665796e+00 8 1.35283001e+01 -1.34598728e+01 3.11239381e+01 9 -1.11296969e+01 -1.12174275e+01 -1.22238326e+01 10 1.94993180e+01 1.23990174e+01 -1.56589341e+01 11 7.71884001e+00 5.77524340e+00 -3.48453357e+00 12 -5.07042083e+00 -1.25953086e+01 1.16923982e+01 13 -2.38882604e+01 2.01586653e+01 -3.53931611e+01 14 1.52297123e+01 3.08000377e+01 -1.69222093e+01 15 9.39032246e+00 -1.65736454e+01 1.26188820e+01 16 -4.38643512e+00 2.48693980e+00 2.33445103e+00 17 -1.36164362e+01 -4.40178028e+01 -6.94018117e-01 18 7.89202831e+01 -1.05675027e+01 4.63919843e+01 19 7.89721625e+01 -7.17564522e+01 7.30499673e+00 20 -5.39513656e+01 7.99373976e+01 -2.54195070e-01 21 4.05646950e+00 -9.99957649e+00 1.88776170e+01 22 -3.17161915e+01 2.93056624e+00 -8.26599188e+00 23 -5.29250015e+00 -2.70509558e+01 1.57023033e+01 24 -2.75635706e+01 -1.75964096e+01 6.49908955e+00 25 -3.07055122e+01 6.32526631e+01 3.07222706e+01 26 4.46829118e+00 -2.17407153e+00 6.22118679e+00 27 -6.21249130e-01 4.34538445e-01 1.12681619e+01 28 4.81798620e-01 -4.76288726e+00 2.71956255e+00 29 1.41227252e-01 -2.58563105e-02 -7.12869727e+00 30 -9.27148039e+00 2.08490539e+00 9.36551443e+00 31 1.28390746e+01 3.87571395e+01 7.16971775e+00 32 1.16814909e+00 4.45386305e+00 2.97056214e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==95561== Memcheck, a memory error detector ==95561== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==95561== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==95561== Command: python runner2.py Tersoff_LAMMPS_Tersoff_1989_SiC__MO_171585019474_004 ==95561== ==96803== Warning: invalid file descriptor 255988 in syscall close() ==96803== Warning: invalid file descriptor 255989 in syscall close() ==96803== Warning: invalid file descriptor 255990 in syscall close() ==96803== Warning: invalid file descriptor 255991 in syscall close() ==96803== Use --log-fd= to select an alternative log fd. ==96803== Warning: invalid file descriptor 255992 in syscall close() ==96803== Warning: invalid file descriptor 255993 in syscall close() ==95561== ==95561== HEAP SUMMARY: ==95561== in use at exit: 2,259,527 bytes in 1,705 blocks ==95561== total heap usage: 89,510 allocs, 87,805 frees, 58,432,724 bytes allocated ==95561== ==95561== LEAK SUMMARY: ==95561== definitely lost: 0 bytes in 0 blocks ==95561== indirectly lost: 0 bytes in 0 blocks ==95561== possibly lost: 180,827 bytes in 103 blocks ==95561== still reachable: 2,078,668 bytes in 1,601 blocks ==95561== of which reachable via heuristic: ==95561== stdstring : 38 bytes in 1 blocks ==95561== suppressed: 32 bytes in 1 blocks ==95561== Rerun with --leak-check=full to see details of leaked memory ==95561== ==95561== For lists of detected and suppressed errors, rerun with: -s ==95561== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8139 from 546) ================================================================================ To pass this verification check the number of bytes that are "definitely lost" or "indirectly lost" must be zero. NOTE that Valgrind will typically report non-zero "possibly lost" bytes due to Python's internal memory allocation and garbage collection that it does not monitor. Full Valgrind output written to auxiliary file "valgrind.out" Grade: P Comment: No memory leak detected.