Enter a model name: === Verification check vc-memory-leak start (2022-11-30 10:16:18) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MunetohMotookaMoriguchi_2007_SiO__MO_501246546792_000 Supported species : O Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = O (Configuration in file "config-F-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 217.61081162453226 Forces: 1 -8.44049728e+00 -1.81643746e+01 -3.84496885e+01 2 -2.94652997e+01 4.25760628e+01 -2.40878316e+01 3 4.34283139e+01 -2.76749352e+01 -2.41628557e+01 4 -2.31104281e+01 2.30669568e+01 7.00036006e+00 5 2.02454732e+01 -5.27980285e+01 -6.18063435e+00 6 1.93896130e+01 -1.41643262e+00 -1.23656769e+01 7 6.16496827e+00 -5.03216333e+01 -5.25694010e+01 8 -4.02247140e+01 -2.77176255e+01 -2.74033255e+00 9 -2.39418855e+01 -8.99668108e+00 -3.61038622e+01 10 -4.61384525e+00 3.85397435e+01 -2.69978040e+01 11 -6.40683854e+00 -2.76020270e+01 2.02743352e+01 12 -1.58910411e+01 1.78565633e+01 1.49188414e+01 13 -2.09850539e+01 -2.54727497e+01 -1.12529376e+02 14 1.68689186e+01 1.67745026e+01 -1.58664392e+01 15 9.84657770e+01 -1.55421670e+01 1.36445605e+01 16 -1.88469417e+01 8.01971369e+01 2.65015130e+01 17 -5.37180624e+01 -7.02104910e+00 4.48203667e+01 18 1.78542845e+01 1.53667629e+01 -6.92840296e+00 19 1.19987713e+01 -3.22519104e+01 1.04546759e+01 20 -2.26456653e+01 1.61718018e+01 2.37861739e+01 21 -2.02675774e+01 -2.91393657e+01 2.76619846e+01 22 5.52067227e+01 2.24668268e+01 3.25778555e+01 23 9.02216959e+00 -2.58598227e+00 1.03477458e+01 24 3.40222812e+00 5.45847941e+00 9.82740994e+00 25 -1.48402680e+01 5.07769537e+00 -4.09999242e+00 26 -2.27700537e+01 3.51745673e+01 -2.99070378e+01 27 4.35547676e+01 -6.83377560e+01 1.27299303e+01 28 -8.19720459e+01 6.00585285e+01 1.06502303e+01 29 -2.63158829e+01 -1.55369544e+01 3.57933723e+01 30 2.76274665e+01 2.53358552e+01 1.26661984e+01 31 3.35173081e+01 -8.12357779e+00 3.37061569e+01 32 2.77093186e+01 1.45817669e+01 4.56276245e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = O (Configuration in file "config-T-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 217.61081162453226 Forces: 1 -8.44049728e+00 -1.81643746e+01 -3.84496885e+01 2 -2.94652997e+01 4.25760628e+01 -2.40878316e+01 3 4.34283139e+01 -2.76749352e+01 -2.41628557e+01 4 -2.31104281e+01 2.30669568e+01 7.00036006e+00 5 2.02454732e+01 -5.27980285e+01 -6.18063435e+00 6 1.93896130e+01 -1.41643262e+00 -1.23656769e+01 7 6.16496827e+00 -5.03216333e+01 -5.25694010e+01 8 -4.02247140e+01 -2.77176255e+01 -2.74033255e+00 9 -2.39418855e+01 -8.99668108e+00 -3.61038622e+01 10 -4.61384525e+00 3.85397435e+01 -2.69978040e+01 11 -6.40683854e+00 -2.76020270e+01 2.02743352e+01 12 -1.58910411e+01 1.78565633e+01 1.49188414e+01 13 -2.09850539e+01 -2.54727497e+01 -1.12529376e+02 14 1.68689186e+01 1.67745026e+01 -1.58664392e+01 15 9.84657770e+01 -1.55421670e+01 1.36445605e+01 16 -1.88469417e+01 8.01971369e+01 2.65015130e+01 17 -5.37180624e+01 -7.02104910e+00 4.48203667e+01 18 1.78542845e+01 1.53667629e+01 -6.92840296e+00 19 1.19987713e+01 -3.22519104e+01 1.04546759e+01 20 -2.26456653e+01 1.61718018e+01 2.37861739e+01 21 -2.02675774e+01 -2.91393657e+01 2.76619846e+01 22 5.52067227e+01 2.24668268e+01 3.25778555e+01 23 9.02216959e+00 -2.58598227e+00 1.03477458e+01 24 3.40222812e+00 5.45847941e+00 9.82740994e+00 25 -1.48402680e+01 5.07769537e+00 -4.09999242e+00 26 -2.27700537e+01 3.51745673e+01 -2.99070378e+01 27 4.35547676e+01 -6.83377560e+01 1.27299303e+01 28 -8.19720459e+01 6.00585285e+01 1.06502303e+01 29 -2.63158829e+01 -1.55369544e+01 3.57933723e+01 30 2.76274665e+01 2.53358552e+01 1.26661984e+01 31 3.35173081e+01 -8.12357779e+00 3.37061569e+01 32 2.77093186e+01 1.45817669e+01 4.56276245e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 195.9128783241771 Forces: 1 -7.36463215e+00 -1.68746191e+01 -1.57042302e+01 2 -6.20495854e+00 -6.47531622e+00 -1.88916185e+01 3 -1.29070172e+01 -2.55625225e+01 -1.37542112e+01 4 -1.49880167e+01 6.50758249e+00 1.14649919e+01 5 -4.48552406e+00 -2.93264658e+01 -2.21204731e+01 6 2.79605129e+01 -8.68482467e-01 -2.60637237e+01 7 2.27786906e+01 -3.14968770e+01 1.94987593e+00 8 -1.67637388e+01 1.93820933e+01 -5.52455889e+01 9 -1.31440301e+01 -1.08761315e+00 -8.58229616e+00 10 1.00964999e+01 9.67287446e+00 -1.92905021e+01 11 -1.98606304e+01 -1.16576822e+00 1.19140721e+01 12 -1.04121798e+01 1.38345101e+01 9.35532277e+00 13 -5.70513833e+00 1.77178674e+01 -5.90025696e+01 14 2.17810037e+01 1.47012312e+01 -2.40374992e+01 15 5.24812239e+01 2.13668846e+01 1.60081987e+01 16 -1.49532624e+01 2.66536386e+01 2.46845691e+01 17 -2.05450525e+01 -1.80278374e+01 6.03618818e+00 18 -1.21568061e+01 1.68839849e+01 -7.06712708e+00 19 -1.34961172e+01 -2.01775127e+01 1.55512973e+01 20 -1.50173977e+01 -1.25577109e+00 1.26966516e+01 21 5.32322450e+00 -9.09470369e+01 2.70807221e+01 22 8.33464352e+01 -1.29637362e+01 -2.11645307e+01 23 1.27302840e+01 -1.61588918e+01 1.08874286e+01 24 -3.45204310e+01 8.20234535e+00 7.25346663e+01 25 -1.57434257e+01 -2.98240893e+00 -6.13366679e+00 26 -1.62714823e+01 2.89495734e+01 -4.54676498e+01 27 -6.42412378e+00 -2.37771526e+01 2.51687720e+01 28 -2.66086365e+01 9.46545104e+00 1.97095131e+01 29 -2.61211441e+01 4.95474193e+01 1.28788652e+01 30 6.44819616e+00 1.94512479e+01 -6.28923625e+00 31 2.08631020e+01 1.79369945e+01 3.47767827e+01 32 4.98845724e+01 1.88743136e+01 3.61170058e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 195.9128783241771 Forces: 1 -7.36463215e+00 -1.68746191e+01 -1.57042302e+01 2 -6.20495854e+00 -6.47531622e+00 -1.88916185e+01 3 -1.29070172e+01 -2.55625225e+01 -1.37542112e+01 4 -1.49880167e+01 6.50758249e+00 1.14649919e+01 5 -4.48552406e+00 -2.93264658e+01 -2.21204731e+01 6 2.79605129e+01 -8.68482467e-01 -2.60637237e+01 7 2.27786906e+01 -3.14968770e+01 1.94987593e+00 8 -1.67637388e+01 1.93820933e+01 -5.52455889e+01 9 -1.31440301e+01 -1.08761315e+00 -8.58229616e+00 10 1.00964999e+01 9.67287446e+00 -1.92905021e+01 11 -1.98606304e+01 -1.16576822e+00 1.19140721e+01 12 -1.04121798e+01 1.38345101e+01 9.35532277e+00 13 -5.70513833e+00 1.77178674e+01 -5.90025696e+01 14 2.17810037e+01 1.47012312e+01 -2.40374992e+01 15 5.24812239e+01 2.13668846e+01 1.60081987e+01 16 -1.49532624e+01 2.66536386e+01 2.46845691e+01 17 -2.05450525e+01 -1.80278374e+01 6.03618818e+00 18 -1.21568061e+01 1.68839849e+01 -7.06712708e+00 19 -1.34961172e+01 -2.01775127e+01 1.55512973e+01 20 -1.50173977e+01 -1.25577109e+00 1.26966516e+01 21 5.32322450e+00 -9.09470369e+01 2.70807221e+01 22 8.33464352e+01 -1.29637362e+01 -2.11645307e+01 23 1.27302840e+01 -1.61588918e+01 1.08874286e+01 24 -3.45204310e+01 8.20234535e+00 7.25346663e+01 25 -1.57434257e+01 -2.98240893e+00 -6.13366679e+00 26 -1.62714823e+01 2.89495734e+01 -4.54676498e+01 27 -6.42412378e+00 -2.37771526e+01 2.51687720e+01 28 -2.66086365e+01 9.46545104e+00 1.97095131e+01 29 -2.61211441e+01 4.95474193e+01 1.28788652e+01 30 6.44819616e+00 1.94512479e+01 -6.28923625e+00 31 2.08631020e+01 1.79369945e+01 3.47767827e+01 32 4.98845724e+01 1.88743136e+01 3.61170058e+01 MIXED STRUCTURE (pbc=False)-- Species = O Si (Configuration in file "config-F-OSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 68.9875798746988 Forces: 1 -3.13137776e+01 -2.68735997e+01 -2.21958760e+01 2 2.63511783e+01 2.24729173e+01 -2.42814539e+01 3 2.41346000e+01 -3.78178660e+01 -3.42169657e+00 4 -2.14752119e+01 1.13111862e+01 6.54138595e+00 5 -1.33773014e+01 -6.63579630e+00 -9.63731822e+00 6 1.31194851e+01 6.44438106e+00 -7.23759783e+00 7 1.25811600e+01 -9.87825041e+00 1.58962956e+01 8 -1.39657757e+01 9.96934063e+00 2.03473176e+00 9 -3.31172455e+01 -2.06690683e+01 -1.97777793e+01 10 2.29782371e+01 1.99692315e+01 -6.13575998e+00 11 3.35099699e+01 2.00518367e+01 -4.35673502e+01 12 -1.20892012e+01 2.37477545e+01 2.97383224e+00 13 -1.44994042e+01 -6.16021237e+00 -1.25495722e+01 14 2.55631918e+01 7.67411965e+00 -3.25910595e+01 15 1.71037085e+01 -1.18975589e+01 2.25626152e+01 16 -2.96485364e+01 9.58844588e+00 9.31067772e+00 17 -2.92690717e+01 -2.98262774e+01 -7.05053002e+00 18 3.99051211e+01 -4.52738229e+01 -9.92263349e-01 19 1.50886096e+01 -1.43304820e+01 2.51003564e+01 20 -1.12970935e+01 5.60616227e+00 9.08773740e+00 21 1.02120427e+01 -2.04060386e+00 3.36239492e+00 22 1.22810290e+01 -1.91520175e+00 -2.49731061e+01 23 6.95154889e-01 -3.92369995e+00 3.13673610e+00 24 -1.14123657e+01 -3.15422331e+01 9.32314851e+00 25 -7.23174699e+01 4.18646248e+01 3.34377303e+01 26 -4.17057134e+00 1.01652082e+01 4.40181094e+00 27 -4.66736966e+00 2.44532070e+01 4.79129028e+01 28 9.29912294e-01 2.52173891e+00 6.84101834e-01 29 8.01620293e+00 4.77635675e+00 -1.55936779e+01 30 3.92833054e+00 6.50655898e+00 1.51824694e+01 31 2.70571875e+01 1.93685200e+01 1.66878609e+01 32 9.16527460e+00 2.29308267e+00 2.36825303e+00 MIXED STRUCTURE (pbc=True)-- Species = O Si (Configuration in file "config-T-OSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 79.19201872378203 Forces: 1 -4.24599669e+01 -2.56684355e+01 -8.76309855e+00 2 3.56143032e+01 2.46241231e+01 -1.49369950e+01 3 2.49837098e+01 -3.12211677e+01 -3.46386907e+00 4 -1.72461057e+01 1.11563678e+01 6.03423401e+00 5 -1.48357154e+01 -3.35317299e+00 -1.21205783e+01 6 8.49602343e+00 6.12911761e+00 -1.08190771e+01 7 1.11132318e+01 -1.04920541e+01 1.64102558e+01 8 -1.30811855e+01 8.56176988e+00 2.67676438e+00 9 -2.70202989e+01 -2.58237885e+01 -2.52363475e+01 10 2.80622342e+01 1.94692723e+01 -1.61497614e+00 11 3.43641704e+01 2.10389622e+01 -4.31574891e+01 12 -1.04254458e+01 1.47081367e+01 -9.80330946e-01 13 -1.79330993e+01 -7.29413448e+00 -1.55910756e+01 14 1.98268805e+01 9.64279580e+00 -3.68246570e+01 15 1.29056086e+01 -1.23687955e+01 2.19436427e+01 16 -2.99232220e+01 6.03755772e+00 1.08318597e+01 17 -1.71707663e+01 -3.43244351e+01 1.05709514e+00 18 4.74365607e+01 -4.54295252e+01 3.02987059e-01 19 3.03458685e+01 -1.72528919e+01 1.64565606e+01 20 -1.43939001e+01 1.00901131e+01 -1.92483302e+00 21 1.09592414e+01 -9.52993888e-01 4.40427954e+00 22 -1.29725639e+01 -7.10957739e-01 -3.06343401e+01 23 -6.99460437e+00 -1.24999755e+01 1.62392758e+00 24 -1.12804836e+01 -3.09040176e+01 8.83085748e+00 25 -5.48004584e+01 5.69675589e+01 3.40912112e+01 26 -1.20102024e+00 3.70072826e+00 -4.52036735e+00 27 -3.13031842e+00 2.50677934e+01 5.30451715e+01 28 -5.37782444e+00 -1.46806367e+00 8.55760551e-02 29 8.31314274e+00 5.09184124e+00 -1.56663033e+01 30 -3.35663255e+00 1.20304116e+01 2.03446460e+01 31 2.12610369e+01 1.99005107e+01 2.14731446e+01 32 9.92159949e+00 5.54734925e+00 6.64212467e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1819517== Memcheck, a memory error detector ==1819517== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1819517== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1819517== Command: python runner2.py Tersoff_LAMMPS_MunetohMotookaMoriguchi_2007_SiO__MO_501246546792_000 ==1819517== ==1820803== Warning: invalid file descriptor 1024 in syscall close() ==1820803== Warning: invalid file descriptor 1025 in syscall close() ==1820803== Warning: invalid file descriptor 1026 in syscall close() ==1820803== Warning: invalid file descriptor 1027 in syscall close() ==1820803== Use --log-fd= to select an alternative log fd. ==1820803== Warning: invalid file descriptor 1028 in syscall close() ==1820803== Warning: invalid file descriptor 1029 in syscall close() ==1819517== ==1819517== HEAP SUMMARY: ==1819517== in use at exit: 2,262,439 bytes in 1,708 blocks ==1819517== total heap usage: 89,520 allocs, 87,812 frees, 66,917,373 bytes allocated ==1819517== ==1819517== LEAK SUMMARY: ==1819517== definitely lost: 0 bytes in 0 blocks ==1819517== indirectly lost: 0 bytes in 0 blocks ==1819517== possibly lost: 180,827 bytes in 103 blocks ==1819517== still reachable: 2,081,580 bytes in 1,604 blocks ==1819517== of which reachable via heuristic: ==1819517== stdstring : 38 bytes in 1 blocks ==1819517== suppressed: 32 bytes in 1 blocks ==1819517== Rerun with --leak-check=full to see details of leaked memory ==1819517== ==1819517== For lists of detected and suppressed errors, rerun with: -s ==1819517== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8151 from 587) ================================================================================ 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. === Verification check vc-memory-leak end (2022-11-30 10:16:49) ===