!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_SiGe__MO_350526375143_004 Supported species : Ge Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ge (Configuration in file "config-F-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 336.07132650818346 Forces: 1 -1.53275356e+01 -3.27264998e+01 -3.85864339e+01 2 -1.61050808e+01 5.95823233e+00 -3.55863032e+01 3 6.68786397e+00 -3.94780405e+01 -1.43397412e+01 4 -2.23343961e+01 3.87733000e+01 1.81413808e+01 5 8.67050763e+00 -3.50086753e+01 -2.15439302e+01 6 2.16669562e+01 5.72316830e+00 -3.16624445e+01 7 2.74104006e+01 -5.65376850e+01 -5.06121826e+01 8 -2.69768761e+01 -3.21110281e+01 5.81721196e+00 9 -3.33541387e+01 -7.12761483e+00 -4.27734575e+01 10 -2.53150969e+01 5.71142817e+01 -4.37319314e+01 11 -3.81763393e+01 -3.42507379e+01 3.98819541e+01 12 -2.38529871e+01 3.32842872e+01 -1.49513763e+01 13 2.99423126e+01 -2.00142166e+01 -9.18125501e+01 14 1.96556967e+01 1.65771745e+01 -1.52318356e+01 15 7.31352928e+01 -4.95717255e+00 -5.19876971e+00 16 1.09259033e+01 7.07756012e+01 3.22115883e+01 17 -3.26093811e+01 -1.86141797e+01 7.57657179e+00 18 4.88872202e+00 2.59848687e+01 2.09196896e+01 19 6.80611076e+00 -2.41421311e+01 1.65356882e+01 20 -1.54712228e+01 1.17404871e+01 1.30781329e+01 21 -2.11376689e+01 -2.87423693e+01 2.20338132e+01 22 4.25085272e+01 4.13565457e+01 4.47472431e+01 23 1.51351543e+01 -9.82485743e+00 2.94085352e+01 24 2.84033129e+00 3.41686617e+00 1.72723383e+01 25 -2.66143841e+01 -2.93897522e+01 1.51987451e+01 26 -2.30473222e+01 5.73202533e+01 -4.39676707e+01 27 6.43422435e+00 -6.92137725e+01 4.05048644e+01 28 -5.45350768e+01 4.46845161e+01 2.39754151e+01 29 -1.49007532e+01 -2.56924730e+01 1.55709317e+01 30 3.23562868e+01 3.38136749e+01 1.38969837e+01 31 5.01160757e+01 -1.34128261e+01 2.55004935e+01 32 3.05778935e+01 3.47207748e+01 4.77270460e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ge (Configuration in file "config-T-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 336.07132650818346 Forces: 1 -1.53275356e+01 -3.27264998e+01 -3.85864339e+01 2 -1.61050808e+01 5.95823233e+00 -3.55863032e+01 3 6.68786397e+00 -3.94780405e+01 -1.43397412e+01 4 -2.23343961e+01 3.87733000e+01 1.81413808e+01 5 8.67050763e+00 -3.50086753e+01 -2.15439302e+01 6 2.16669562e+01 5.72316830e+00 -3.16624445e+01 7 2.74104006e+01 -5.65376850e+01 -5.06121826e+01 8 -2.69768761e+01 -3.21110281e+01 5.81721196e+00 9 -3.33541387e+01 -7.12761483e+00 -4.27734575e+01 10 -2.53150969e+01 5.71142817e+01 -4.37319314e+01 11 -3.81763393e+01 -3.42507379e+01 3.98819541e+01 12 -2.38529871e+01 3.32842872e+01 -1.49513763e+01 13 2.99423126e+01 -2.00142166e+01 -9.18125501e+01 14 1.96556967e+01 1.65771745e+01 -1.52318356e+01 15 7.31352928e+01 -4.95717255e+00 -5.19876971e+00 16 1.09259033e+01 7.07756012e+01 3.22115883e+01 17 -3.26093811e+01 -1.86141797e+01 7.57657179e+00 18 4.88872202e+00 2.59848687e+01 2.09196896e+01 19 6.80611076e+00 -2.41421311e+01 1.65356882e+01 20 -1.54712228e+01 1.17404871e+01 1.30781329e+01 21 -2.11376689e+01 -2.87423693e+01 2.20338132e+01 22 4.25085272e+01 4.13565457e+01 4.47472431e+01 23 1.51351543e+01 -9.82485743e+00 2.94085352e+01 24 2.84033129e+00 3.41686617e+00 1.72723383e+01 25 -2.66143841e+01 -2.93897522e+01 1.51987451e+01 26 -2.30473222e+01 5.73202533e+01 -4.39676707e+01 27 6.43422435e+00 -6.92137725e+01 4.05048644e+01 28 -5.45350768e+01 4.46845161e+01 2.39754151e+01 29 -1.49007532e+01 -2.56924730e+01 1.55709317e+01 30 3.23562868e+01 3.38136749e+01 1.38969837e+01 31 5.01160757e+01 -1.34128261e+01 2.55004935e+01 32 3.05778935e+01 3.47207748e+01 4.77270460e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 213.5418665357061 Forces: 1 -1.45014499e+01 -1.26561506e+01 -1.75997006e+01 2 -1.87390145e+01 -2.75160845e+01 -6.41361072e+01 3 1.61246375e+00 -2.12799028e+01 -5.40728619e+00 4 -4.57412120e+01 -4.46583404e+00 7.28275428e+00 5 5.52492834e+00 -3.21081841e+01 -2.47365855e+01 6 1.32178114e+01 4.93029312e+00 -9.84006627e+00 7 1.32844948e+01 -1.26397702e+01 -1.47116390e-01 8 3.89745678e+01 -2.34712674e+01 3.24703312e+01 9 -2.03990287e+01 6.37711383e+00 -1.68060008e+01 10 -3.98857792e+01 6.74410269e+01 -1.43805650e+01 11 -2.75558630e+01 2.90564780e+01 2.61423582e+00 12 -2.82422797e+01 4.77041892e+01 -5.47140163e+01 13 4.34435079e+01 -3.03398554e+01 -5.03162078e+01 14 2.10021302e+01 5.74708129e+00 -1.35923270e+01 15 2.83409731e+01 1.64912994e+01 -1.75410237e+01 16 3.80744541e+00 2.36274167e+01 1.87982312e+01 17 -4.51413161e+01 -1.38473156e+01 -1.51606786e+01 18 2.50446782e+01 -3.11681358e+01 7.70556359e+00 19 2.75960134e+01 -2.03641251e+01 2.68620028e+01 20 -2.75161611e+01 1.10969833e+01 3.41666259e+01 21 1.49377748e+01 -9.13001453e+00 1.14026200e+01 22 2.27291459e+01 -1.54293302e+01 -3.33147390e+00 23 3.50011183e+00 -5.10985087e+00 3.84968662e+00 24 2.32062931e+00 -3.17250549e+01 2.03622911e+01 25 -3.34585674e+01 -5.04220746e+01 2.34157854e+01 26 3.94907118e+01 5.81795727e+01 5.34648086e+00 27 -2.68228247e+01 1.46412642e+01 2.27046064e+01 28 -2.64094741e+01 1.24979014e+01 3.64371528e+01 29 2.01737914e+01 9.15646299e+00 4.00499392e+01 30 2.06088569e+01 1.08381294e+01 -1.89811995e+01 31 2.53824695e+01 9.55309520e-01 1.41420166e+01 32 -1.65795354e+01 2.29324287e+01 1.90800312e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 213.5418665357061 Forces: 1 -1.45014499e+01 -1.26561506e+01 -1.75997006e+01 2 -1.87390145e+01 -2.75160845e+01 -6.41361072e+01 3 1.61246375e+00 -2.12799028e+01 -5.40728619e+00 4 -4.57412120e+01 -4.46583404e+00 7.28275428e+00 5 5.52492834e+00 -3.21081841e+01 -2.47365855e+01 6 1.32178114e+01 4.93029312e+00 -9.84006627e+00 7 1.32844948e+01 -1.26397702e+01 -1.47116390e-01 8 3.89745678e+01 -2.34712674e+01 3.24703312e+01 9 -2.03990287e+01 6.37711383e+00 -1.68060008e+01 10 -3.98857792e+01 6.74410269e+01 -1.43805650e+01 11 -2.75558630e+01 2.90564780e+01 2.61423582e+00 12 -2.82422797e+01 4.77041892e+01 -5.47140163e+01 13 4.34435079e+01 -3.03398554e+01 -5.03162078e+01 14 2.10021302e+01 5.74708129e+00 -1.35923270e+01 15 2.83409731e+01 1.64912994e+01 -1.75410237e+01 16 3.80744541e+00 2.36274167e+01 1.87982312e+01 17 -4.51413161e+01 -1.38473156e+01 -1.51606786e+01 18 2.50446782e+01 -3.11681358e+01 7.70556359e+00 19 2.75960134e+01 -2.03641251e+01 2.68620028e+01 20 -2.75161611e+01 1.10969833e+01 3.41666259e+01 21 1.49377748e+01 -9.13001453e+00 1.14026200e+01 22 2.27291459e+01 -1.54293302e+01 -3.33147390e+00 23 3.50011183e+00 -5.10985087e+00 3.84968662e+00 24 2.32062931e+00 -3.17250549e+01 2.03622911e+01 25 -3.34585674e+01 -5.04220746e+01 2.34157854e+01 26 3.94907118e+01 5.81795727e+01 5.34648086e+00 27 -2.68228247e+01 1.46412642e+01 2.27046064e+01 28 -2.64094741e+01 1.24979014e+01 3.64371528e+01 29 2.01737914e+01 9.15646299e+00 4.00499392e+01 30 2.06088569e+01 1.08381294e+01 -1.89811995e+01 31 2.53824695e+01 9.55309520e-01 1.41420166e+01 32 -1.65795354e+01 2.29324287e+01 1.90800312e+01 MIXED STRUCTURE (pbc=False)-- Species = Ge Si (Configuration in file "config-F-GeSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 386.36777107783865 Forces: 1 -7.57055116e+01 -7.98748721e+01 -4.08882004e+01 2 5.92200807e+01 5.85126741e+01 -4.86849333e+01 3 2.51169094e+00 -4.86491420e+01 2.27059229e+01 4 -4.33794592e+01 2.56608491e+01 3.19759660e+01 5 1.28565002e+01 -3.18482998e+01 -3.42303349e+01 6 2.49835380e+01 2.89889773e+01 -4.96413255e+01 7 3.50755976e+01 -3.59116238e+01 2.28692489e+01 8 -5.28767080e+00 -6.40162710e+00 -9.76780012e+00 9 -3.15147572e+01 8.65545289e+00 -1.77219911e+01 10 -2.70205292e+01 2.24056085e+01 -5.17612983e+01 11 -3.57352492e+01 -3.65639524e+01 -2.61449056e+01 12 -3.81794849e+01 2.64074920e+01 -9.65559106e+00 13 2.07693317e+01 -1.41988731e+01 -4.79632771e+01 14 1.09131532e+01 1.59770767e+01 -1.35270001e+01 15 2.71568434e+01 -1.79651283e+00 9.86483098e+00 16 3.39951535e+01 6.75106707e+01 -4.00316401e+00 17 -4.61877739e+01 -7.72228502e+01 -3.32056468e+01 18 1.99223035e+01 1.55872161e+01 -4.34747178e+01 19 2.91121689e+01 -6.40178405e+01 5.61323933e+01 20 -6.08021861e+01 2.98870647e+01 7.52510638e+01 21 -9.89670263e+00 -5.43744728e+01 7.46484999e+00 22 7.45327743e+01 2.08099788e+01 -2.26535531e+01 23 1.88207627e+01 -2.07369980e+01 1.68579416e+01 24 -2.11813837e+01 1.53863187e+01 5.49435953e+01 25 -7.58105466e+01 9.46273803e+00 -3.18590690e+01 26 -3.49203590e+01 8.10121850e+01 2.35844933e+01 27 3.62784960e+01 1.91788554e+00 6.05674387e+01 28 -1.96408282e+01 2.19066842e+01 1.32053439e+01 29 5.99007562e+01 -2.01219160e+01 2.65321895e+01 30 3.05170455e+01 1.84733499e+01 -1.06021444e+01 31 1.21576567e+01 1.33344488e+00 2.53411634e+01 32 1.65385893e+01 2.18233135e+01 4.84885109e+01 MIXED STRUCTURE (pbc=True)-- Species = Ge Si (Configuration in file "config-T-GeSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 619.737289064665 Forces: 1 -4.56394876e+01 -8.61438663e+01 -2.76826437e+01 2 6.87813256e+01 6.67201233e+01 -8.61021004e+00 3 6.66747902e+00 -1.26979622e+01 2.62021601e+01 4 2.32459432e+01 5.52116129e+01 5.15564853e+01 5 -3.13898492e+00 -5.79626978e+00 -3.03132991e+01 6 -1.84856879e+01 4.27006928e+01 -4.82428277e+01 7 -2.66329902e+01 -5.26516546e+01 5.83490140e+01 8 -1.03027612e+01 -5.10438811e+00 -8.86232794e+00 9 6.87801588e+00 4.68854160e+00 4.60902618e+00 10 -2.02051301e+01 1.60995319e+01 -3.49997126e+01 11 -2.48952578e+01 -3.83291133e+01 -2.45414960e+01 12 -2.22745563e+01 2.10982967e+01 3.58866559e+00 13 1.76869623e+01 -1.66977087e+01 -3.98352017e+01 14 8.86318894e+00 -1.55554509e+01 -9.33255111e+00 15 -2.21906895e+01 -5.57369173e+00 2.41039249e+01 16 4.13563880e+01 2.67437591e+01 6.40224112e-01 17 -2.59967242e+01 -7.01488720e+01 -5.10138600e+01 18 2.14220435e+01 2.08017588e+01 -5.33621757e+01 19 3.41627007e+01 -6.26568795e+01 3.50101805e+01 20 -4.44578668e+01 4.28089664e+01 4.79912059e+01 21 -1.54127089e+01 -3.40627459e+01 7.50060178e+00 22 5.36444737e+01 2.18318279e+01 -2.70262696e+01 23 1.70094239e-01 -1.63242904e+01 -1.57918573e+01 24 -2.31807336e+01 1.94110806e+01 4.63628290e+01 25 -4.18805148e+01 2.30163230e+00 -5.70643424e+01 26 -3.42434745e+01 6.44931786e+01 2.46469757e+01 27 5.33906042e+01 -6.23196821e+00 4.27159734e+01 28 -7.33449793e+00 1.31741785e+01 2.50145813e+00 29 5.84836286e+01 -2.41397862e+01 2.65935014e+01 30 -3.44318240e+00 2.05857503e+01 -2.46982213e+01 31 -2.77464283e+01 -9.04321830e-02 1.71677097e+01 32 2.27088289e+01 1.35341483e+01 4.18370604e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1819513== Memcheck, a memory error detector ==1819513== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1819513== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1819513== Command: python runner2.py Tersoff_LAMMPS_Tersoff_1989_SiGe__MO_350526375143_004 ==1819513== ==1820796== Warning: invalid file descriptor 1024 in syscall close() ==1820796== Warning: invalid file descriptor 1025 in syscall close() ==1820796== Warning: invalid file descriptor 1026 in syscall close() ==1820796== Warning: invalid file descriptor 1027 in syscall close() ==1820796== Use --log-fd= to select an alternative log fd. ==1820796== Warning: invalid file descriptor 1028 in syscall close() ==1820796== Warning: invalid file descriptor 1029 in syscall close() ==1819513== ==1819513== HEAP SUMMARY: ==1819513== in use at exit: 2,259,511 bytes in 1,705 blocks ==1819513== total heap usage: 88,579 allocs, 86,874 frees, 66,818,433 bytes allocated ==1819513== ==1819513== LEAK SUMMARY: ==1819513== definitely lost: 0 bytes in 0 blocks ==1819513== indirectly lost: 0 bytes in 0 blocks ==1819513== possibly lost: 180,827 bytes in 103 blocks ==1819513== still reachable: 2,078,652 bytes in 1,601 blocks ==1819513== of which reachable via heuristic: ==1819513== stdstring : 38 bytes in 1 blocks ==1819513== suppressed: 32 bytes in 1 blocks ==1819513== Rerun with --leak-check=full to see details of leaked memory ==1819513== ==1819513== For lists of detected and suppressed errors, rerun with: -s ==1819513== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8003 from 539) ================================================================================ 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.