!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_1990_SiC__MO_444207127575_000 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 = -77.86386437415786 Forces: 1 2.20474081e+00 -9.02649803e-01 -4.71663108e-01 2 -1.37501346e+00 6.12941666e-01 1.17745968e+00 3 -1.75325741e-01 5.12398856e-01 -9.22232097e-01 4 1.27210691e+00 1.92487613e+00 1.46946605e+00 5 1.10549174e+00 1.71792929e+00 2.08694178e+00 6 -1.93551041e+00 -1.08652410e+00 2.07840489e+00 7 -8.07197191e-01 -4.20840163e+00 -5.77529706e+00 8 -3.72152681e+00 -2.74189292e+00 -5.23675260e-01 9 -6.18496518e-03 -3.28686346e-02 1.11358041e+00 10 -6.85802493e+00 4.14068036e+00 -7.27662002e+00 11 -1.71305049e+00 -5.94496738e+00 3.90897673e+00 12 1.28711209e+00 -2.57406803e+00 2.64418904e-01 13 -2.13599801e+00 -1.74602847e+00 -6.97148404e+00 14 -1.29923036e+00 -1.41764091e+00 1.12542629e+00 15 6.86582403e+00 2.86105717e+00 4.67069514e+00 16 1.05880141e+01 5.12584574e+00 2.59283194e+00 17 3.03092176e-01 -4.16620095e-01 -1.43159461e+00 18 1.13136941e+00 2.06764434e+00 -4.58807319e-01 19 1.60282537e+00 9.80150684e-01 -7.08935819e-01 20 1.19112717e-01 5.70094547e-01 -5.99508761e-01 21 -1.85622674e+00 1.07465754e+00 1.53962952e+00 22 1.65681731e+00 3.25676539e+00 3.58206590e+00 23 -2.25646906e+00 1.75477143e+00 -2.31885089e+00 24 2.91030710e-01 -2.58487421e-01 -1.47340315e+00 25 -2.18056217e+00 -1.14217132e+00 1.66683417e-01 26 -6.47605718e+00 5.88516000e+00 3.76342357e+00 27 6.64165975e+00 -3.87044421e+00 -3.81188927e-01 28 -3.60188072e+00 2.98845637e+00 -1.40273552e+00 29 4.28250534e+00 -6.40461312e+00 2.38663168e+00 30 -1.47556256e+00 -1.46734198e+00 -3.13778225e-01 31 -1.75610350e+00 1.08311489e-01 1.46559882e-01 32 2.78221835e-01 -1.36702099e+00 -1.04342097e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -77.86386437415786 Forces: 1 2.20474081e+00 -9.02649803e-01 -4.71663108e-01 2 -1.37501346e+00 6.12941666e-01 1.17745968e+00 3 -1.75325741e-01 5.12398856e-01 -9.22232097e-01 4 1.27210691e+00 1.92487613e+00 1.46946605e+00 5 1.10549174e+00 1.71792929e+00 2.08694178e+00 6 -1.93551041e+00 -1.08652410e+00 2.07840489e+00 7 -8.07197191e-01 -4.20840163e+00 -5.77529706e+00 8 -3.72152681e+00 -2.74189292e+00 -5.23675260e-01 9 -6.18496518e-03 -3.28686346e-02 1.11358041e+00 10 -6.85802493e+00 4.14068036e+00 -7.27662002e+00 11 -1.71305049e+00 -5.94496738e+00 3.90897673e+00 12 1.28711209e+00 -2.57406803e+00 2.64418904e-01 13 -2.13599801e+00 -1.74602847e+00 -6.97148404e+00 14 -1.29923036e+00 -1.41764091e+00 1.12542629e+00 15 6.86582403e+00 2.86105717e+00 4.67069514e+00 16 1.05880141e+01 5.12584574e+00 2.59283194e+00 17 3.03092176e-01 -4.16620095e-01 -1.43159461e+00 18 1.13136941e+00 2.06764434e+00 -4.58807319e-01 19 1.60282537e+00 9.80150684e-01 -7.08935819e-01 20 1.19112717e-01 5.70094547e-01 -5.99508761e-01 21 -1.85622674e+00 1.07465754e+00 1.53962952e+00 22 1.65681731e+00 3.25676539e+00 3.58206590e+00 23 -2.25646906e+00 1.75477143e+00 -2.31885089e+00 24 2.91030710e-01 -2.58487421e-01 -1.47340315e+00 25 -2.18056217e+00 -1.14217132e+00 1.66683417e-01 26 -6.47605718e+00 5.88516000e+00 3.76342357e+00 27 6.64165975e+00 -3.87044421e+00 -3.81188927e-01 28 -3.60188072e+00 2.98845637e+00 -1.40273552e+00 29 4.28250534e+00 -6.40461312e+00 2.38663168e+00 30 -1.47556256e+00 -1.46734198e+00 -3.13778225e-01 31 -1.75610350e+00 1.08311489e-01 1.46559882e-01 32 2.78221835e-01 -1.36702099e+00 -1.04342097e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 131.28093180392122 Forces: 1 -5.12486588e+00 -3.95695413e+00 -3.52916552e+00 2 -2.38751245e+01 2.38944831e+01 -5.47132982e+00 3 8.17537554e+00 -1.05052742e+01 -3.08695712e+01 4 -1.07158553e+01 -8.89740734e+00 -1.05336666e+01 5 1.54625747e+01 -3.23977264e+01 -1.27698807e+01 6 2.16347298e+01 -7.03878023e+00 -2.05976528e+01 7 2.32438588e+01 -3.34487038e+01 -2.25751267e+00 8 -2.94485338e+01 1.56036842e+01 7.26532139e+00 9 -9.25735212e+00 -8.38622673e+00 -8.14065892e+00 10 1.27546092e+01 1.02519528e+01 -1.30248441e+01 11 -1.94022029e+01 -1.08724709e+00 -2.99432695e+01 12 -1.12506721e+01 8.93377315e+00 8.71733792e+00 13 -4.90458923e+01 -9.99651082e+00 -4.46403668e+01 14 1.40994255e+01 1.77027402e+01 -2.29422601e+01 15 6.78594300e+01 -2.11070545e+01 3.47028494e+01 16 -2.67370388e+01 5.59661976e+01 -1.12771107e+01 17 -2.53356934e+01 -3.78828330e+00 2.15187547e+01 18 -2.07161632e+00 -1.65768471e+01 7.06837002e+00 19 -3.79904667e+01 -3.60843150e+01 1.99667017e+01 20 -4.01314313e+00 -1.17724356e+01 1.39263424e+01 21 1.61079055e+01 -1.93470088e+01 -9.15859662e+00 22 2.00949339e+01 8.90719924e+00 1.03839369e+01 23 1.10122224e+01 -7.80417409e+00 1.01704906e+01 24 2.85505764e+01 3.78462121e+01 1.76864216e+01 25 -1.77701224e+01 1.12443035e+01 -1.98227620e+00 26 -3.52626265e+01 4.26294269e+01 -1.56824087e+01 27 -2.30009050e+00 -1.22788504e+01 2.32077509e+01 28 -1.00690693e+01 1.36889047e+01 3.23399744e+00 29 2.12848160e+01 -3.73987281e+01 5.70268107e+00 30 2.77468432e+01 1.76613084e+01 4.78367692e+00 31 1.38010410e+01 -6.75893720e+00 1.59977092e+01 32 1.78420241e+01 2.43012790e+01 3.84882288e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 131.28093180392122 Forces: 1 -5.12486588e+00 -3.95695413e+00 -3.52916552e+00 2 -2.38751245e+01 2.38944831e+01 -5.47132982e+00 3 8.17537554e+00 -1.05052742e+01 -3.08695712e+01 4 -1.07158553e+01 -8.89740734e+00 -1.05336666e+01 5 1.54625747e+01 -3.23977264e+01 -1.27698807e+01 6 2.16347298e+01 -7.03878023e+00 -2.05976528e+01 7 2.32438588e+01 -3.34487038e+01 -2.25751267e+00 8 -2.94485338e+01 1.56036842e+01 7.26532139e+00 9 -9.25735212e+00 -8.38622673e+00 -8.14065892e+00 10 1.27546092e+01 1.02519528e+01 -1.30248441e+01 11 -1.94022029e+01 -1.08724709e+00 -2.99432695e+01 12 -1.12506721e+01 8.93377315e+00 8.71733792e+00 13 -4.90458923e+01 -9.99651082e+00 -4.46403668e+01 14 1.40994255e+01 1.77027402e+01 -2.29422601e+01 15 6.78594300e+01 -2.11070545e+01 3.47028494e+01 16 -2.67370388e+01 5.59661976e+01 -1.12771107e+01 17 -2.53356934e+01 -3.78828330e+00 2.15187547e+01 18 -2.07161632e+00 -1.65768471e+01 7.06837002e+00 19 -3.79904667e+01 -3.60843150e+01 1.99667017e+01 20 -4.01314313e+00 -1.17724356e+01 1.39263424e+01 21 1.61079055e+01 -1.93470088e+01 -9.15859662e+00 22 2.00949339e+01 8.90719924e+00 1.03839369e+01 23 1.10122224e+01 -7.80417409e+00 1.01704906e+01 24 2.85505764e+01 3.78462121e+01 1.76864216e+01 25 -1.77701224e+01 1.12443035e+01 -1.98227620e+00 26 -3.52626265e+01 4.26294269e+01 -1.56824087e+01 27 -2.30009050e+00 -1.22788504e+01 2.32077509e+01 28 -1.00690693e+01 1.36889047e+01 3.23399744e+00 29 2.12848160e+01 -3.73987281e+01 5.70268107e+00 30 2.77468432e+01 1.76613084e+01 4.78367692e+00 31 1.38010410e+01 -6.75893720e+00 1.59977092e+01 32 1.78420241e+01 2.43012790e+01 3.84882288e+01 MIXED STRUCTURE (pbc=False)-- Species = C Si (Configuration in file "config-F-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 54.97746293780294 Forces: 1 -6.80992910e+00 -1.71578456e+00 -1.01632036e+01 2 -5.46027816e+00 8.01159851e+00 -4.06610422e+00 3 1.24977659e+01 -8.49131414e+00 3.85906381e+00 4 -7.14299994e+00 1.64413883e+01 -3.25437110e+00 5 2.66054341e+00 -9.54824856e+00 -6.89876607e+00 6 1.10695829e+01 -8.23576912e+00 -1.07045286e+01 7 2.12237401e+01 -2.46752750e+01 -5.57331637e+00 8 -2.61851732e+01 3.60931113e+01 -3.40355006e+01 9 -1.14861180e+01 -1.34440417e+01 -3.31386380e+00 10 3.32514271e-01 2.83234560e+01 -2.79406554e+01 11 -1.29939819e+01 -4.22744444e+01 1.77819426e+01 12 -2.65375447e+01 2.01922975e+01 -8.83980698e+00 13 -1.30346496e+01 -7.38230896e+00 -4.55341386e+01 14 2.54292784e+00 9.32281617e+00 -5.90066987e+00 15 2.87565659e+01 -1.12864687e+01 1.51715047e+01 16 1.56891748e+01 3.07447472e+01 9.06077642e+00 17 -6.17622210e+00 -1.23767054e+01 8.58478336e+00 18 -2.50837245e+01 1.54033525e+01 -1.47924167e+01 19 -9.91118965e+00 -3.07128936e+01 1.55031993e+01 20 -1.56675032e+01 1.07963782e+01 -2.64366522e+00 21 -7.57503447e+00 -5.68645392e+01 3.72322997e+00 22 4.10342816e+01 1.33146368e+01 4.99528935e+00 23 7.19140440e+00 -1.08889418e+01 1.37290111e+01 24 1.49783730e+01 1.89273747e+01 3.79849025e+01 25 -5.21078176e-01 -1.65601955e+01 1.65310317e+01 26 6.77458997e+00 6.69990287e+00 7.81851863e+00 27 -8.08235825e+00 -8.53054408e+00 9.68989786e+00 28 -1.08572670e+01 8.19491176e+00 4.43734888e+00 29 1.19556433e+01 1.21966923e+01 -1.18725001e+01 30 7.87791511e+00 1.73287582e+01 1.55305078e+01 31 7.52584266e+00 2.53558617e+00 8.73004872e+00 32 1.41418656e+00 8.46046619e+00 2.40245061e+00 MIXED STRUCTURE (pbc=True)-- Species = C Si (Configuration in file "config-T-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 100.7254136900226 Forces: 1 -5.64271573e+00 -8.41317659e+00 -1.05907602e+01 2 -1.07303577e+01 1.27300558e+01 7.11448844e+00 3 1.37225250e+01 -7.97402935e+00 5.71367060e+00 4 -4.19034675e+00 1.74293652e+01 -1.32139834e+00 5 6.29404374e+00 -1.63170484e+01 -2.10973320e+00 6 4.21951943e+00 -7.44611389e+00 -1.18083624e+01 7 2.27528196e+01 -2.69248464e+01 -6.57895018e+00 8 -2.69391860e+01 3.74102386e+01 -3.38004788e+01 9 -1.23039782e+01 -1.75217884e+01 -4.11743741e+00 10 2.27525349e+01 3.22070251e+01 1.55989012e+01 11 -1.36329052e+01 -4.21653954e+01 1.86013296e+01 12 1.94638770e+01 2.62946790e+01 -2.98764677e+01 13 -2.02027013e+01 -5.16850876e+00 -3.83253575e+01 14 4.75312677e+00 1.54182101e+01 -7.93750468e+00 15 1.17661302e+01 -2.31241858e+01 1.25198058e+01 16 1.73281755e+01 3.12448392e+01 9.92718360e+00 17 -6.30711716e+00 -1.36957755e+01 1.04515406e+01 18 -2.36991431e+01 1.54575492e+01 -1.44809648e+01 19 -7.38272388e+00 -2.71509729e+01 8.03288170e+00 20 -1.89086993e+01 1.43876134e+01 1.45316487e-01 21 -9.68623255e+00 -5.35272720e+01 6.48643368e-02 22 3.75877106e+01 1.58734841e+01 1.39543158e+00 23 1.17369477e+01 -1.76293322e+01 1.93349103e+01 24 1.87712004e+01 2.43272989e+01 2.18489020e+01 25 1.98132370e+00 -2.05677600e+01 1.81117516e+01 26 7.42068305e+00 6.48496960e+00 7.65711809e+00 27 -8.29403679e+00 -1.24122060e+01 8.61048016e+00 28 -3.09074015e+01 4.97871989e+00 -3.65336819e+01 29 1.19208467e+01 1.12780050e+01 -1.41085430e+01 30 -2.64910626e+01 2.55498511e+01 4.29533209e+01 31 7.04214320e+00 2.60849660e-01 -5.52610852e-01 32 5.80500047e+00 8.70565799e+00 4.06035388e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==26112== Memcheck, a memory error detector ==26112== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==26112== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==26112== Command: python runner2.py Tersoff_LAMMPS_Tersoff_1990_SiC__MO_444207127575_000 ==26112== ==26258== Warning: invalid file descriptor 4096 in syscall close() ==26258== Warning: invalid file descriptor 4097 in syscall close() ==26258== Warning: invalid file descriptor 4098 in syscall close() ==26258== Warning: invalid file descriptor 4099 in syscall close() ==26258== Use --log-fd= to select an alternative log fd. ==26258== Warning: invalid file descriptor 4100 in syscall close() ==26258== Warning: invalid file descriptor 4101 in syscall close() ==26112== ==26112== HEAP SUMMARY: ==26112== in use at exit: 2,206,687 bytes in 1,649 blocks ==26112== total heap usage: 90,589 allocs, 88,940 frees, 64,810,237 bytes allocated ==26112== ==26112== LEAK SUMMARY: ==26112== definitely lost: 0 bytes in 0 blocks ==26112== indirectly lost: 0 bytes in 0 blocks ==26112== possibly lost: 198,622 bytes in 101 blocks ==26112== still reachable: 2,008,033 bytes in 1,547 blocks ==26112== suppressed: 32 bytes in 1 blocks ==26112== Rerun with --leak-check=full to see details of leaked memory ==26112== ==26112== For lists of detected and suppressed errors, rerun with: -s ==26112== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 9202 from 564) ================================================================================ 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.