!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : SNAP_LiHuChen_2018_NiMo__MO_468686727341_000 Supported species : Mo Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mo (Configuration in file "config-F-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = -120.13263834247589 Forces: 1 -6.53033096e+00 -9.38763773e+00 -1.19162957e+01 2 -3.47954236e+00 3.67287811e+00 -1.23202132e+01 3 4.63558459e+00 -1.31117164e+01 6.00828731e-01 4 -1.09922141e+01 8.35973371e+00 4.26914805e+00 5 5.84876187e+00 -1.19204015e+01 -4.63408412e+00 6 5.88826224e+00 -5.78595932e+00 -9.82180048e+00 7 8.91352894e+00 -1.80378925e+01 -1.40955050e+01 8 -1.61472307e+01 -1.50184617e+01 4.15674815e+00 9 -7.43697553e+00 -4.97441597e+00 -1.44773020e+01 10 -2.37470495e+00 1.70553984e+01 -1.62174557e+01 11 -9.08586068e+00 -1.25804882e+01 4.21929021e+00 12 -1.11319810e+01 1.06716699e+01 5.83023329e+00 13 -5.61889387e-02 1.67735832e+00 -3.21845476e+01 14 6.82980232e+00 6.15765255e+00 -2.72229098e+00 15 3.09299523e+01 9.63242810e+00 7.14512015e+00 16 5.59019366e+00 2.62858947e+01 7.92495493e+00 17 -1.81469080e+01 -1.15143953e+01 -3.61841554e+00 18 6.38408587e+00 8.71260324e+00 -4.33035094e+00 19 7.17655922e+00 -1.21225421e+01 1.21634444e+01 20 -8.17600642e+00 5.50416802e+00 1.24497276e+01 21 -7.08389926e+00 -1.12089184e+01 4.34996881e+00 22 1.85374166e+01 8.92753703e+00 8.13169944e+00 23 6.15083459e+00 -4.06021275e+00 9.86043958e+00 24 -2.59752522e+00 1.45738215e+00 6.78434571e+00 25 -1.39707022e+01 -5.94563130e+00 -1.09134955e+01 26 3.33147406e+00 1.96971334e+01 -6.86121806e+00 27 1.13886874e+01 -2.16210119e+01 1.79092796e+01 28 -2.11421631e+01 2.08345991e+01 1.08258052e+01 29 -5.40233367e+00 -8.34316157e+00 8.37731428e+00 30 8.13526574e+00 1.00325117e+01 -2.79269246e+00 31 1.15320641e+01 -4.49979163e+00 9.86035523e+00 32 2.48209368e+00 1.14536896e+01 1.20469638e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mo (Configuration in file "config-T-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = -120.13263834247589 Forces: 1 -6.53033096e+00 -9.38763773e+00 -1.19162957e+01 2 -3.47954236e+00 3.67287811e+00 -1.23202132e+01 3 4.63558459e+00 -1.31117164e+01 6.00828731e-01 4 -1.09922141e+01 8.35973371e+00 4.26914805e+00 5 5.84876187e+00 -1.19204015e+01 -4.63408412e+00 6 5.88826224e+00 -5.78595932e+00 -9.82180048e+00 7 8.91352894e+00 -1.80378925e+01 -1.40955050e+01 8 -1.61472307e+01 -1.50184617e+01 4.15674815e+00 9 -7.43697553e+00 -4.97441597e+00 -1.44773020e+01 10 -2.37470495e+00 1.70553984e+01 -1.62174557e+01 11 -9.08586068e+00 -1.25804882e+01 4.21929021e+00 12 -1.11319810e+01 1.06716699e+01 5.83023329e+00 13 -5.61889387e-02 1.67735832e+00 -3.21845476e+01 14 6.82980232e+00 6.15765255e+00 -2.72229098e+00 15 3.09299523e+01 9.63242810e+00 7.14512015e+00 16 5.59019366e+00 2.62858947e+01 7.92495493e+00 17 -1.81469080e+01 -1.15143953e+01 -3.61841554e+00 18 6.38408587e+00 8.71260324e+00 -4.33035094e+00 19 7.17655922e+00 -1.21225421e+01 1.21634444e+01 20 -8.17600642e+00 5.50416802e+00 1.24497276e+01 21 -7.08389926e+00 -1.12089184e+01 4.34996881e+00 22 1.85374166e+01 8.92753703e+00 8.13169944e+00 23 6.15083459e+00 -4.06021275e+00 9.86043958e+00 24 -2.59752522e+00 1.45738215e+00 6.78434571e+00 25 -1.39707022e+01 -5.94563130e+00 -1.09134955e+01 26 3.33147406e+00 1.96971334e+01 -6.86121806e+00 27 1.13886874e+01 -2.16210119e+01 1.79092796e+01 28 -2.11421631e+01 2.08345991e+01 1.08258052e+01 29 -5.40233367e+00 -8.34316157e+00 8.37731428e+00 30 8.13526574e+00 1.00325117e+01 -2.79269246e+00 31 1.15320641e+01 -4.49979163e+00 9.86035523e+00 32 2.48209368e+00 1.14536896e+01 1.20469638e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -132.3153741569802 Forces: 1 -2.21966878e+00 -1.99895022e+00 -3.01091257e+00 2 3.24680087e+00 -1.52885608e+00 -3.19808950e+00 3 1.15157759e+00 -1.49078191e+00 6.25199634e-01 4 -1.67142165e+00 -1.43495526e+00 6.61198319e-01 5 1.38630449e+00 -4.71621815e-01 -1.22706882e+00 6 1.71360758e+00 -1.41638358e+00 -1.07639848e+00 7 8.00868570e-01 -2.31029450e+00 -9.45307478e-01 8 -4.85480938e-01 1.62841813e+00 -1.45333152e+00 9 -5.46758482e+00 2.12850530e+00 -3.77957060e+00 10 -5.56203428e-01 2.91665124e-01 -3.61430553e-01 11 2.51531303e+00 9.60348291e-01 2.79997284e+00 12 -2.06906864e+00 1.98962948e+00 -1.34564114e+00 13 -4.43624579e+00 -1.92772033e+00 -2.20846174e+00 14 3.36359757e+00 4.28968137e+00 -1.28251895e+00 15 2.80744036e+00 -3.18948575e+00 -1.67145479e+00 16 8.71631103e-01 3.81748624e+00 -1.99991328e+00 17 -2.38111445e+00 -1.41383399e+00 4.38097806e-01 18 3.38095267e-01 2.37958353e+00 -2.10101285e+00 19 2.30526825e+00 -4.39958384e+00 3.10925433e+00 20 -3.48815060e+00 2.14416485e+00 1.60299188e+00 21 1.75545845e+00 -2.67545107e+00 5.22991764e-01 22 1.50995175e+00 -1.83919142e+00 1.64003382e+00 23 2.40418735e+00 -1.83165813e+00 -2.12738471e-01 24 -8.75778354e-01 3.08711333e+00 8.90179171e-01 25 -1.81692942e+00 1.58132668e+00 2.89151021e+00 26 5.52651167e-01 9.30279547e-01 1.57913648e+00 27 2.08935032e-01 -2.28586678e+00 8.96737637e-01 28 -2.44407550e+00 1.21511934e+00 6.45477960e-01 29 -2.98346699e+00 -3.09668728e+00 3.22780835e+00 30 2.59157549e+00 4.06373109e+00 5.12705622e-01 31 3.24470762e-01 -1.57265035e-01 2.60437125e+00 32 1.04745467e+00 2.96153469e+00 1.22618367e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -132.3153741569802 Forces: 1 -2.21966878e+00 -1.99895022e+00 -3.01091257e+00 2 3.24680087e+00 -1.52885608e+00 -3.19808950e+00 3 1.15157759e+00 -1.49078191e+00 6.25199634e-01 4 -1.67142165e+00 -1.43495526e+00 6.61198319e-01 5 1.38630449e+00 -4.71621815e-01 -1.22706882e+00 6 1.71360758e+00 -1.41638358e+00 -1.07639848e+00 7 8.00868570e-01 -2.31029450e+00 -9.45307478e-01 8 -4.85480938e-01 1.62841813e+00 -1.45333152e+00 9 -5.46758482e+00 2.12850530e+00 -3.77957060e+00 10 -5.56203428e-01 2.91665124e-01 -3.61430553e-01 11 2.51531303e+00 9.60348291e-01 2.79997284e+00 12 -2.06906864e+00 1.98962948e+00 -1.34564114e+00 13 -4.43624579e+00 -1.92772033e+00 -2.20846174e+00 14 3.36359757e+00 4.28968137e+00 -1.28251895e+00 15 2.80744036e+00 -3.18948575e+00 -1.67145479e+00 16 8.71631103e-01 3.81748624e+00 -1.99991328e+00 17 -2.38111445e+00 -1.41383399e+00 4.38097806e-01 18 3.38095267e-01 2.37958353e+00 -2.10101285e+00 19 2.30526825e+00 -4.39958384e+00 3.10925433e+00 20 -3.48815060e+00 2.14416485e+00 1.60299188e+00 21 1.75545845e+00 -2.67545107e+00 5.22991764e-01 22 1.50995175e+00 -1.83919142e+00 1.64003382e+00 23 2.40418735e+00 -1.83165813e+00 -2.12738471e-01 24 -8.75778354e-01 3.08711333e+00 8.90179171e-01 25 -1.81692942e+00 1.58132668e+00 2.89151021e+00 26 5.52651167e-01 9.30279547e-01 1.57913648e+00 27 2.08935032e-01 -2.28586678e+00 8.96737637e-01 28 -2.44407550e+00 1.21511934e+00 6.45477960e-01 29 -2.98346699e+00 -3.09668728e+00 3.22780835e+00 30 2.59157549e+00 4.06373109e+00 5.12705622e-01 31 3.24470762e-01 -1.57265035e-01 2.60437125e+00 32 1.04745467e+00 2.96153469e+00 1.22618367e+00 MIXED STRUCTURE (pbc=False)-- Species = Mo Ni (Configuration in file "config-F-MoNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = -124.73093596150049 Forces: 1 -3.82493745e+00 -2.80930021e+00 -2.48471197e+00 2 -5.00978251e+00 4.50870568e+00 -1.37794977e+01 3 -4.62561119e+00 -1.76801741e+01 -3.22652686e+00 4 -7.14124654e+00 2.51218881e+00 1.17655141e+00 5 8.75565649e+00 -8.17545832e+00 -7.90296477e+00 6 3.88934652e+00 1.22332298e+00 -3.65029792e+00 7 3.78211612e+00 -4.31444833e+00 -3.78912969e-01 8 7.19208543e+00 -6.04289015e+00 -2.65561130e+00 9 -7.24213121e+00 8.87482641e-01 -5.71580898e+00 10 -2.55498299e-01 2.14846645e+00 -3.46574419e+00 11 -9.12242525e+00 4.59555250e-01 -8.86285248e+00 12 -2.66882328e+00 2.21209772e+00 1.98365052e+00 13 3.01238173e-01 1.24415833e+00 -5.68650882e+00 14 1.20883030e+01 2.12455021e+00 -1.09922461e+01 15 1.14078968e+01 -1.24022897e+00 -4.34706075e+00 16 -6.84805284e+00 1.07823417e+01 6.74814647e+00 17 -5.72556730e+00 -3.57728288e+00 3.73763366e+00 18 -6.48722914e+00 6.41735877e+00 5.36880779e+00 19 -2.96978469e+00 -2.23971701e+00 4.96558738e+00 20 -4.81520626e+00 -7.35948192e+00 6.36166216e+00 21 1.02552632e+01 -1.40024113e+01 1.90278063e+00 22 5.83832339e+00 2.06913170e+00 -2.35349242e+00 23 2.89403495e+00 -4.13243299e+00 2.65078178e+00 24 -1.03492019e+00 3.94229005e+00 7.89720340e+00 25 -1.25006531e+01 2.80033775e+00 -5.15986446e+00 26 -6.57525181e+00 1.72947153e+01 6.27134189e+00 27 7.01453877e+00 1.25104862e+00 9.36093000e+00 28 -1.97364898e+00 2.56274615e+00 2.02958117e+00 29 6.81377897e+00 -1.89750431e+00 9.05137124e+00 30 4.43604887e+00 1.54364896e+01 -4.61171940e+00 31 2.84580977e+00 -8.87561993e+00 1.19064020e+01 32 1.30632963e+00 2.46996270e+00 3.86138969e+00 MIXED STRUCTURE (pbc=True)-- Species = Mo Ni (Configuration in file "config-T-MoNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = -29.583561321576724 Forces: 1 5.10300737e-01 -1.38904231e+00 2.81997252e+00 2 -1.95668086e+00 -3.02902739e+00 3.20066337e-01 3 -3.75736974e+00 -1.08701389e+00 -1.17225688e+00 4 -1.38317786e+00 -4.94868705e-01 -4.81996985e-01 5 1.94133152e+00 3.62652087e+00 -3.01490629e+00 6 1.90149187e+00 -7.65380489e-01 -9.15866712e-01 7 -1.22851587e+00 -3.00973459e-01 -1.20958269e+00 8 1.20493868e+00 -4.45616262e+00 -2.81478703e-02 9 -4.67325844e+00 -5.86814515e-01 -1.98911411e+00 10 4.31138146e-01 1.15152947e+00 -6.15630781e-01 11 -9.08559911e-01 -4.37871759e-01 -4.52635754e+00 12 2.20280176e-01 1.91591204e+00 -1.40266604e-01 13 5.15995731e-01 -1.05218789e+00 -8.54716457e-01 14 9.25318780e+00 1.68606652e+00 -2.28753083e+00 15 1.10681795e+00 -4.37320016e-01 -2.92256834e+00 16 -3.01515737e+00 -3.20944485e+00 4.41705688e+00 17 -5.29449783e-01 -5.55855425e-01 8.11638770e-01 18 -1.76259732e+00 1.96365564e+00 7.32824869e-01 19 5.82783790e-01 2.55183783e+00 4.27205169e-01 20 -2.64747632e+00 -1.33888729e-01 1.41222159e+00 21 3.60012186e+00 -3.85631507e+00 1.84638003e+00 22 1.30500157e-01 -1.76069737e-01 9.38440825e-01 23 -2.64495938e+00 -6.33683571e-02 1.32182275e+00 24 8.24603004e-01 -4.17749187e-01 -8.53026923e-02 25 -1.43620011e+00 2.10135647e+00 -1.05185072e-01 26 -3.88866058e-01 2.54627479e+00 9.91833740e-01 27 1.11528851e+00 1.41675575e+00 6.99252331e-01 28 1.03419665e+00 1.18529322e+00 1.16599317e+00 29 2.62795381e+00 2.61388135e+00 3.13198526e+00 30 8.42937001e-02 2.99731633e+00 -4.90453584e+00 31 -3.20232708e+00 -2.94615481e+00 4.04955197e+00 32 2.44937202e+00 -3.60891067e-01 1.67719478e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==38716== Memcheck, a memory error detector ==38716== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==38716== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==38716== Command: python runner2.py SNAP_LiHuChen_2018_NiMo__MO_468686727341_000 ==38716== ==39310== Warning: invalid file descriptor 255988 in syscall close() ==39310== Warning: invalid file descriptor 255989 in syscall close() ==39310== Warning: invalid file descriptor 255990 in syscall close() ==39310== Warning: invalid file descriptor 255991 in syscall close() ==39310== Use --log-fd= to select an alternative log fd. ==39310== Warning: invalid file descriptor 255992 in syscall close() ==39310== Warning: invalid file descriptor 255993 in syscall close() ==38716== ==38716== HEAP SUMMARY: ==38716== in use at exit: 2,257,767 bytes in 1,704 blocks ==38716== total heap usage: 86,354 allocs, 84,650 frees, 62,369,911 bytes allocated ==38716== ==38716== LEAK SUMMARY: ==38716== definitely lost: 0 bytes in 0 blocks ==38716== indirectly lost: 0 bytes in 0 blocks ==38716== possibly lost: 180,827 bytes in 103 blocks ==38716== still reachable: 2,076,908 bytes in 1,600 blocks ==38716== of which reachable via heuristic: ==38716== stdstring : 38 bytes in 1 blocks ==38716== suppressed: 32 bytes in 1 blocks ==38716== Rerun with --leak-check=full to see details of leaked memory ==38716== ==38716== For lists of detected and suppressed errors, rerun with: -s ==38716== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8042 from 554) ================================================================================ 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.