!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_Dynamo_SetyawanGaoKurtz_2018_ReW__MO_680820064987_000 Supported species : Re W random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Re (Configuration in file "config-F-Re.xyz") ----------------------------------------------------------------------------------------------------- Energy = 190.22171821117158 Forces: 1 -1.51524218e+01 -1.60376418e+01 -2.11138161e+01 2 -1.70137441e+01 -7.60848446e+00 -4.37739665e+01 3 1.15305996e+01 -4.81764350e+01 -9.42084845e+00 4 -3.81023432e+01 1.95792683e+01 -1.12515056e+01 5 -1.05580067e+00 -3.94531831e+01 -2.93309574e+01 6 3.40640006e+01 -3.78936969e+00 -3.29691178e+01 7 1.87759305e+01 -2.37197500e+01 -1.38011556e+01 8 1.36981101e+01 -1.90204355e+01 -5.65388237e+00 9 -2.81579021e+01 -1.10030425e+01 -3.62543288e+01 10 3.52287279e+00 4.91070335e+01 -3.05727399e+01 11 -3.97818447e+01 -1.57963448e+01 -8.75885078e-01 12 -3.31211329e+01 3.02567636e+01 1.47335669e+00 13 2.04551355e+01 -3.15963710e-01 -5.54663742e+01 14 2.53745025e+01 2.96769957e+01 -2.22429071e+01 15 5.03610556e+01 -2.26845914e+01 -5.94612672e+00 16 -2.96683899e+01 5.01914910e+01 -8.09322904e-01 17 -3.06680172e+01 -1.94030614e+01 1.08209296e+01 18 1.13395177e+01 -9.18091544e+00 1.63236997e+01 19 3.33722242e+00 -2.42259144e+01 1.42076047e+01 20 -2.53672331e+01 2.92653356e+00 3.02206681e+01 21 -8.70703245e+00 -2.94168407e+01 1.64373744e+01 22 4.37493707e+01 -8.34564879e+00 1.25279412e+01 23 1.39531107e+01 -1.25206408e+01 2.25511218e+01 24 9.13300555e-01 -5.74337406e+00 2.69981293e+01 25 -3.75729645e+01 1.18726819e+01 1.54987093e+01 26 5.35335129e+00 3.55436627e+01 1.21255707e+00 27 -3.72282692e+00 -9.84379243e+00 3.04775306e+01 28 -2.93988717e+01 1.86209064e+01 2.03086532e+01 29 1.30717245e+01 1.36638894e+00 2.61243958e+01 30 3.88518152e+01 4.27907494e+01 1.63832039e+01 31 2.65221929e+01 -1.33379779e+00 2.19896261e+01 32 2.61671237e+00 3.56867530e+01 3.59274330e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Re (Configuration in file "config-T-Re.xyz") ----------------------------------------------------------------------------------------------------- Energy = 190.22171821117158 Forces: 1 -1.51524218e+01 -1.60376418e+01 -2.11138161e+01 2 -1.70137441e+01 -7.60848446e+00 -4.37739665e+01 3 1.15305996e+01 -4.81764350e+01 -9.42084845e+00 4 -3.81023432e+01 1.95792683e+01 -1.12515056e+01 5 -1.05580067e+00 -3.94531831e+01 -2.93309574e+01 6 3.40640006e+01 -3.78936969e+00 -3.29691178e+01 7 1.87759305e+01 -2.37197500e+01 -1.38011556e+01 8 1.36981101e+01 -1.90204355e+01 -5.65388237e+00 9 -2.81579021e+01 -1.10030425e+01 -3.62543288e+01 10 3.52287279e+00 4.91070335e+01 -3.05727399e+01 11 -3.97818447e+01 -1.57963448e+01 -8.75885078e-01 12 -3.31211329e+01 3.02567636e+01 1.47335669e+00 13 2.04551355e+01 -3.15963710e-01 -5.54663742e+01 14 2.53745025e+01 2.96769957e+01 -2.22429071e+01 15 5.03610556e+01 -2.26845914e+01 -5.94612672e+00 16 -2.96683899e+01 5.01914910e+01 -8.09322904e-01 17 -3.06680172e+01 -1.94030614e+01 1.08209296e+01 18 1.13395177e+01 -9.18091544e+00 1.63236997e+01 19 3.33722242e+00 -2.42259144e+01 1.42076047e+01 20 -2.53672331e+01 2.92653356e+00 3.02206681e+01 21 -8.70703245e+00 -2.94168407e+01 1.64373744e+01 22 4.37493707e+01 -8.34564879e+00 1.25279412e+01 23 1.39531107e+01 -1.25206408e+01 2.25511218e+01 24 9.13300555e-01 -5.74337406e+00 2.69981293e+01 25 -3.75729645e+01 1.18726819e+01 1.54987093e+01 26 5.35335129e+00 3.55436627e+01 1.21255707e+00 27 -3.72282692e+00 -9.84379243e+00 3.04775306e+01 28 -2.93988717e+01 1.86209064e+01 2.03086532e+01 29 1.30717245e+01 1.36638894e+00 2.61243958e+01 30 3.88518152e+01 4.27907494e+01 1.63832039e+01 31 2.65221929e+01 -1.33379779e+00 2.19896261e+01 32 2.61671237e+00 3.56867530e+01 3.59274330e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = W (Configuration in file "config-F-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 74.57852072504785 Forces: 1 -2.74031386e+01 -2.25942481e+01 -2.91725789e+01 2 1.17966355e+00 2.85372806e+01 -2.72043987e+01 3 1.27060155e+01 -2.54520075e+01 1.63472763e+01 4 -2.35257196e+01 -9.08997798e+00 1.11538893e+01 5 2.08376173e+01 -2.76462024e+01 -2.06135821e+01 6 1.07348211e+01 -2.05298830e+00 -8.01091110e+00 7 9.51098297e+00 -1.29932207e+01 -7.41461077e+00 8 6.22867155e+00 8.47084235e+00 1.42565529e+01 9 -2.45392544e+01 4.08707258e+00 -3.59243168e+01 10 -8.49503089e+00 1.97861657e+01 -2.20876797e+01 11 1.32403298e+01 -2.34185636e+01 1.04405033e+01 12 -2.99218534e+01 2.72637346e+01 -6.70487795e+00 13 -1.61051432e+01 -2.29931836e+01 -3.80254026e+01 14 3.33809793e+01 3.30515973e+01 -2.00595234e+01 15 3.26823337e+01 -1.90930275e+01 -1.22919133e+01 16 -3.68809212e+00 3.92530484e+01 1.10876916e+01 17 -2.82876943e+01 -2.43909283e+01 -1.19802981e+00 18 1.91550901e+01 2.74917628e+01 -2.12717513e+01 19 1.64221642e+01 -3.25491141e+01 3.13981976e+01 20 -3.15946300e+01 1.56167431e+01 2.16289619e+01 21 -9.95970349e-01 -1.75343485e+01 -9.16760761e+00 22 2.08508146e+01 -2.18475264e+01 3.13770564e+00 23 2.46452975e+01 -2.39953032e+01 8.46592414e+00 24 -1.48889188e+01 2.32777569e+01 1.51424250e+01 25 -1.73445892e+01 4.54591986e+00 2.17793867e+01 26 1.09165239e+01 1.89611692e+01 1.05193008e+01 27 9.24000823e+00 -1.22647660e+01 1.25403829e+01 28 -2.07000571e+01 1.27079383e+01 9.51522612e+00 29 -3.94752459e+01 -2.81271964e+01 1.13591013e+01 30 3.63913993e+01 4.23750397e+01 -6.73630766e+00 31 1.91747567e+01 -8.62101017e+00 3.31830299e+01 32 -1.03321315e+01 2.92375416e+01 2.39279366e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = W (Configuration in file "config-T-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 74.57852072504785 Forces: 1 -2.74031386e+01 -2.25942481e+01 -2.91725789e+01 2 1.17966355e+00 2.85372806e+01 -2.72043987e+01 3 1.27060155e+01 -2.54520075e+01 1.63472763e+01 4 -2.35257196e+01 -9.08997798e+00 1.11538893e+01 5 2.08376173e+01 -2.76462024e+01 -2.06135821e+01 6 1.07348211e+01 -2.05298830e+00 -8.01091110e+00 7 9.51098297e+00 -1.29932207e+01 -7.41461077e+00 8 6.22867155e+00 8.47084235e+00 1.42565529e+01 9 -2.45392544e+01 4.08707258e+00 -3.59243168e+01 10 -8.49503089e+00 1.97861657e+01 -2.20876797e+01 11 1.32403298e+01 -2.34185636e+01 1.04405033e+01 12 -2.99218534e+01 2.72637346e+01 -6.70487795e+00 13 -1.61051432e+01 -2.29931836e+01 -3.80254026e+01 14 3.33809793e+01 3.30515973e+01 -2.00595234e+01 15 3.26823337e+01 -1.90930275e+01 -1.22919133e+01 16 -3.68809212e+00 3.92530484e+01 1.10876916e+01 17 -2.82876943e+01 -2.43909283e+01 -1.19802981e+00 18 1.91550901e+01 2.74917628e+01 -2.12717513e+01 19 1.64221642e+01 -3.25491141e+01 3.13981976e+01 20 -3.15946300e+01 1.56167431e+01 2.16289619e+01 21 -9.95970349e-01 -1.75343485e+01 -9.16760761e+00 22 2.08508146e+01 -2.18475264e+01 3.13770564e+00 23 2.46452975e+01 -2.39953032e+01 8.46592414e+00 24 -1.48889188e+01 2.32777569e+01 1.51424250e+01 25 -1.73445892e+01 4.54591986e+00 2.17793867e+01 26 1.09165239e+01 1.89611692e+01 1.05193008e+01 27 9.24000823e+00 -1.22647660e+01 1.25403829e+01 28 -2.07000571e+01 1.27079383e+01 9.51522612e+00 29 -3.94752459e+01 -2.81271964e+01 1.13591013e+01 30 3.63913993e+01 4.23750397e+01 -6.73630766e+00 31 1.91747567e+01 -8.62101017e+00 3.31830299e+01 32 -1.03321315e+01 2.92375416e+01 2.39279366e+01 MIXED STRUCTURE (pbc=False)-- Species = Re W (Configuration in file "config-F-ReW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1939.1294797702453 Forces: 1 -6.90270120e+02 -6.94632820e+02 1.15187635e+02 2 6.97131665e+02 8.52652236e+02 -4.87887909e+02 3 -2.08108436e+02 -2.66249162e+02 3.92073263e+02 4 -1.54002529e+02 2.77631165e+01 7.49095016e+01 5 2.88031306e+02 -3.08830936e+02 -4.72310679e+02 6 1.61869758e+02 -1.31931096e+01 -1.03726495e+02 7 3.05483433e+02 -1.28485659e+02 -2.48477778e+02 8 -3.25022073e+01 -3.15689565e+02 7.39281547e+02 9 -1.70026107e+02 -4.97857539e+01 -7.93543280e+01 10 -8.72573584e+01 7.31838956e+01 -3.28704640e+02 11 1.13417444e+01 -2.85469760e+02 -5.43165823e+01 12 -1.94353618e+02 1.53001564e+02 4.05729681e+01 13 -1.05631449e+02 5.11228553e+02 -5.74658816e+02 14 6.81928053e+01 1.90884156e+01 -5.25365875e+01 15 9.92403652e+01 2.97947085e+01 -4.24430000e+01 16 2.57658202e+02 3.67444495e+02 1.09490760e+02 17 -2.60395063e+02 -7.63114287e+02 -3.58630657e+02 18 1.29386861e+02 4.06455001e+02 -3.03085561e+02 19 3.44834379e+02 -5.17005717e+02 3.26257653e+02 20 -2.84366892e+02 7.21205892e+02 4.66240929e+02 21 -2.36358753e+02 -3.76533320e+01 1.82408808e+02 22 3.66658588e+02 5.95246537e+01 -4.70135289e+02 23 6.26613663e+01 -1.65661412e+02 1.93969652e+02 24 -5.32374653e+02 8.21047079e+01 4.04899442e+02 25 -7.47405451e+01 -7.13111112e+01 -5.92712670e+01 26 -6.91718429e+02 4.08754134e+02 -2.13159739e+02 27 -5.48287698e+01 -3.00789479e+02 4.86491891e+01 28 -1.67617494e+02 2.52958838e+02 1.39511301e+02 29 2.77957049e+02 -4.52124600e+02 5.05178328e+01 30 1.92782379e+02 6.69331927e+01 3.48270769e+01 31 1.67917267e+02 1.02781731e+02 5.76055831e+01 32 5.13405256e+02 2.35121569e+02 4.72296186e+02 MIXED STRUCTURE (pbc=True)-- Species = Re W (Configuration in file "config-T-ReW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 2554.1372323149376 Forces: 1 -4.56923703e+02 -7.85246441e+02 1.05724089e+02 2 7.65314504e+02 8.40854707e+02 -3.45751196e+02 3 -1.88590107e+02 -1.98888282e+02 4.10465500e+02 4 5.81534949e+02 3.44725385e+02 2.74597910e+02 5 2.87215894e+02 -2.73615954e+02 -4.81107010e+02 6 -3.92684091e+02 1.13807101e+02 -3.43594460e+02 7 -1.31574182e+02 -4.41830008e+02 -1.45770760e+02 8 -2.97676754e+01 -3.06918961e+02 7.31892583e+02 9 -7.11620706e+01 -4.84722487e+01 -9.04071350e+01 10 -7.50368162e+01 2.73371034e+01 -3.11856365e+02 11 1.34851721e+01 -2.81828649e+02 -5.74288390e+01 12 -1.68812611e+02 1.18641355e+02 3.58339841e+01 13 -1.02837616e+02 5.10736982e+02 -5.57043647e+02 14 2.89695870e+01 6.29796907e+00 -6.66246280e+01 15 4.88366174e+00 2.56939692e+01 5.43335439e+00 16 2.51811941e+02 3.20763652e+02 1.05052443e+02 17 -2.19143445e+02 -7.54132177e+02 -3.59627794e+02 18 1.34486528e+02 4.02052270e+02 -2.98694307e+02 19 3.52075873e+02 -5.03453625e+02 3.02995913e+02 20 -2.21129026e+02 7.82270229e+02 3.16147586e+02 21 -2.18148229e+02 -1.50756614e+01 1.95358709e+02 22 3.04409967e+02 5.29156265e+01 -4.75478136e+02 23 -6.05638347e+01 -2.38262176e+02 1.96511157e+02 24 -5.26949331e+02 8.09679168e+01 3.93320766e+02 25 -6.00061334e+01 -6.48281395e+01 -4.69000947e+01 26 -6.75907701e+02 3.80512656e+02 -1.97462196e+02 27 -4.68950389e+01 -3.05097118e+02 -1.40302672e+01 28 -1.35315609e+02 2.58383846e+02 1.36208939e+02 29 2.77387306e+02 -4.47745059e+02 4.90286527e+01 30 1.40030148e+02 4.93539240e+01 2.11405260e+01 31 1.21895861e+02 1.22355606e+02 4.57122011e+01 32 5.17945830e+02 2.27724202e+02 4.66352523e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==4102== Memcheck, a memory error detector ==4102== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4102== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==4102== Command: python runner2.py EAM_Dynamo_SetyawanGaoKurtz_2018_ReW__MO_680820064987_000 ==4102== ==4355== Warning: invalid file descriptor 4096 in syscall close() ==4355== Warning: invalid file descriptor 4097 in syscall close() ==4355== Warning: invalid file descriptor 4098 in syscall close() ==4355== Warning: invalid file descriptor 4099 in syscall close() ==4355== Use --log-fd= to select an alternative log fd. ==4355== Warning: invalid file descriptor 4100 in syscall close() ==4355== Warning: invalid file descriptor 4101 in syscall close() ==4102== ==4102== HEAP SUMMARY: ==4102== in use at exit: 2,203,207 bytes in 1,644 blocks ==4102== total heap usage: 86,386 allocs, 84,742 frees, 171,026,565 bytes allocated ==4102== ==4102== LEAK SUMMARY: ==4102== definitely lost: 0 bytes in 0 blocks ==4102== indirectly lost: 0 bytes in 0 blocks ==4102== possibly lost: 198,622 bytes in 101 blocks ==4102== still reachable: 2,004,553 bytes in 1,542 blocks ==4102== suppressed: 32 bytes in 1 blocks ==4102== Rerun with --leak-check=full to see details of leaked memory ==4102== ==4102== For lists of detected and suppressed errors, rerun with: -s ==4102== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 9176 from 565) ================================================================================ 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.