!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 ----------------------------------------------------------------------------------------------------- Results for KIM Model : Tersoff_LAMMPS_Tersoff_PRB39_1989_GeSi__MO_350526375143_000 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 = 364.894570747 Forces: 1 -4.09306895e+01 -4.35189616e+01 -6.21008313e+01 2 4.71969256e+00 1.99149061e+00 -5.17250427e+01 3 3.31918008e+01 -6.54239817e+01 9.00509976e+00 4 -5.04700893e+01 6.10377250e+01 2.81369349e+01 5 6.79534196e+00 -4.01593007e+01 -1.96671570e+01 6 1.86837344e+01 5.97964857e+00 -2.86395802e+01 7 2.25799484e+01 -5.02892405e+01 -2.63684361e+01 8 9.23354170e+00 -4.22287356e+01 -2.00882097e+01 9 -2.77687903e+01 -1.76871406e+00 -5.21575907e+01 10 -2.00024912e+01 3.79803372e+01 -4.82236025e+01 11 -2.66898312e+01 6.51582093e+00 2.97306737e+01 12 -2.62896332e+01 2.68289404e+01 2.19012054e+00 13 1.27901354e+01 -1.13570729e+01 -6.56275283e+01 14 9.34907213e+00 1.30110436e+01 -1.26611226e+01 15 8.56031839e+01 -4.60548098e+00 -6.79527245e+00 16 3.96304971e+01 5.63108722e+01 -2.20440647e+01 17 -4.19361049e+01 -2.59899809e+01 9.89673087e+00 18 -9.49545338e-01 3.10610280e+01 -7.94538982e+00 19 8.72354596e+00 -6.13935410e+01 3.56501501e+01 20 -3.64533580e+01 2.53607231e+01 2.64136380e+01 21 -3.39941593e+00 -2.91570984e+01 3.69905559e+00 22 4.28678410e+01 2.62200776e+01 4.26589661e+01 23 7.10832741e+00 -4.33618064e+00 1.37661038e+01 24 2.00661953e+01 1.07285126e+01 3.58282509e+01 25 -3.00116210e+01 -1.31820252e+01 5.01774712e+00 26 -5.88096329e+01 5.80038073e+01 3.59644128e+01 27 -1.33383230e+00 -3.05909177e+01 2.09518954e+01 28 -3.84143265e+01 2.89883849e+01 1.31766461e+01 29 -1.34261209e+01 -8.90145970e+00 3.10268294e+01 30 2.64303409e+01 4.28650586e+01 -9.48554082e+00 31 5.33200396e+01 -3.55906446e+01 5.30183578e+01 32 1.57922439e+01 3.56098656e+01 3.73977560e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ge (Configuration in file "config-T-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 704.288253597 Forces: 1 9.71045671e+00 -5.91939892e+01 -3.31039724e+01 2 -6.86477713e+00 8.39420489e+00 -2.97267416e+00 3 4.85096369e+01 -3.37921881e+01 9.38740948e+00 4 -8.76980750e+00 8.06344285e+01 2.72054289e+01 5 1.70850566e+01 8.42139613e+00 -2.15773311e+01 6 -3.43095797e+01 4.83547521e+01 -1.44594503e+01 7 -1.41215439e+01 -4.51204062e+01 -1.68667147e+01 8 7.57926202e+00 -4.15203499e+01 -2.00484168e+01 9 -5.14209422e+01 -1.27464616e+01 7.25908492e+00 10 -4.11453829e+01 1.74794256e+01 -1.45389051e+01 11 -2.56783729e+01 1.92388189e+00 3.23753576e+01 12 1.02760964e+01 -3.45025751e-01 2.60759735e+01 13 1.60401978e+01 -1.80004602e+01 -4.44244365e+01 14 -3.44976864e+01 -3.09616597e+00 -5.16649323e-01 15 6.23295160e+01 -2.09391686e+01 -4.89490057e+00 16 3.51320788e+01 2.85253838e+01 -2.99589510e+00 17 2.25204695e+01 -5.29292371e+01 1.09418037e+01 18 9.69797018e-01 4.01309928e+01 -8.90876069e+00 19 1.34875260e+01 -5.22339035e+01 2.19539212e+01 20 -1.25755039e+01 5.97205903e+01 -8.86313726e+00 21 6.43670278e-01 2.27516844e+01 8.46612326e+00 22 -2.33199156e+01 7.77453237e+01 5.35405084e+01 23 -2.90435578e+01 -1.03533529e+00 -2.41869755e+01 24 4.17281627e+01 6.00182262e+00 -1.48823172e+01 25 6.51240690e+00 -3.04476880e+01 2.06430891e+00 26 -6.94805195e+01 1.01972332e+01 4.16188648e+01 27 2.42929083e+01 -3.48478579e+01 -3.32691993e+01 28 -2.18758469e+00 1.51660045e+01 -3.02578829e+00 29 -2.18682259e+01 -2.11549892e+01 3.04325057e+01 30 -3.51844924e+00 2.78703832e+01 -2.40783699e+01 31 2.68609539e+01 -5.43907262e+01 3.97962900e+01 32 3.51236535e+01 2.84764450e+01 -1.75036864e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 294.335558667 Forces: 1 -2.06143813e+00 -2.12359429e+00 -4.68113180e+00 2 -1.30720198e+01 7.39840950e-01 -2.32048050e+01 3 1.05964153e+01 -4.14935659e+01 -3.60887647e+01 4 -4.33924117e+01 -5.85608862e+01 -8.87528298e+00 5 -5.99807305e+01 -6.41741204e+01 -5.44346253e+01 6 3.44528142e+01 -1.83229405e+01 -6.09488976e+01 7 7.40063501e+01 -2.35040507e+01 5.09313286e+01 8 1.87729484e+00 3.67389053e+01 -1.77749917e+01 9 -3.48347420e+01 1.05621154e+01 -6.33198154e+01 10 1.10118505e+01 2.61081616e+01 -2.93783345e+01 11 4.82781986e+01 9.52369262e+00 1.54357368e+01 12 -1.64960844e+01 3.16897114e+01 5.05923994e+00 13 -3.42781238e+01 2.49581249e+01 -3.33008733e+01 14 8.97941809e+00 1.47001576e+01 -9.58138389e+00 15 5.14846334e+01 3.68354353e+01 3.80241485e+01 16 7.32447533e+00 7.55207224e+01 -5.30772364e+01 17 -5.52091406e+01 -3.71034541e+01 2.45663003e+01 18 1.87215874e+01 1.55410893e+01 3.20607859e+01 19 -1.54283216e+01 -2.71839078e+01 1.37335533e+01 20 -1.53293724e+01 -9.94692037e+00 1.25237821e+01 21 1.64122750e+01 -6.02449936e+01 1.07414081e+01 22 3.13018904e+01 -2.69518867e+01 -3.86725319e+01 23 1.49681011e+01 -1.45661108e+01 1.34263638e+01 24 -4.24508381e-02 2.01267769e+01 3.00223443e+01 25 -4.53892656e+01 2.89315184e+01 3.95186807e+01 26 -2.62868757e+00 2.65147519e+01 -2.58329623e+01 27 -1.21791647e+00 -1.04649616e+01 2.37784193e+01 28 -2.92698460e+01 1.08421946e+01 1.57505453e+01 29 -1.88122440e+01 -3.75266176e+01 3.86679905e+01 30 2.88798402e+01 1.51466619e+01 1.25419818e+01 31 6.32676030e+00 2.62068799e+01 5.63932145e+01 32 2.28208906e+01 2.14812701e+01 2.59958133e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 579.624168487 Forces: 1 3.75698999e+01 5.33537901e+01 -2.73593960e-01 2 -1.18000601e+01 1.65782790e+01 3.41305599e+01 3 3.87878165e+01 -1.15887519e+01 -3.06981897e+01 4 1.14571497e+01 -6.86363843e+01 2.84253590e+00 5 -7.27195485e+01 -4.19907252e+01 -4.19594143e+01 6 1.76006532e+00 -3.56297065e+01 -3.96794268e+01 7 3.93832402e+01 -1.31904523e+01 7.10750073e+01 8 9.77236273e-01 3.75641972e+01 -1.77931051e+01 9 9.81217130e-01 4.42019646e+01 -3.71753782e+01 10 2.14186470e+01 2.93266108e+01 2.22202485e+01 11 5.24611254e+01 2.24757671e+00 1.85599188e+01 12 -1.33389676e+01 -1.07439236e+01 1.92087765e+00 13 -4.88552241e+01 2.39572795e+01 -3.21138806e+00 14 -3.42499854e+01 -3.36779272e+01 1.36183107e+01 15 -6.10110662e+00 5.31974094e+01 5.47888110e+01 16 4.73415201e-02 5.45699026e+01 -5.11701813e+01 17 -4.38023768e+01 -1.62289204e+01 5.02551317e+01 18 3.03757727e+01 1.51566567e+01 3.01971333e+01 19 -9.91500767e+00 -4.68588508e+00 -1.21154934e+01 20 -4.90027043e+00 -4.01999505e+01 -3.23153670e+01 21 1.27993463e+01 -3.80685457e+01 1.51353776e+01 22 4.83910360e-01 -3.06355560e+01 -4.66536011e+01 23 5.86377545e+00 2.68918147e+00 -2.38665274e+01 24 1.05991823e+01 2.73191872e+01 6.74468741e-01 25 -1.22666625e+01 2.88312138e+01 4.37630568e+01 26 7.01141265e+00 9.23085353e+00 -3.80475879e+01 27 5.35749418e+00 -4.07447427e+01 -1.91375968e+01 28 -3.05229257e+01 -7.12897630e+00 -2.83865633e+01 29 -2.09944772e+01 -5.11198803e+01 3.88123888e+01 30 2.05378670e+00 9.76261938e+00 3.17889125e+00 31 8.51824254e-01 3.46067447e+01 1.32576408e+01 32 2.92263687e+01 1.67686140e+00 8.05305578e+00 MIXED STRUCTURE (pbc=False)-- Species = Ge Si (Configuration in file "config-F-GeSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 380.891170889 Forces: 1 -8.40830658e+01 -4.92755366e+01 -6.66250634e+01 2 4.22798630e+01 7.86424545e+01 -1.00721649e+02 3 2.36619452e+01 -1.07606916e+02 4.92565369e+01 4 -6.37640242e+01 5.10062584e+01 2.60058272e+01 5 2.79652956e+01 -4.17317933e+01 -3.07836528e+01 6 4.43810331e+01 -2.25828594e+01 -3.47942612e+01 7 3.50407735e+01 -2.09198454e+01 -1.94953658e+01 8 2.80760241e+01 -3.26967937e+01 3.23617194e+01 9 -1.17121071e+01 -2.42872188e+00 -1.46292565e+01 10 -5.47206471e+00 1.11872294e+01 -1.49258974e+01 11 -2.50532395e+01 4.43779108e+01 -1.95328986e+01 12 -1.15181422e+01 1.66012127e+01 -1.06858811e+01 13 -1.25859047e+01 4.11228349e+01 -6.58345829e+01 14 7.02875785e+00 7.67812194e+00 -5.51061691e+00 15 5.49943831e+01 2.06116221e+01 -1.39826911e+01 16 1.27694317e+01 2.18416936e+01 -3.28835979e+01 17 -3.85713189e+01 -5.18120200e+01 3.67640132e+01 18 1.64909859e+01 -1.12749904e+01 1.78147942e+01 19 2.55946076e+00 -1.49525801e+01 1.01495193e+01 20 -3.30039144e+01 5.69778714e+00 2.81040390e+01 21 -6.29225059e+01 -6.25339593e+01 -1.23729328e+01 22 6.14982219e+01 2.72211250e+01 -1.76128963e+01 23 4.29746321e+01 -3.53928993e+01 4.06761278e+01 24 -3.17517215e+01 -8.60217990e+00 5.01740012e+01 25 -3.64472080e+01 2.73302990e+00 1.69956417e+01 26 -1.86507966e+01 3.27033314e+01 1.94413073e+01 27 -1.14780774e+01 -3.23389785e+01 2.33404174e+01 28 -1.98895120e+01 2.51378199e+01 9.73962243e+00 29 -2.17076794e+01 2.61507748e+01 3.70131373e+01 30 2.72449046e+01 2.20935337e+01 1.65043183e+01 31 3.44325182e+01 2.55321110e+01 2.85267027e+01 32 2.72130519e+01 3.38112227e+01 1.75235189e+01 MIXED STRUCTURE (pbc=True)-- Species = Ge Si (Configuration in file "config-T-GeSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 640.762707408 Forces: 1 -8.17309997e+01 -4.85244344e+01 -5.78875037e+01 2 4.77169373e+01 8.63932216e+01 -8.53835001e+01 3 2.91637642e+01 -7.73216519e+01 4.26987157e+01 4 -2.76443380e+01 7.07745067e+01 2.75497385e+01 5 3.35795153e+01 -8.86395418e+00 -4.73805594e+01 6 2.11085855e+01 -3.47496238e+01 -4.58769452e+00 7 -1.65238806e+01 -2.30077574e+00 -3.21308594e+01 8 2.69776249e+01 -2.36526706e+01 3.54624347e+01 9 1.85147934e+01 -8.61363297e+00 5.47228027e+00 10 -4.45415452e-01 1.02116209e+01 3.88432180e+01 11 -2.49665882e+01 4.29390496e+01 -1.92639511e+01 12 2.03187881e+01 -2.62773766e+01 -1.96697877e+01 13 -1.64623989e+01 4.78448006e+01 -3.19807847e+01 14 -2.09258805e+01 2.16133661e+01 -1.26096610e+01 15 3.00593608e+01 2.16110169e+01 -1.11654505e+01 16 6.06931856e+00 -2.32851809e+01 -1.24214151e+01 17 6.02489374e+00 -3.26281783e+01 4.66695142e+01 18 1.76233909e+01 -2.41504863e+00 1.82459837e+01 19 2.71116392e+01 1.97508525e+01 -1.24849863e+01 20 9.30602500e+00 2.24395210e+01 1.88147602e+01 21 -8.54660183e+01 -2.32892400e+01 -6.89544195e-01 22 4.39980992e+01 4.51955079e+01 -2.92735342e+01 23 1.61730014e+01 -4.02545455e+01 5.25359661e+01 24 -5.06981551e+01 -1.75622668e+01 1.60135827e+01 25 -1.92834145e+01 2.96612724e+00 2.00818992e+01 26 -1.89352249e+01 -3.80576849e+00 3.38419046e+01 27 -8.90285154e-01 -6.26815988e+01 -1.18407045e+01 28 -3.60589389e+01 -1.58805863e+00 -9.30524583e+00 29 -2.58644635e+01 2.55952411e+01 3.56274410e+01 30 1.93291981e+01 -4.70029406e+01 2.81329232e+01 31 9.89814505e+00 3.59816163e+01 -4.66916147e+00 32 4.29229209e+01 3.15004984e+01 -1.72460184e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==26542== Memcheck, a memory error detector ==26542== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al. ==26542== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info ==26542== Command: python runner2.py Tersoff_LAMMPS_Tersoff_PRB39_1989_GeSi__MO_350526375143_000 ==26542== ==26542== Warning: set address range perms: large range [0x20fe9000, 0x314e9000) (defined) ==26542== Warning: set address range perms: large range [0x2122d000, 0x314e9000) (defined) ==26542== Warning: set address range perms: large range [0x20fe9000, 0x314e9000) (noaccess) ==26542== Warning: set address range perms: large range [0x23029000, 0x33529000) (defined) ==26542== Warning: set address range perms: large range [0x2326d000, 0x33529000) (defined) ==26542== Warning: set address range perms: large range [0x23029000, 0x33529000) (noaccess) ==26542== Warning: set address range perms: large range [0x23029000, 0x33529000) (defined) ==26542== Warning: set address range perms: large range [0x2326d000, 0x33529000) (defined) ==26542== Warning: set address range perms: large range [0x23029000, 0x33529000) (noaccess) ==26542== Warning: set address range perms: large range [0x23029000, 0x33529000) (defined) ==26542== Warning: set address range perms: large range [0x2326d000, 0x33529000) (defined) ==26542== Warning: set address range perms: large range [0x23029000, 0x33529000) (noaccess) ==26542== Warning: set address range perms: large range [0x23429000, 0x33929000) (defined) ==26542== Warning: set address range perms: large range [0x2366d000, 0x33929000) (defined) ==26542== Warning: set address range perms: large range [0x23429000, 0x33929000) (noaccess) ==26542== Warning: set address range perms: large range [0x23429000, 0x33929000) (defined) ==26542== Warning: set address range perms: large range [0x2366d000, 0x33929000) (defined) ==26542== Warning: set address range perms: large range [0x23429000, 0x33929000) (noaccess) ==26542== Warning: set address range perms: large range [0x23429000, 0x33929000) (defined) ==26542== Warning: set address range perms: large range [0x2366d000, 0x33929000) (defined) ==26542== Warning: set address range perms: large range [0x23429000, 0x33929000) (noaccess) ==26542== ==26542== HEAP SUMMARY: ==26542== in use at exit: 4,043,539 bytes in 5,784 blocks ==26542== total heap usage: 153,343 allocs, 147,559 frees, 59,598,875 bytes allocated ==26542== ==26542== LEAK SUMMARY: ==26542== definitely lost: 0 bytes in 0 blocks ==26542== indirectly lost: 0 bytes in 0 blocks ==26542== possibly lost: 162,822 bytes in 96 blocks ==26542== still reachable: 3,880,717 bytes in 5,688 blocks ==26542== suppressed: 0 bytes in 0 blocks ==26542== Rerun with --leak-check=full to see details of leaked memory ==26542== ==26542== For counts of detected and suppressed errors, rerun with: -v ==26542== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2408 from 156) ================================================================================ 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.