Model Extended KIM ID = === Verification check vc-memory-leak start (2018-06-18 20:21:01) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Erhart_Juslin_Goy_Nordlund_Mueller_Albe_ZnO__MO_616776018688_001 Supported species : O Zn random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = O (Configuration in file "config-F-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = -2.18202142957 Forces: 1 3.09097604e-01 -1.91816213e+00 -2.41918646e+00 2 -1.59778626e+00 -8.81623174e-01 -2.07089831e+00 3 1.50103028e+00 -4.65024448e+00 -6.21601378e+00 4 -2.31833612e+00 2.59233868e+00 2.10322812e+00 5 2.37805920e+00 -1.35890335e+00 -8.83421481e-01 6 4.23259068e-01 -1.72867333e+00 -1.03312163e+00 7 4.72835175e-01 -4.41033311e+00 -6.03861905e+00 8 -1.97477665e+00 -1.55044681e+00 8.36986880e-01 9 -7.51169209e-01 4.52696174e-01 -3.68515033e-01 10 -2.08413858e+00 3.42884030e-01 -1.77914219e+00 11 -1.21972208e-01 -1.07030287e+00 -2.26817263e+00 12 -2.83012826e-01 3.81888481e-01 -1.85322049e+00 13 -3.93273568e+00 -2.17114063e+00 -6.04206693e+00 14 1.60770387e+00 2.70268376e+00 -2.07812618e+00 15 5.31378410e+00 -7.33725590e-01 2.61374108e+00 16 2.48654496e+00 3.84060102e+00 2.11334167e-01 17 -5.22553063e+00 -2.90632950e+00 1.92369368e+00 18 3.12277323e+00 5.39589654e+00 3.70733061e+00 19 1.09935863e+00 -2.05065493e+00 1.83667326e+00 20 -1.98481047e+00 7.58280911e-01 4.48753718e-01 21 -1.64127306e-01 -1.06308225e+00 1.38342942e+00 22 3.70059440e+00 1.87517532e+00 4.55326113e+00 23 1.29841254e-01 -5.95265751e-02 -2.03117238e-01 24 6.74590152e-02 -2.22848112e-01 2.64078899e-01 25 -4.01804219e+00 4.32400021e-01 2.16217950e+00 26 -1.43548056e+00 3.49344148e+00 3.11474526e+00 27 1.67252298e+00 -2.82725806e+00 1.40664300e+00 28 -3.71274929e+00 3.16055323e+00 -2.50213675e-01 29 1.69221600e+00 1.29619662e+00 3.18758623e+00 30 6.51991838e-01 1.79060849e+00 2.78966312e+00 31 5.32493036e-01 2.22150843e-01 4.19953225e-01 32 2.44310334e+00 8.65459297e-01 5.40553762e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = O (Configuration in file "config-T-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 20.1013859505 Forces: 1 3.26139720e+00 -5.69603088e+00 -3.14416489e+00 2 -3.53427182e+00 1.74555507e-01 2.04432099e+00 3 3.26155648e+00 -4.31329767e+00 -6.54076083e+00 4 3.00250065e-01 5.37553917e+00 3.91635854e+00 5 2.63000078e+00 -1.45261928e+00 1.50854048e-01 6 -4.37723669e+00 2.38410999e+00 -1.37454234e+00 7 -4.46231441e-01 -4.65869601e+00 -6.33031895e+00 8 -2.74128833e+00 -1.36895982e+00 6.67783224e-01 9 -1.35866455e+00 -8.08118316e-01 9.46207245e-01 10 -2.52191820e+00 -9.21654712e-01 -4.45463086e-01 11 1.23330511e-01 -1.76574368e+00 -2.36068316e+00 12 1.69343383e+00 9.91820235e-01 -3.06338895e+00 13 -4.63045793e+00 -2.93321865e+00 -5.26686043e+00 14 1.58017698e+00 3.46881415e+00 -2.78434810e+00 15 3.79580671e+00 -2.47039517e+00 3.06440108e+00 16 2.55698884e+00 2.51100567e+00 5.32322253e-01 17 -5.16264240e+00 -5.69624266e+00 1.62416925e+00 18 5.31430040e+00 6.91315465e+00 3.26633586e+00 19 3.56593605e+00 -3.04872834e+00 1.49957635e+00 20 -5.23666433e-01 4.75075544e+00 4.48107622e-01 21 -1.82230566e+00 -7.49800055e-01 2.04143859e+00 22 3.58755122e-01 5.39929649e+00 5.73359722e+00 23 -1.73725678e+00 -2.82938664e+00 -1.73778742e+00 24 1.82358867e+00 3.17908887e-01 -3.18004679e+00 25 -9.87050897e-01 -1.78278024e+00 2.05551925e+00 26 -8.29812825e-01 3.57781414e+00 2.64935925e+00 27 3.19398256e+00 -4.98732786e+00 -4.17287805e-01 28 -5.66248719e+00 5.45055113e+00 -7.60273605e-01 29 1.45757054e+00 5.43701532e-01 2.88387970e+00 30 -2.18209593e+00 2.54238746e+00 3.94751135e+00 31 -7.02372289e-02 -1.57603585e-01 2.56223440e-01 32 3.67054953e+00 1.23918911e+00 -3.22038922e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Zn (Configuration in file "config-F-Zn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 126.943855193 Forces: 1 -1.82453146e+01 -1.48964214e+01 -1.29121152e+01 2 1.74959348e+01 2.23884581e+01 -1.50898129e+01 3 8.14471380e+00 -3.21558706e+01 -1.63477256e+01 4 -2.11478471e+01 1.50104577e+01 -9.26744227e+00 5 -5.01399805e+00 -8.24911441e+00 -7.99307582e+00 6 1.60576846e+01 3.36395843e+00 -1.15096589e+01 7 1.71470443e+01 -2.41209219e+01 -9.68612930e-01 8 -1.11486126e+01 1.31828944e+01 -2.37675034e+00 9 -4.94778484e+00 2.53168815e+00 -7.47568094e+00 10 -5.88884319e+00 3.08731189e+00 -2.04010726e+00 11 1.60180956e+01 -1.00454103e+01 -1.41024440e+01 12 -1.98819658e+01 2.49781737e+01 -2.68925127e+01 13 -4.30058537e+00 2.37366239e+00 -4.70102362e+00 14 6.73179837e+00 4.60140149e+00 -4.41537047e+00 15 1.33056680e+01 -6.89044458e+00 -6.68637265e+00 16 -8.08019810e+00 9.83158291e+00 -8.46444376e-01 17 -2.28088478e+01 -3.23800676e+01 1.58521996e+01 18 8.91377978e+00 3.01438640e+01 5.37204105e+00 19 -1.23970012e+01 -1.53875814e+01 2.60782659e+01 20 -1.55248575e+01 -1.53036907e+00 1.72028265e+01 21 1.85277271e+01 -2.01432217e+01 -6.13567719e+00 22 9.96401836e+00 1.10667253e+01 6.95953746e-01 23 4.68211602e-01 -8.81183318e+00 1.07165555e+01 24 7.73517116e+00 -2.30769306e+00 1.76377670e+01 25 -3.55185219e+01 -3.51946886e+01 -5.52196251e+00 26 3.16862811e+01 2.93135777e+01 -8.51446353e+00 27 2.22440649e+01 -1.66335782e+01 2.31613646e+01 28 -2.64348713e+01 3.33999715e+01 3.69272216e+01 29 -2.05747285e+00 7.26719291e+00 -1.24891041e+01 30 1.73587798e+01 1.18063052e+01 -5.53435313e+00 31 1.07984550e+01 -5.30836715e+00 1.65244283e+01 32 -9.20070618e+00 9.70835747e+00 1.16520868e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zn (Configuration in file "config-T-Zn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 249.538954787 Forces: 1 -1.28705281e+01 -1.94653353e+01 1.20145589e+00 2 1.74968765e+01 2.53444780e+01 -9.81933440e+00 3 9.47698714e+00 -2.85129177e+01 -1.73521157e+01 4 3.64563190e+00 2.44706089e+01 -1.25276869e+01 5 -2.96944133e+01 4.64395932e+01 1.18433571e+01 6 4.84037938e+00 6.30767405e+00 -1.20375085e+01 7 5.67821513e+00 -2.57943178e+01 -1.26961568e+00 8 -1.25550028e+01 1.41080184e+01 -1.94898621e+00 9 1.69062962e+00 5.02199281e+00 -4.24765889e+00 10 -1.87173176e+01 -1.22192460e+01 1.35885786e+01 11 1.70542816e+01 -1.09814686e+01 -1.39892647e+01 12 -6.05970461e+00 2.68865262e+01 -3.18182725e+01 13 -1.98947875e+01 4.45002565e+00 2.09586007e+01 14 3.86218731e+01 -4.42314201e+01 8.96516686e+00 15 -1.15463685e+01 -1.61044703e+01 -1.43749596e+01 16 -1.07844133e+01 -5.30593709e+00 -3.13521399e+00 17 -6.41714907e+00 -2.99637564e+01 1.24598158e+01 18 1.09613903e+01 3.28420680e+01 4.57964406e+00 19 -2.77560403e+01 9.95889848e+00 1.95088698e+01 20 -1.75221403e+00 8.44455815e+00 1.66582237e+01 21 1.65033679e+01 6.41111431e+00 -1.73677102e+01 22 -2.54853341e+01 1.78145741e+01 3.38659146e+00 23 7.40341224e+00 7.76197293e+00 -1.88706910e+00 24 6.43785405e+00 -7.44865447e+00 5.97072834e+00 25 -1.67676836e+01 -4.25514014e+01 1.19293981e+00 26 3.15201215e+01 1.34343135e+01 -1.17459351e+01 27 2.27043930e+01 -1.95125982e+01 1.91704257e+01 28 -1.93692413e+01 3.08273287e+01 4.04915157e+01 29 -3.60617814e+00 6.17464262e+00 -1.38088840e+01 30 1.29582482e+00 8.92523151e+00 -1.14186150e+01 31 2.21110731e+01 -9.11519739e+00 -4.35938059e+00 32 5.83406512e+00 -2.44168988e+01 3.13229761e+00 MIXED STRUCTURE (pbc=False)-- Species = O Zn (Configuration in file "config-F-OZn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 720.571947295 Forces: 1 -1.05196127e+01 -2.03865813e+01 -2.25547259e+01 2 -2.75996866e+01 -1.03431836e+01 -8.99402675e+01 3 -2.62379360e+01 -6.64222419e+01 6.56112100e+01 4 -2.25795311e+01 -2.62080988e+00 -8.83449881e+00 5 2.33594673e+01 -1.48863191e+01 -3.55499976e+01 6 4.64059814e+01 -3.92604725e+01 -6.20195929e+01 7 7.60479021e+00 -5.52628962e+01 -1.38359063e+01 8 -2.47086453e+01 -1.28400862e+02 7.30282212e+00 9 -2.45767458e+01 3.22284829e+00 -4.02000964e+01 10 -1.29113090e+01 7.55838615e+01 -5.72087676e+01 11 -2.10421618e+01 3.78196873e+01 1.79453700e+01 12 -9.36491253e+00 3.74057576e+01 -8.09074762e+00 13 3.38927327e+01 4.24528279e+01 -8.51998147e+01 14 8.79804293e+00 1.82621064e+00 -6.96319134e+00 15 1.03927674e+02 7.28830770e+01 -1.88599936e+01 16 -1.31129902e+01 1.05267722e+02 -2.88638937e+00 17 -6.32680817e+01 -8.24508470e+01 1.24420599e+01 18 -5.56720535e+01 3.37082195e+01 -5.72496996e+01 19 -5.72880308e+00 -1.20544333e+02 6.75056927e+01 20 -5.55910692e+01 2.59425140e+01 2.87519775e+01 21 7.94069621e+01 -1.26666775e+02 -2.60684715e+01 22 1.06365860e+02 2.25456088e+01 4.10717502e+01 23 2.37035783e+01 -2.25961881e+01 1.15546397e+01 24 6.27479600e+01 -2.75036212e+01 1.09506266e+02 25 -6.58658326e+01 -7.40546692e+00 6.19035900e+01 26 -2.91277212e+01 4.45436391e+01 -2.67693197e+00 27 -8.07668369e+01 1.41957062e+02 3.67315281e+01 28 -2.77035470e+00 1.30458027e+01 5.87117139e+00 29 -3.83414436e+01 2.11939358e+01 1.83160844e+01 30 3.65806919e+01 8.92640614e+00 2.24070005e+01 31 3.43382056e+01 1.19858871e+01 1.11060922e+01 32 2.26537813e+01 2.44395306e+01 2.01118379e+01 MIXED STRUCTURE (pbc=True)-- Species = O Zn (Configuration in file "config-T-OZn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1468.93905018 Forces: 1 2.25383101e+01 -1.15621332e+01 8.86095540e+01 2 -3.08229024e+01 -1.00921774e+01 -4.84613625e+01 3 -1.90500771e+01 -1.70211489e+01 8.48859370e+01 4 4.34380184e+01 2.98448866e+01 2.04550543e+01 5 1.16094718e+01 -1.60317390e+01 1.85274797e+01 6 2.43636421e+01 -5.91311168e+01 -5.51773150e+01 7 -4.38275028e+01 -4.13626904e+01 -1.06462696e+01 8 -2.90660670e+01 -1.28851233e+02 1.95684006e+01 9 6.45015069e+01 6.61170335e+00 8.02651345e+01 10 1.56940095e+01 5.40644611e+01 -1.95868842e+01 11 -1.87723851e+01 3.66499111e+01 2.30683850e+01 12 -3.18245928e+01 -3.70767875e+01 -3.25142520e+01 13 3.26144976e+01 2.16604124e+01 -4.18748590e+01 14 -4.14633827e+00 -9.78038479e+01 5.68136501e+01 15 6.82867267e+01 8.96148541e+01 -7.34377726e+00 16 -2.24723511e+00 8.74855256e+01 -1.63998026e+00 17 -6.85234509e+01 5.03449040e+01 1.07160068e+01 18 -5.14460244e+01 3.52328544e+01 -6.48293367e+01 19 1.23493716e+01 -7.97326151e+01 6.59072909e+01 20 -4.74052030e+01 9.92527560e+01 -1.52899603e+01 21 6.44980841e+01 -5.54942903e+01 -4.40013878e+01 22 4.32066687e+01 3.62689107e+01 7.55552059e+00 23 8.79208798e+01 1.29647626e+02 -4.67720801e+01 24 9.81765683e+01 1.56952621e+01 3.74515650e+01 25 2.12527634e+01 -7.79604611e+01 1.51198330e+01 26 -2.75633883e+01 -1.07382537e+01 -3.50208076e+01 27 -9.42669659e+01 1.45081271e+02 2.01491115e+01 28 1.22694506e+01 -6.40374606e+01 -4.59987886e+01 29 -5.88895195e+01 1.74088727e+01 1.52432176e+01 30 -2.14553559e+01 -1.80757296e+01 -9.57863320e+00 31 -6.68174167e+01 -2.37490456e+01 -7.17458574e+01 32 -6.59554447e+00 -1.06143482e+02 -1.38545892e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==20102== Memcheck, a memory error detector ==20102== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al. ==20102== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info ==20102== Command: python runner2.py Tersoff_LAMMPS_Erhart_Juslin_Goy_Nordlund_Mueller_Albe_ZnO__MO_616776018688_001 ==20102== ==20102== ==20102== HEAP SUMMARY: ==20102== in use at exit: 4,107,467 bytes in 5,848 blocks ==20102== total heap usage: 96,246 allocs, 90,398 frees, 64,961,890 bytes allocated ==20102== ==20102== LEAK SUMMARY: ==20102== definitely lost: 0 bytes in 0 blocks ==20102== indirectly lost: 0 bytes in 0 blocks ==20102== possibly lost: 172,751 bytes in 105 blocks ==20102== still reachable: 3,934,716 bytes in 5,743 blocks ==20102== suppressed: 0 bytes in 0 blocks ==20102== Rerun with --leak-check=full to see details of leaked memory ==20102== ==20102== For counts of detected and suppressed errors, rerun with: -v ==20102== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2414 from 126) ================================================================================ 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. === Verification check vc-memory-leak end (2018-06-18 20:21:22) ===