!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_BonnyBakaevTerentyev_2017_WRe__MO_234187151804_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 = 240.93506172595653 Forces: 1 -1.19663426e+01 -4.34775299e+01 -3.48542812e+01 2 -1.50641802e+01 2.33055294e+01 -2.61967412e+01 3 1.24571542e+01 -2.42276809e+01 -4.41322409e+00 4 -2.05172565e+01 3.37481844e+01 3.18635617e+01 5 7.03471532e+00 -4.51128991e+01 -1.52019378e+01 6 2.24698525e+01 8.51830616e+00 -2.58266701e+01 7 1.28582376e+01 -8.21504982e+01 -6.62786247e+01 8 -2.98047272e+01 -2.73136048e+01 9.63990244e+00 9 -1.96933755e+01 -4.37485273e+01 -4.99074620e+01 10 3.93774029e+01 4.51309652e+01 -4.46436333e+01 11 -2.23349002e+01 -3.52161399e+01 -1.75882256e+01 12 -5.68309824e+01 3.65960135e+01 4.55904298e+01 13 -3.79355299e+01 -1.37372383e+01 -1.07336056e+02 14 2.05764554e+01 2.72166531e+01 -1.78366692e+01 15 9.57749813e+01 -1.23050889e+01 3.23770985e+01 16 7.96014066e+00 7.57423360e+01 1.55954127e+01 17 -4.40388070e+01 -2.37821831e+01 -1.43429194e+01 18 1.71282847e+01 2.36599326e+01 -1.26087823e+01 19 1.36998875e+01 -3.99206993e+01 2.87222162e+01 20 -2.33418194e+01 1.99446867e+01 2.92736856e+01 21 -2.90539057e+01 -2.85870291e+01 1.09639614e+01 22 5.55767396e+01 6.77697847e+01 6.48022644e+01 23 1.43196909e+01 -7.40353036e+00 1.87489086e+01 24 6.27066884e+00 1.03020511e+01 2.01862125e+01 25 -6.79965170e+01 -3.53220392e+01 -1.99317326e+01 26 1.83275234e+01 7.45354206e+01 -2.19223888e+01 27 5.86879663e+01 -9.24590537e+01 4.84321481e+01 28 -9.01475959e+01 7.85043530e+01 3.40108865e+01 29 -1.02347276e+01 -2.57593073e+01 2.32250975e+01 30 2.43879255e+01 3.76454503e+01 5.65220107e+00 31 3.81548488e+01 -2.02587687e+01 3.06744661e+01 32 1.38981915e+01 3.81621512e+01 2.91308953e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Re (Configuration in file "config-T-Re.xyz") ----------------------------------------------------------------------------------------------------- Energy = 240.93506172595653 Forces: 1 -1.19663426e+01 -4.34775299e+01 -3.48542812e+01 2 -1.50641802e+01 2.33055294e+01 -2.61967412e+01 3 1.24571542e+01 -2.42276809e+01 -4.41322409e+00 4 -2.05172565e+01 3.37481844e+01 3.18635617e+01 5 7.03471532e+00 -4.51128991e+01 -1.52019378e+01 6 2.24698525e+01 8.51830616e+00 -2.58266701e+01 7 1.28582376e+01 -8.21504982e+01 -6.62786247e+01 8 -2.98047272e+01 -2.73136048e+01 9.63990244e+00 9 -1.96933755e+01 -4.37485273e+01 -4.99074620e+01 10 3.93774029e+01 4.51309652e+01 -4.46436333e+01 11 -2.23349002e+01 -3.52161399e+01 -1.75882256e+01 12 -5.68309824e+01 3.65960135e+01 4.55904298e+01 13 -3.79355299e+01 -1.37372383e+01 -1.07336056e+02 14 2.05764554e+01 2.72166531e+01 -1.78366692e+01 15 9.57749813e+01 -1.23050889e+01 3.23770985e+01 16 7.96014066e+00 7.57423360e+01 1.55954127e+01 17 -4.40388070e+01 -2.37821831e+01 -1.43429194e+01 18 1.71282847e+01 2.36599326e+01 -1.26087823e+01 19 1.36998875e+01 -3.99206993e+01 2.87222162e+01 20 -2.33418194e+01 1.99446867e+01 2.92736856e+01 21 -2.90539057e+01 -2.85870291e+01 1.09639614e+01 22 5.55767396e+01 6.77697847e+01 6.48022644e+01 23 1.43196909e+01 -7.40353036e+00 1.87489086e+01 24 6.27066884e+00 1.03020511e+01 2.01862125e+01 25 -6.79965170e+01 -3.53220392e+01 -1.99317326e+01 26 1.83275234e+01 7.45354206e+01 -2.19223888e+01 27 5.86879663e+01 -9.24590537e+01 4.84321481e+01 28 -9.01475959e+01 7.85043530e+01 3.40108865e+01 29 -1.02347276e+01 -2.57593073e+01 2.32250975e+01 30 2.43879255e+01 3.76454503e+01 5.65220107e+00 31 3.81548488e+01 -2.02587687e+01 3.06744661e+01 32 1.38981915e+01 3.81621512e+01 2.91308953e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = W (Configuration in file "config-F-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 124.87364135091863 Forces: 1 -1.82782238e+01 -2.29282111e+01 -2.17545208e+01 2 2.32882868e+01 -2.28498768e+01 -3.27685463e+01 3 1.86823823e+01 -5.70028621e+01 -1.84496906e+01 4 -4.36766727e+01 1.61668254e+01 -1.25943316e+01 5 -5.66858162e+01 -2.54247715e+01 -5.62938851e+01 6 3.19916255e+01 1.01185399e+01 -1.63967741e+01 7 6.35067507e+01 -2.32248758e+01 5.01731374e+01 8 2.87526668e+01 5.54148035e+01 -7.79145370e+01 9 -5.54456236e+01 1.45541803e+01 -3.53933549e+01 10 1.39401314e+01 1.95630539e+01 -2.18320635e+01 11 4.11033662e+01 2.50015602e+01 2.56684060e+01 12 -1.83688605e+01 9.55587183e+00 9.97768625e+00 13 -1.11852972e+01 6.83391112e+00 -1.34077613e+01 14 1.80769292e+01 1.50939385e+01 -1.35663595e+01 15 3.49197937e+01 -1.92128278e+01 -1.21558788e+01 16 -2.76607677e+01 2.70690316e+01 -6.44005722e-02 17 -3.13039636e+01 -3.41083576e+01 9.54062935e+00 18 -2.86587998e+01 2.06428224e+01 4.82776907e+01 19 1.70678408e+01 -1.83468783e+01 9.12101640e+00 20 -1.78767328e+01 2.57841311e+01 2.24959309e+01 21 1.05662513e+01 -8.25688538e+01 6.21725533e+01 22 3.61697132e+01 3.41595810e+01 -4.80953433e+01 23 1.30759480e+01 -5.84477993e+01 5.20390881e+01 24 -2.19207869e+01 -2.49969173e+00 3.36628027e+01 25 -2.88838227e+01 1.39480847e+01 8.65959668e+00 26 1.06398167e+01 2.44263282e+01 -1.62888462e+01 27 4.43157858e+00 -1.91264852e+01 3.08797618e+01 28 -2.91322234e+01 1.53800206e+01 1.21860215e+01 29 -1.30110828e+01 1.10954705e+01 -1.49604429e+01 30 1.27175245e+01 1.85148772e+01 2.87523431e+00 31 4.57533862e+01 -1.90970608e+01 2.00652601e+01 32 -2.25953180e+01 4.15155199e+01 1.41419211e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = W (Configuration in file "config-T-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 124.87364135091863 Forces: 1 -1.82782238e+01 -2.29282111e+01 -2.17545208e+01 2 2.32882868e+01 -2.28498768e+01 -3.27685463e+01 3 1.86823823e+01 -5.70028621e+01 -1.84496906e+01 4 -4.36766727e+01 1.61668254e+01 -1.25943316e+01 5 -5.66858162e+01 -2.54247715e+01 -5.62938851e+01 6 3.19916255e+01 1.01185399e+01 -1.63967741e+01 7 6.35067507e+01 -2.32248758e+01 5.01731374e+01 8 2.87526668e+01 5.54148035e+01 -7.79145370e+01 9 -5.54456236e+01 1.45541803e+01 -3.53933549e+01 10 1.39401314e+01 1.95630539e+01 -2.18320635e+01 11 4.11033662e+01 2.50015602e+01 2.56684060e+01 12 -1.83688605e+01 9.55587183e+00 9.97768625e+00 13 -1.11852972e+01 6.83391112e+00 -1.34077613e+01 14 1.80769292e+01 1.50939385e+01 -1.35663595e+01 15 3.49197937e+01 -1.92128278e+01 -1.21558788e+01 16 -2.76607677e+01 2.70690316e+01 -6.44005722e-02 17 -3.13039636e+01 -3.41083576e+01 9.54062935e+00 18 -2.86587998e+01 2.06428224e+01 4.82776907e+01 19 1.70678408e+01 -1.83468783e+01 9.12101640e+00 20 -1.78767328e+01 2.57841311e+01 2.24959309e+01 21 1.05662513e+01 -8.25688538e+01 6.21725533e+01 22 3.61697132e+01 3.41595810e+01 -4.80953433e+01 23 1.30759480e+01 -5.84477993e+01 5.20390881e+01 24 -2.19207869e+01 -2.49969173e+00 3.36628027e+01 25 -2.88838227e+01 1.39480847e+01 8.65959668e+00 26 1.06398167e+01 2.44263282e+01 -1.62888462e+01 27 4.43157858e+00 -1.91264852e+01 3.08797618e+01 28 -2.91322234e+01 1.53800206e+01 1.21860215e+01 29 -1.30110828e+01 1.10954705e+01 -1.49604429e+01 30 1.27175245e+01 1.85148772e+01 2.87523431e+00 31 4.57533862e+01 -1.90970608e+01 2.00652601e+01 32 -2.25953180e+01 4.15155199e+01 1.41419211e+01 MIXED STRUCTURE (pbc=False)-- Species = Re W (Configuration in file "config-F-ReW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 143.14041927479064 Forces: 1 -1.06115573e+01 -9.37020074e+00 -9.08075203e+00 2 -3.98078300e+01 -1.54784314e+01 -1.51787166e+01 3 -1.97706989e+01 -3.07726739e+01 -1.50817974e+01 4 -2.63800453e+01 -1.20656074e+01 -2.48379699e+01 5 1.08541068e+01 -2.66119030e+01 -2.19847970e+01 6 4.69307565e+01 -4.55197390e+00 -3.30577506e+01 7 2.00728521e+01 -3.17338506e+01 -1.01329885e+01 8 -9.23566301e+00 1.30706996e+01 1.82581508e+01 9 -1.82157046e+01 -6.50012395e+00 -2.78146558e+01 10 2.81144766e+01 2.17481956e+01 -4.89968590e+01 11 7.87317207e+01 -7.66647387e+01 7.11555337e+00 12 -1.15989275e+02 8.95908105e+01 1.74968976e+01 13 1.40099454e+01 4.80577921e+01 -2.69925300e+01 14 2.57323154e+01 1.17864570e+01 -1.81509831e+01 15 1.87652495e+01 -1.41400865e+01 -3.51410864e+00 16 -1.82147455e+01 2.30685197e+01 8.33231203e+00 17 -3.39642890e+01 -2.99050948e+01 -2.37747702e+00 18 5.15059150e+00 2.71895224e+01 1.39195967e+00 19 9.94567168e+00 -1.80214602e+01 2.65853665e+01 20 -3.24078004e+01 -8.79088935e+00 2.11331487e+01 21 9.47542814e+00 -4.97767698e+01 1.45457641e+01 22 2.91982766e+01 2.72449818e+01 -6.51630825e+00 23 5.43434939e+01 -7.92208601e+01 3.17818231e+01 24 -4.29012331e+01 6.58838227e+01 2.63070262e+01 25 -2.47983874e+01 1.85919989e+01 2.18457200e+01 26 3.72182400e+01 1.95640368e+01 -3.00284748e+01 27 2.00259389e+01 1.72115174e+01 1.47325156e+01 28 -3.76658471e+01 1.83062029e+00 4.56586514e+01 29 -1.83517041e+01 -3.75872744e+00 -4.32753731e-01 30 2.97251166e+01 3.07198528e+01 -7.39441277e+00 31 2.71626920e+01 -3.43517648e+01 3.34476385e+01 32 -1.71420912e+01 3.61563289e+01 1.29408075e+01 MIXED STRUCTURE (pbc=True)-- Species = Re W (Configuration in file "config-T-ReW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 374.3283568055613 Forces: 1 -1.84149858e-01 7.04109924e+00 1.35875127e+00 2 -2.65747836e+01 -3.15532512e+01 2.66363801e+01 3 -1.32193586e+01 3.66987015e+00 -6.85685204e+00 4 3.79028948e+00 -8.63768660e+00 -2.23178794e+01 5 6.10818288e+00 9.06345640e+00 -2.27630188e+01 6 1.28413307e+01 -8.59551428e+00 -2.52941024e+01 7 2.11694410e+00 -3.95548058e+00 1.32834025e+01 8 -7.46167070e+00 1.46343121e+01 1.79520874e+01 9 -1.11505452e-01 3.80585806e+01 2.49348323e+01 10 4.00266215e+01 -1.41490519e+01 -2.59849905e+01 11 7.51059409e+01 -7.51552563e+01 5.09554447e+00 12 -1.02708340e+02 7.21367593e+01 1.93448060e+01 13 1.82338154e+01 5.06197771e+01 -5.34333407e+00 14 8.27745360e+00 -1.82449539e+01 -2.67092492e+01 15 3.69586339e+00 -1.14391775e+01 -5.91529892e+00 16 -1.65894914e+01 -2.34695008e+01 1.78439453e+01 17 2.05767207e+01 -4.69327253e+01 3.83023284e+00 18 7.06956379e+00 2.79020812e+01 1.29394350e+00 19 2.88463563e+01 2.73736909e+01 7.67129646e+00 20 -2.95987837e+01 -3.87164628e+01 -4.05171170e+01 21 1.46614817e+01 -2.64595405e+01 8.28526972e+00 22 -5.28641601e+01 5.17172185e+01 -9.41871053e+00 23 4.99194352e+01 -6.85227480e+01 2.15289125e+01 24 -3.71016742e+01 6.34761738e+01 4.57205793e+00 25 4.48484896e+00 1.64459184e+01 2.02126380e+01 26 3.86445164e+01 -1.63876342e+01 -3.36963784e+01 27 1.67997339e+01 3.07909250e+01 -2.49207535e+01 28 -5.61255277e+01 -3.11880576e+01 2.66553873e+01 29 -1.60089108e+01 -2.60123600e+00 4.39572876e-01 30 6.13130306e+00 2.85531119e+01 -5.81312479e+00 31 1.55366137e+01 -3.01563008e+01 2.42937774e+01 32 -1.43186597e+01 1.46816032e+01 1.03179718e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==4159348== Memcheck, a memory error detector ==4159348== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4159348== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==4159348== Command: python runner2.py EAM_Dynamo_BonnyBakaevTerentyev_2017_WRe__MO_234187151804_000 ==4159348== ==4161035== Warning: invalid file descriptor 1024 in syscall close() ==4161035== Warning: invalid file descriptor 1025 in syscall close() ==4161035== Warning: invalid file descriptor 1026 in syscall close() ==4161035== Warning: invalid file descriptor 1027 in syscall close() ==4161035== Use --log-fd= to select an alternative log fd. ==4161035== Warning: invalid file descriptor 1028 in syscall close() ==4161035== Warning: invalid file descriptor 1029 in syscall close() ==4159348== ==4159348== HEAP SUMMARY: ==4159348== in use at exit: 2,257,767 bytes in 1,704 blocks ==4159348== total heap usage: 82,856 allocs, 81,152 frees, 120,546,867 bytes allocated ==4159348== ==4159348== LEAK SUMMARY: ==4159348== definitely lost: 0 bytes in 0 blocks ==4159348== indirectly lost: 0 bytes in 0 blocks ==4159348== possibly lost: 180,827 bytes in 103 blocks ==4159348== still reachable: 2,076,908 bytes in 1,600 blocks ==4159348== of which reachable via heuristic: ==4159348== stdstring : 38 bytes in 1 blocks ==4159348== suppressed: 32 bytes in 1 blocks ==4159348== Rerun with --leak-check=full to see details of leaked memory ==4159348== ==4159348== For lists of detected and suppressed errors, rerun with: -s ==4159348== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8066 from 567) ================================================================================ 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.