!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouZimmermanWong_2008_PdH__MO_114797992931_000 Supported species : H Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -4.650505069432963 Forces: 1 -2.22831369e+00 -1.75005271e+00 -3.09282775e+00 2 -2.87252470e+00 6.43207878e+00 -1.71813391e+00 3 1.02185488e+00 -2.16772728e+00 3.48039122e+00 4 -2.53684169e+00 2.32316295e+00 9.87862377e-02 5 5.21970861e+00 -5.54347782e+00 -8.37165676e-01 6 5.98364009e-01 5.43485227e-01 -1.00331226e+00 7 6.94453033e-01 -8.59550380e+00 -9.37387309e+00 8 -4.93803286e+00 -3.60842919e+00 -5.15831663e-02 9 -8.90514388e-01 -2.58484395e+00 -2.56778306e+00 10 -1.75138600e+00 2.98855180e+00 -4.24747978e+00 11 7.91283803e-03 -2.86894544e+00 -2.59317470e+00 12 -1.63031798e+00 2.74172463e+00 1.30999403e+00 13 -4.52596665e+00 -4.11516778e+00 -1.18062141e+01 14 1.54867878e+00 2.29830296e+00 -1.27070115e+00 15 1.08677008e+01 -2.22568177e+00 3.52219055e+00 16 1.64721865e+00 8.27075331e+00 4.22283419e+00 17 -3.82474432e+00 -3.04936704e+00 -1.96655139e+00 18 4.51036499e+00 2.52397886e+00 7.25126503e-01 19 2.06113159e+00 -2.22688048e+00 1.78079418e+00 20 -1.13200744e+00 2.33512203e+00 1.85613200e+00 21 -4.00682538e+00 -2.99475975e+00 9.80802813e-01 22 5.05900870e+00 8.10555347e+00 6.86803525e+00 23 1.15019437e+00 -4.81414030e-01 1.48537053e+00 24 -9.04500374e-01 2.23714644e+00 1.18625163e+00 25 -4.82775796e+00 -1.23119109e+00 2.29516048e+00 26 -1.88968724e+00 5.24459267e+00 -2.35922647e+00 27 5.07311249e+00 -1.08408753e+01 1.78751979e+00 28 -7.79870790e+00 6.98529486e+00 1.41997080e+00 29 -1.71619361e+00 -3.24388549e+00 2.60499985e+00 30 1.58779546e+00 3.35750451e+00 1.25263285e+00 31 3.94902644e+00 -2.37421910e+00 2.48330549e+00 32 2.47779655e+00 3.51516953e+00 3.52772815e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -4.650505069432963 Forces: 1 -2.22831369e+00 -1.75005271e+00 -3.09282775e+00 2 -2.87252470e+00 6.43207878e+00 -1.71813391e+00 3 1.02185488e+00 -2.16772728e+00 3.48039122e+00 4 -2.53684169e+00 2.32316295e+00 9.87862377e-02 5 5.21970861e+00 -5.54347782e+00 -8.37165676e-01 6 5.98364009e-01 5.43485227e-01 -1.00331226e+00 7 6.94453033e-01 -8.59550380e+00 -9.37387309e+00 8 -4.93803286e+00 -3.60842919e+00 -5.15831663e-02 9 -8.90514388e-01 -2.58484395e+00 -2.56778306e+00 10 -1.75138600e+00 2.98855180e+00 -4.24747978e+00 11 7.91283803e-03 -2.86894544e+00 -2.59317470e+00 12 -1.63031798e+00 2.74172463e+00 1.30999403e+00 13 -4.52596665e+00 -4.11516778e+00 -1.18062141e+01 14 1.54867878e+00 2.29830296e+00 -1.27070115e+00 15 1.08677008e+01 -2.22568177e+00 3.52219055e+00 16 1.64721865e+00 8.27075331e+00 4.22283419e+00 17 -3.82474432e+00 -3.04936704e+00 -1.96655139e+00 18 4.51036499e+00 2.52397886e+00 7.25126503e-01 19 2.06113159e+00 -2.22688048e+00 1.78079418e+00 20 -1.13200744e+00 2.33512203e+00 1.85613200e+00 21 -4.00682538e+00 -2.99475975e+00 9.80802813e-01 22 5.05900870e+00 8.10555347e+00 6.86803525e+00 23 1.15019437e+00 -4.81414030e-01 1.48537053e+00 24 -9.04500374e-01 2.23714644e+00 1.18625163e+00 25 -4.82775796e+00 -1.23119109e+00 2.29516048e+00 26 -1.88968724e+00 5.24459267e+00 -2.35922647e+00 27 5.07311249e+00 -1.08408753e+01 1.78751979e+00 28 -7.79870790e+00 6.98529486e+00 1.41997080e+00 29 -1.71619361e+00 -3.24388549e+00 2.60499985e+00 30 1.58779546e+00 3.35750451e+00 1.25263285e+00 31 3.94902644e+00 -2.37421910e+00 2.48330549e+00 32 2.47779655e+00 3.51516953e+00 3.52772815e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 26.178921776676333 Forces: 1 -4.10647845e+00 -3.58238679e+00 -3.80168265e+00 2 -7.06164608e+00 -1.08962431e+00 -1.08140240e+01 3 -6.32944587e+00 -1.41272157e+01 -5.24516075e+00 4 -9.30474543e+00 -1.05371664e+00 -3.59770008e+00 5 -1.89021042e+00 -9.42867492e+00 -8.85765236e+00 6 1.02338822e+01 2.76534252e+00 -9.30939046e+00 7 8.45898713e+00 -9.82674570e+00 4.09572734e+00 8 7.45519353e-01 -7.50405301e+00 -1.10493391e+01 9 -4.69064637e+00 -2.83973565e+00 -3.33976190e+00 10 2.40361800e+00 5.34102385e+00 -7.41968784e+00 11 -1.02143330e+01 6.50120580e+00 -2.81346572e+00 12 -4.44547295e+00 6.88872293e+00 1.97997397e+00 13 1.71287191e+00 4.27358745e+00 -1.92183963e+01 14 3.76469718e+00 3.01628560e+00 -4.60822129e+00 15 2.11307925e+01 3.75957905e+00 -4.52367666e+00 16 -3.04922326e+00 1.75561881e+01 1.11102897e+00 17 -5.17093495e+00 -6.45738682e+00 1.45878073e+00 18 -1.23465548e+01 8.06781452e-01 4.23724896e+00 19 -5.06272661e+00 -8.13221162e+00 9.28185037e+00 20 -5.80150865e+00 6.40976309e-01 6.03231616e+00 21 4.66971566e+00 -2.22694322e+01 2.16618344e+00 22 2.36207892e+01 -5.84424690e+00 4.49484323e+00 23 3.13836747e+00 -2.65315046e+00 2.65960011e+00 24 5.54381438e-01 3.51649361e-01 1.86380834e+01 25 -9.64265906e+00 2.32409340e+00 1.54838047e+00 26 -6.79387001e-01 1.11378169e+01 -9.44833737e+00 27 -3.10986933e+00 -6.45162533e+00 1.22958700e+01 28 -8.95524377e+00 4.43739461e+00 5.96045287e+00 29 -2.27359538e+00 1.26022356e+01 7.42879351e+00 30 5.71311024e+00 6.89448608e+00 4.44235876e-01 31 8.62552554e+00 3.17212252e+00 1.16501909e+01 32 9.36242351e+00 8.79071457e+00 8.56293626e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 26.178921776676333 Forces: 1 -4.10647845e+00 -3.58238679e+00 -3.80168265e+00 2 -7.06164608e+00 -1.08962431e+00 -1.08140240e+01 3 -6.32944587e+00 -1.41272157e+01 -5.24516075e+00 4 -9.30474543e+00 -1.05371664e+00 -3.59770008e+00 5 -1.89021042e+00 -9.42867492e+00 -8.85765236e+00 6 1.02338822e+01 2.76534252e+00 -9.30939046e+00 7 8.45898713e+00 -9.82674570e+00 4.09572734e+00 8 7.45519353e-01 -7.50405301e+00 -1.10493391e+01 9 -4.69064637e+00 -2.83973565e+00 -3.33976190e+00 10 2.40361800e+00 5.34102385e+00 -7.41968784e+00 11 -1.02143330e+01 6.50120580e+00 -2.81346572e+00 12 -4.44547295e+00 6.88872293e+00 1.97997397e+00 13 1.71287191e+00 4.27358745e+00 -1.92183963e+01 14 3.76469718e+00 3.01628560e+00 -4.60822129e+00 15 2.11307925e+01 3.75957905e+00 -4.52367666e+00 16 -3.04922326e+00 1.75561881e+01 1.11102897e+00 17 -5.17093495e+00 -6.45738682e+00 1.45878073e+00 18 -1.23465548e+01 8.06781452e-01 4.23724896e+00 19 -5.06272661e+00 -8.13221162e+00 9.28185037e+00 20 -5.80150865e+00 6.40976309e-01 6.03231616e+00 21 4.66971566e+00 -2.22694322e+01 2.16618344e+00 22 2.36207892e+01 -5.84424690e+00 4.49484323e+00 23 3.13836747e+00 -2.65315046e+00 2.65960011e+00 24 5.54381438e-01 3.51649361e-01 1.86380834e+01 25 -9.64265906e+00 2.32409340e+00 1.54838047e+00 26 -6.79387001e-01 1.11378169e+01 -9.44833737e+00 27 -3.10986933e+00 -6.45162533e+00 1.22958700e+01 28 -8.95524377e+00 4.43739461e+00 5.96045287e+00 29 -2.27359538e+00 1.26022356e+01 7.42879351e+00 30 5.71311024e+00 6.89448608e+00 4.44235876e-01 31 8.62552554e+00 3.17212252e+00 1.16501909e+01 32 9.36242351e+00 8.79071457e+00 8.56293626e+00 MIXED STRUCTURE (pbc=False)-- Species = H Pd (Configuration in file "config-F-HPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = -29.40532824448978 Forces: 1 -2.19191396e+00 -1.72789285e+00 1.82165264e+00 2 1.18742147e-01 3.09843538e-01 -4.43382460e+00 3 2.71116467e+00 -5.06794830e+00 -3.05499997e+00 4 -7.67386246e+00 6.42807972e+00 -6.59373050e+00 5 3.22893534e+00 -9.56355212e-01 -1.53974141e+00 6 -1.11727208e-03 -1.56728116e+00 3.94028885e-01 7 2.74315840e+00 -1.09035494e+00 6.00485362e-01 8 -6.79487237e-02 8.84999583e-02 3.70041968e+00 9 -5.16428098e+00 -6.65772886e+00 -2.71530574e+00 10 3.86647285e+00 6.33032148e+00 -4.35830644e+00 11 -9.86296131e+00 -1.45650546e+01 -3.73654290e+00 12 -2.75529233e+00 3.47432163e+00 7.91360504e+00 13 -1.18857190e+00 -4.05097641e+00 -1.95804143e+00 14 4.28331974e+00 3.70920578e+00 -4.08778016e-01 15 3.61551031e+00 -4.62283327e-01 9.17436399e-01 16 1.15399544e+01 1.41009148e+01 -2.17661522e+00 17 -4.94256958e+00 -9.63321138e+00 6.70385254e+00 18 7.34579057e+00 4.90228338e+00 3.95179274e+00 19 5.20909402e+00 -3.91983070e+00 -8.15410436e-01 20 -5.14628722e+00 2.82988514e+00 -1.16206299e+00 21 -3.19855569e+00 -3.63278195e+00 -4.88903085e+00 22 2.35310858e+00 7.85111538e+00 -6.73145607e+00 23 3.58662194e+00 -7.10693580e+00 7.38074330e+00 24 -2.30918280e+00 2.96573624e+00 3.27410842e+00 25 -5.11653801e+00 1.40548764e+00 2.00050603e+00 26 -2.56558064e+00 5.38984065e+00 3.42911504e+00 27 -2.68765221e-01 -2.91413113e+00 4.71848184e+00 28 -4.99277803e+00 3.98095644e+00 2.91223736e-01 29 1.55906418e+00 -2.10800619e+00 -4.33596961e+00 30 2.48830846e+00 3.18814643e+00 -1.60775124e+00 31 1.04892678e+00 -1.65746975e+00 2.14601668e+00 32 1.74803371e+00 1.63604324e-01 1.27409913e+00 MIXED STRUCTURE (pbc=True)-- Species = H Pd (Configuration in file "config-T-HPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 28.58276859283649 Forces: 1 -9.20477689e+00 -2.17046751e+00 8.48745656e+00 2 7.10823531e+00 4.91885893e+00 3.64756741e+00 3 3.17091180e+00 -4.78489320e+00 -2.22891788e+00 4 -4.62211028e+00 6.56121164e+00 -3.45531416e+00 5 3.82167577e+00 -3.51444813e+00 9.80500598e-01 6 -2.42727079e+00 -5.74240506e-01 -3.07520341e+00 7 9.04387065e-01 7.11335591e+00 4.49075433e+00 8 -1.50748943e+00 1.81647226e+00 5.37373820e+00 9 -4.46771167e+00 -1.53405381e+01 5.59833762e+00 10 1.17143160e+01 1.02275152e+01 6.64270700e+00 11 -9.28662664e+00 -1.52043439e+01 -2.87565424e+00 12 7.75532695e+00 2.00632587e+00 1.21373758e+01 13 -4.04749505e+00 -6.26878277e+00 1.44438897e+00 14 -3.64156827e+00 7.67697428e+00 -7.25371475e+00 15 2.83285338e+00 -2.06097704e+00 1.50631687e+00 16 1.12086607e+01 1.42408400e+01 -1.23695078e+00 17 -5.88104623e+00 -9.47883835e+00 5.60222176e+00 18 7.92476114e+00 5.26598057e+00 2.96375299e+00 19 1.05231848e+01 -6.54770163e+00 -1.24933028e+01 20 -9.84105336e+00 5.33717094e+00 -1.14877081e+01 21 -2.45411115e+00 -2.74272874e+00 -4.93136660e+00 22 1.20027509e+00 8.37957428e+00 -5.87380768e+00 23 3.84585809e+00 -7.85443426e+00 8.04384521e+00 24 -8.68370740e-01 4.95377249e+00 -8.15899082e-02 25 -5.06999795e+00 5.03790497e-01 1.98330718e+00 26 -1.19198157e+00 3.70238668e+00 3.48284195e+00 27 2.44953951e+00 -6.15525615e+00 -3.23669728e+00 28 -4.95205765e+00 6.69232228e+00 -1.29434492e+01 29 4.22977163e-01 -3.82260641e+00 -6.34998969e+00 30 -3.13606107e+00 2.29545213e+00 6.35353181e+00 31 -4.74065792e+00 -6.32211662e+00 -2.94646033e+00 32 2.45742390e+00 1.15036930e+00 1.73148262e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==207480== Memcheck, a memory error detector ==207480== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==207480== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==207480== Command: python runner2.py EAM_Dynamo_ZhouZimmermanWong_2008_PdH__MO_114797992931_000 ==207480== ==209364== Warning: invalid file descriptor 1024 in syscall close() ==209364== Warning: invalid file descriptor 1025 in syscall close() ==209364== Warning: invalid file descriptor 1026 in syscall close() ==209364== Warning: invalid file descriptor 1027 in syscall close() ==209364== Use --log-fd= to select an alternative log fd. ==209364== Warning: invalid file descriptor 1028 in syscall close() ==209364== Warning: invalid file descriptor 1029 in syscall close() ==207480== ==207480== HEAP SUMMARY: ==207480== in use at exit: 2,257,767 bytes in 1,704 blocks ==207480== total heap usage: 82,926 allocs, 81,222 frees, 73,383,054 bytes allocated ==207480== ==207480== LEAK SUMMARY: ==207480== definitely lost: 0 bytes in 0 blocks ==207480== indirectly lost: 0 bytes in 0 blocks ==207480== possibly lost: 180,827 bytes in 103 blocks ==207480== still reachable: 2,076,908 bytes in 1,600 blocks ==207480== of which reachable via heuristic: ==207480== stdstring : 38 bytes in 1 blocks ==207480== suppressed: 32 bytes in 1 blocks ==207480== Rerun with --leak-check=full to see details of leaked memory ==207480== ==207480== For lists of detected and suppressed errors, rerun with: -s ==207480== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8020 from 562) ================================================================================ 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.