!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Sim_LAMMPS_MEAM_Lenosky_2017_W__SM_631352869360_000 Supported species : W random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = W (Configuration in file "config-F-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 121.24222490258704 Forces: 1 -1.63520371e+01 -1.19655699e+01 -1.17504691e+01 2 4.94390607e+00 6.99458900e+00 -2.27931021e+01 3 2.48631232e-01 -2.00089275e+01 7.47476090e+00 4 -2.08467259e+01 1.43331680e+00 3.56051257e+00 5 -2.17517934e+00 -2.34851017e+01 -1.91423557e+01 6 2.31472223e+01 4.19648294e+00 -2.27553964e+01 7 1.55881954e+01 -1.45977465e+01 2.16240152e+00 8 -1.22200543e+00 -4.68617788e+00 4.77012829e-01 9 -1.27430857e+01 -1.08645751e+00 -2.26800871e+01 10 2.68974454e+00 2.48537575e+01 -2.28704637e+01 11 -8.14467149e+00 -1.78517692e+01 1.43016061e+01 12 -2.55412293e+01 2.29064216e+01 7.77415645e-01 13 4.27837405e+00 -5.76723643e+00 -2.78864866e+01 14 2.04230933e+01 1.75706832e+01 -1.57709987e+01 15 2.55742615e+01 -1.07130159e+01 -1.89024972e+00 16 -6.65223190e+00 2.57643167e+01 1.65018167e+00 17 -2.28795541e+01 -1.41146572e+01 -6.97313592e+00 18 7.20490185e+00 -3.52259322e-02 -7.04971238e+00 19 2.16982188e+00 -2.59914551e+01 1.47642611e+01 20 -1.90865031e+01 1.00516878e+01 1.91853276e+01 21 -8.16409348e+00 -2.08237264e+01 5.15869154e+00 22 1.99713051e+01 1.11591227e+01 3.31934976e-01 23 9.31021891e+00 -6.09776565e+00 1.70627040e+01 24 1.43172716e+01 1.97310305e+00 1.87862459e+01 25 -2.47115194e+01 -5.83905253e+00 -8.17490342e+00 26 4.62260234e+00 3.00255405e+01 -4.95833172e+00 27 -4.62668714e+00 -4.07164128e+00 2.36294394e+01 28 -1.95947099e+01 1.32025867e+01 1.90218502e+01 29 1.40151819e+00 -1.43372869e+01 6.65344191e+00 30 1.96709500e+01 2.12750656e+01 2.92487907e+00 31 1.32161826e+01 -7.30543136e+00 1.49648851e+01 32 3.96203262e+00 1.73715707e+01 2.18081404e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = W (Configuration in file "config-T-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 121.24222490258704 Forces: 1 -1.63520371e+01 -1.19655699e+01 -1.17504691e+01 2 4.94390607e+00 6.99458900e+00 -2.27931021e+01 3 2.48631232e-01 -2.00089275e+01 7.47476090e+00 4 -2.08467259e+01 1.43331680e+00 3.56051257e+00 5 -2.17517934e+00 -2.34851017e+01 -1.91423557e+01 6 2.31472223e+01 4.19648294e+00 -2.27553964e+01 7 1.55881954e+01 -1.45977465e+01 2.16240152e+00 8 -1.22200543e+00 -4.68617788e+00 4.77012829e-01 9 -1.27430857e+01 -1.08645751e+00 -2.26800871e+01 10 2.68974454e+00 2.48537575e+01 -2.28704637e+01 11 -8.14467149e+00 -1.78517692e+01 1.43016061e+01 12 -2.55412293e+01 2.29064216e+01 7.77415645e-01 13 4.27837405e+00 -5.76723643e+00 -2.78864866e+01 14 2.04230933e+01 1.75706832e+01 -1.57709987e+01 15 2.55742615e+01 -1.07130159e+01 -1.89024972e+00 16 -6.65223190e+00 2.57643167e+01 1.65018167e+00 17 -2.28795541e+01 -1.41146572e+01 -6.97313592e+00 18 7.20490185e+00 -3.52259322e-02 -7.04971238e+00 19 2.16982188e+00 -2.59914551e+01 1.47642611e+01 20 -1.90865031e+01 1.00516878e+01 1.91853276e+01 21 -8.16409348e+00 -2.08237264e+01 5.15869154e+00 22 1.99713051e+01 1.11591227e+01 3.31934976e-01 23 9.31021891e+00 -6.09776565e+00 1.70627040e+01 24 1.43172716e+01 1.97310305e+00 1.87862459e+01 25 -2.47115194e+01 -5.83905253e+00 -8.17490342e+00 26 4.62260234e+00 3.00255405e+01 -4.95833172e+00 27 -4.62668714e+00 -4.07164128e+00 2.36294394e+01 28 -1.95947099e+01 1.32025867e+01 1.90218502e+01 29 1.40151819e+00 -1.43372869e+01 6.65344191e+00 30 1.96709500e+01 2.12750656e+01 2.92487907e+00 31 1.32161826e+01 -7.30543136e+00 1.49648851e+01 32 3.96203262e+00 1.73715707e+01 2.18081404e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==62469== Memcheck, a memory error detector ==62469== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==62469== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==62469== Command: python runner2.py Sim_LAMMPS_MEAM_Lenosky_2017_W__SM_631352869360_000 ==62469== ==63505== Warning: invalid file descriptor 1048564 in syscall close() ==63505== Warning: invalid file descriptor 1048565 in syscall close() ==63505== Warning: invalid file descriptor 1048566 in syscall close() ==63505== Warning: invalid file descriptor 1048567 in syscall close() ==63505== Use --log-fd= to select an alternative log fd. ==63505== Warning: invalid file descriptor 1048568 in syscall close() ==63505== Warning: invalid file descriptor 1048569 in syscall close() ==63524== Warning: invalid file descriptor 1048564 in syscall close() ==63524== Warning: invalid file descriptor 1048565 in syscall close() ==63524== Warning: invalid file descriptor 1048566 in syscall close() ==63524== Warning: invalid file descriptor 1048567 in syscall close() ==63524== Use --log-fd= to select an alternative log fd. ==63524== Warning: invalid file descriptor 1048568 in syscall close() ==63524== Warning: invalid file descriptor 1048569 in syscall close() ==63532== Warning: invalid file descriptor 1048564 in syscall close() ==63532== Warning: invalid file descriptor 1048565 in syscall close() ==63532== Warning: invalid file descriptor 1048566 in syscall close() ==63532== Warning: invalid file descriptor 1048567 in syscall close() ==63532== Use --log-fd= to select an alternative log fd. ==63532== Warning: invalid file descriptor 1048568 in syscall close() ==63532== Warning: invalid file descriptor 1048569 in syscall close() ==63538== Warning: invalid file descriptor 1048564 in syscall close() ==63538== Warning: invalid file descriptor 1048565 in syscall close() ==63538== Warning: invalid file descriptor 1048566 in syscall close() ==63538== Warning: invalid file descriptor 1048567 in syscall close() ==63538== Use --log-fd= to select an alternative log fd. ==63538== Warning: invalid file descriptor 1048568 in syscall close() ==63538== Warning: invalid file descriptor 1048569 in syscall close() ==63556== Warning: invalid file descriptor 1048564 in syscall close() ==63556== Warning: invalid file descriptor 1048565 in syscall close() ==63556== Warning: invalid file descriptor 1048566 in syscall close() ==63556== Warning: invalid file descriptor 1048567 in syscall close() ==63556== Use --log-fd= to select an alternative log fd. ==63556== Warning: invalid file descriptor 1048568 in syscall close() ==63556== Warning: invalid file descriptor 1048569 in syscall close() ==63567== Warning: invalid file descriptor 1048564 in syscall close() ==63567== Warning: invalid file descriptor 1048565 in syscall close() ==63567== Warning: invalid file descriptor 1048566 in syscall close() ==63567== Warning: invalid file descriptor 1048567 in syscall close() ==63567== Use --log-fd= to select an alternative log fd. ==63567== Warning: invalid file descriptor 1048568 in syscall close() ==63567== Warning: invalid file descriptor 1048569 in syscall close() ==63572== Warning: invalid file descriptor 1048564 in syscall close() ==63572== Warning: invalid file descriptor 1048565 in syscall close() ==63572== Warning: invalid file descriptor 1048566 in syscall close() ==63572== Warning: invalid file descriptor 1048567 in syscall close() ==63572== Use --log-fd= to select an alternative log fd. ==63572== Warning: invalid file descriptor 1048568 in syscall close() ==63572== Warning: invalid file descriptor 1048569 in syscall close() ==63576== Warning: invalid file descriptor 1048564 in syscall close() ==63576== Warning: invalid file descriptor 1048565 in syscall close() ==63576== Warning: invalid file descriptor 1048566 in syscall close() ==63576== Warning: invalid file descriptor 1048567 in syscall close() ==63576== Use --log-fd= to select an alternative log fd. ==63576== Warning: invalid file descriptor 1048568 in syscall close() ==63576== Warning: invalid file descriptor 1048569 in syscall close() ==62469== ==62469== HEAP SUMMARY: ==62469== in use at exit: 1,780,563 bytes in 1,488 blocks ==62469== total heap usage: 28,445 allocs, 26,957 frees, 42,730,011 bytes allocated ==62469== ==62469== LEAK SUMMARY: ==62469== definitely lost: 0 bytes in 0 blocks ==62469== indirectly lost: 0 bytes in 0 blocks ==62469== possibly lost: 178,423 bytes in 96 blocks ==62469== still reachable: 1,602,140 bytes in 1,392 blocks ==62469== suppressed: 0 bytes in 0 blocks ==62469== Rerun with --leak-check=full to see details of leaked memory ==62469== ==62469== For counts of detected and suppressed errors, rerun with: -v ==62469== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11334 from 599) ================================================================================ 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.