!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_FernandezPascuet_2014_U__SM_176800861722_000 Supported species : U random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = U (Configuration in file "config-F-U.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1139.7067119480128 Forces: 1 -1.81352621e+01 -6.98648266e+01 -7.65543305e+01 2 -6.93647385e+01 1.02656197e+02 -3.18841225e+01 3 4.29034143e+01 -6.19008657e+01 -3.40589225e+01 4 -5.75380699e+01 5.14113431e+01 3.68225658e+01 5 5.66471658e+01 -1.37178811e+02 -2.64629382e+01 6 5.07488425e+01 1.16125996e+01 -5.18471112e+01 7 4.95049811e+00 -2.21314322e+02 -2.52129817e+02 8 -1.37877581e+02 -7.69459722e+01 4.35881293e+01 9 -3.34972922e+01 -6.34888237e+01 -8.29522953e+01 10 -1.21707436e+02 1.22706131e+02 -2.42940172e+02 11 3.29369251e+02 -1.59238567e+02 -3.19780854e+02 12 -8.86406596e+01 1.08405842e+02 2.51182218e+01 13 -1.34632114e+02 -6.45153686e+00 -3.02599338e+02 14 4.99330433e+01 5.26779417e+01 -6.03710207e+01 15 2.61571338e+02 -7.23675940e+01 1.38191660e+02 16 1.08091944e+02 6.12684636e+01 1.83980915e+02 17 -1.15792597e+02 -6.36181531e+01 -4.60218984e+01 18 6.88016701e+01 9.01905886e+01 -3.46265397e+01 19 3.84630927e+01 -9.79202984e+01 9.01717312e+01 20 -5.46152216e+01 6.52147603e+01 7.18239749e+01 21 -1.27997625e+02 -1.13776112e+02 5.13414333e+01 22 2.01482955e+02 2.31758284e+02 1.85374040e+02 23 6.26442673e+01 -3.11037531e+01 5.29960487e+01 24 -7.06825249e+00 5.51287456e+01 4.98988926e+01 25 -3.48399787e+02 3.22532509e+01 3.18883938e+02 26 -1.12540370e+01 1.21729221e+02 -4.52900074e+01 27 1.56444109e+02 -2.92710275e+02 6.40349134e+01 28 -2.85578856e+02 2.51213278e+02 9.72199550e+01 29 -9.75704873e+01 -1.06810463e+02 -1.45346631e+02 30 5.93363088e+01 1.27366062e+02 8.54162802e+01 31 1.86985475e+02 -3.92014690e+01 1.28066467e+02 32 3.12966429e+01 1.28299133e+02 1.29936833e+02 MONOATOMIC STRUCTURE (pbc=True)-- Species = U (Configuration in file "config-T-U.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1139.7067119480128 Forces: 1 -1.81352621e+01 -6.98648266e+01 -7.65543305e+01 2 -6.93647385e+01 1.02656197e+02 -3.18841225e+01 3 4.29034143e+01 -6.19008657e+01 -3.40589225e+01 4 -5.75380699e+01 5.14113431e+01 3.68225658e+01 5 5.66471658e+01 -1.37178811e+02 -2.64629382e+01 6 5.07488425e+01 1.16125996e+01 -5.18471112e+01 7 4.95049811e+00 -2.21314322e+02 -2.52129817e+02 8 -1.37877581e+02 -7.69459722e+01 4.35881293e+01 9 -3.34972922e+01 -6.34888237e+01 -8.29522953e+01 10 -1.21707436e+02 1.22706131e+02 -2.42940172e+02 11 3.29369251e+02 -1.59238567e+02 -3.19780854e+02 12 -8.86406596e+01 1.08405842e+02 2.51182218e+01 13 -1.34632114e+02 -6.45153686e+00 -3.02599338e+02 14 4.99330433e+01 5.26779417e+01 -6.03710207e+01 15 2.61571338e+02 -7.23675940e+01 1.38191660e+02 16 1.08091944e+02 6.12684636e+01 1.83980915e+02 17 -1.15792597e+02 -6.36181531e+01 -4.60218984e+01 18 6.88016701e+01 9.01905886e+01 -3.46265397e+01 19 3.84630927e+01 -9.79202984e+01 9.01717312e+01 20 -5.46152216e+01 6.52147603e+01 7.18239749e+01 21 -1.27997625e+02 -1.13776112e+02 5.13414333e+01 22 2.01482955e+02 2.31758284e+02 1.85374040e+02 23 6.26442673e+01 -3.11037531e+01 5.29960487e+01 24 -7.06825249e+00 5.51287456e+01 4.98988926e+01 25 -3.48399787e+02 3.22532509e+01 3.18883938e+02 26 -1.12540370e+01 1.21729221e+02 -4.52900074e+01 27 1.56444109e+02 -2.92710275e+02 6.40349134e+01 28 -2.85578856e+02 2.51213278e+02 9.72199550e+01 29 -9.75704873e+01 -1.06810463e+02 -1.45346631e+02 30 5.93363088e+01 1.27366062e+02 8.54162802e+01 31 1.86985475e+02 -3.92014690e+01 1.28066467e+02 32 3.12966429e+01 1.28299133e+02 1.29936833e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==31763== Memcheck, a memory error detector ==31763== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==31763== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==31763== Command: python runner2.py Sim_LAMMPS_MEAM_FernandezPascuet_2014_U__SM_176800861722_000 ==31763== ==32867== Warning: invalid file descriptor 1048564 in syscall close() ==32867== Warning: invalid file descriptor 1048565 in syscall close() ==32867== Warning: invalid file descriptor 1048566 in syscall close() ==32867== Warning: invalid file descriptor 1048567 in syscall close() ==32867== Use --log-fd= to select an alternative log fd. ==32867== Warning: invalid file descriptor 1048568 in syscall close() ==32867== Warning: invalid file descriptor 1048569 in syscall close() ==32875== Warning: invalid file descriptor 1048564 in syscall close() ==32875== Warning: invalid file descriptor 1048565 in syscall close() ==32875== Warning: invalid file descriptor 1048566 in syscall close() ==32875== Warning: invalid file descriptor 1048567 in syscall close() ==32875== Use --log-fd= to select an alternative log fd. ==32875== Warning: invalid file descriptor 1048568 in syscall close() ==32875== Warning: invalid file descriptor 1048569 in syscall close() ==32879== Warning: invalid file descriptor 1048564 in syscall close() ==32879== Warning: invalid file descriptor 1048565 in syscall close() ==32879== Warning: invalid file descriptor 1048566 in syscall close() ==32879== Warning: invalid file descriptor 1048567 in syscall close() ==32879== Use --log-fd= to select an alternative log fd. ==32879== Warning: invalid file descriptor 1048568 in syscall close() ==32879== Warning: invalid file descriptor 1048569 in syscall close() ==32887== Warning: invalid file descriptor 1048564 in syscall close() ==32887== Warning: invalid file descriptor 1048565 in syscall close() ==32887== Warning: invalid file descriptor 1048566 in syscall close() ==32887== Warning: invalid file descriptor 1048567 in syscall close() ==32887== Use --log-fd= to select an alternative log fd. ==32887== Warning: invalid file descriptor 1048568 in syscall close() ==32887== Warning: invalid file descriptor 1048569 in syscall close() ==32894== Warning: invalid file descriptor 1048564 in syscall close() ==32894== Warning: invalid file descriptor 1048565 in syscall close() ==32894== Warning: invalid file descriptor 1048566 in syscall close() ==32894== Warning: invalid file descriptor 1048567 in syscall close() ==32894== Use --log-fd= to select an alternative log fd. ==32894== Warning: invalid file descriptor 1048568 in syscall close() ==32894== Warning: invalid file descriptor 1048569 in syscall close() ==32899== Warning: invalid file descriptor 1048564 in syscall close() ==32899== Warning: invalid file descriptor 1048565 in syscall close() ==32899== Warning: invalid file descriptor 1048566 in syscall close() ==32899== Warning: invalid file descriptor 1048567 in syscall close() ==32899== Use --log-fd= to select an alternative log fd. ==32899== Warning: invalid file descriptor 1048568 in syscall close() ==32899== Warning: invalid file descriptor 1048569 in syscall close() ==32906== Warning: invalid file descriptor 1048564 in syscall close() ==32906== Warning: invalid file descriptor 1048565 in syscall close() ==32906== Warning: invalid file descriptor 1048566 in syscall close() ==32906== Warning: invalid file descriptor 1048567 in syscall close() ==32906== Use --log-fd= to select an alternative log fd. ==32906== Warning: invalid file descriptor 1048568 in syscall close() ==32906== Warning: invalid file descriptor 1048569 in syscall close() ==32910== Warning: invalid file descriptor 1048564 in syscall close() ==32910== Warning: invalid file descriptor 1048565 in syscall close() ==32910== Warning: invalid file descriptor 1048566 in syscall close() ==32910== Warning: invalid file descriptor 1048567 in syscall close() ==32910== Use --log-fd= to select an alternative log fd. ==32910== Warning: invalid file descriptor 1048568 in syscall close() ==32910== Warning: invalid file descriptor 1048569 in syscall close() ==31763== ==31763== HEAP SUMMARY: ==31763== in use at exit: 1,780,671 bytes in 1,488 blocks ==31763== total heap usage: 28,627 allocs, 27,139 frees, 48,625,825 bytes allocated ==31763== ==31763== LEAK SUMMARY: ==31763== definitely lost: 0 bytes in 0 blocks ==31763== indirectly lost: 0 bytes in 0 blocks ==31763== possibly lost: 178,423 bytes in 96 blocks ==31763== still reachable: 1,602,248 bytes in 1,392 blocks ==31763== suppressed: 0 bytes in 0 blocks ==31763== Rerun with --leak-check=full to see details of leaked memory ==31763== ==31763== For counts of detected and suppressed errors, rerun with: -v ==31763== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16450 from 607) ================================================================================ 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.