!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_SMTBQ_SallesPolitanoAmzallag_2016_Al__SM_404097633924_000 Supported species : Al random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 97.00065493354714 Forces: 1 -5.70048871e+00 -1.01788367e+01 -1.05623667e+01 2 -9.71816626e+00 1.45643635e+01 -1.44715871e+01 3 -1.55269598e+00 -1.54479365e+01 -1.62108525e+00 4 -9.22604778e+00 4.47888618e+00 4.83810106e+00 5 1.41172604e+01 -2.28475052e+01 -5.66314983e+00 6 5.89100782e+00 1.16345122e+00 -9.19656981e+00 7 9.03115220e+00 -3.20844841e+01 -2.77778298e+01 8 -9.17523627e+00 -1.15702204e+01 -5.51320528e+00 9 -1.23089292e+01 -1.62826126e+01 -2.83919260e+01 10 -1.45033046e+00 2.47013799e+01 -2.48217255e+01 11 -4.94742879e+00 -1.65874715e+01 9.79930762e+00 12 -1.80737458e+01 2.35090654e+01 1.23776482e+01 13 -4.09369238e+00 -1.22980374e+01 -4.72029267e+01 14 1.01251282e+01 1.22350863e+01 -8.51658290e+00 15 4.25372140e+01 -4.70119289e+00 9.45721947e+00 16 5.22697258e+00 3.49368768e+01 1.45391206e+01 17 -1.41262819e+01 -6.95219389e+00 -4.70820881e+00 18 -7.54726748e+00 8.77790527e+00 7.16956949e+00 19 5.75540254e+00 -1.21001259e+01 9.62424797e+00 20 -6.54965329e+00 8.42370613e+00 7.70139805e+00 21 -1.01320665e+01 -1.56307770e+01 9.78330049e+00 22 2.33823676e+01 2.29073532e+01 2.21855065e+01 23 5.29880225e+00 -2.61635627e+00 8.70123543e+00 24 3.01259248e+00 4.72517822e-01 8.99203352e+00 25 -1.37287183e+01 -3.89849531e+00 9.31415099e+00 26 -8.49150008e+00 2.25904886e+01 -9.54713106e+00 27 8.71155304e+00 -3.24380741e+01 1.30571744e+01 28 -2.87728128e+01 2.33864800e+01 5.56035338e+00 29 -7.04949196e+00 -1.05578885e+01 8.90721390e+00 30 1.16353694e+01 1.68335416e+01 1.51979044e+00 31 1.81855979e+01 -1.00661351e+01 1.56631929e+01 32 9.73413345e+00 1.72772414e+01 1.88037303e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 97.00065493354714 Forces: 1 -5.70048871e+00 -1.01788367e+01 -1.05623667e+01 2 -9.71816626e+00 1.45643635e+01 -1.44715871e+01 3 -1.55269598e+00 -1.54479365e+01 -1.62108525e+00 4 -9.22604778e+00 4.47888618e+00 4.83810106e+00 5 1.41172604e+01 -2.28475052e+01 -5.66314983e+00 6 5.89100782e+00 1.16345122e+00 -9.19656981e+00 7 9.03115220e+00 -3.20844841e+01 -2.77778298e+01 8 -9.17523627e+00 -1.15702204e+01 -5.51320528e+00 9 -1.23089292e+01 -1.62826126e+01 -2.83919260e+01 10 -1.45033046e+00 2.47013799e+01 -2.48217255e+01 11 -4.94742879e+00 -1.65874715e+01 9.79930762e+00 12 -1.80737458e+01 2.35090654e+01 1.23776482e+01 13 -4.09369238e+00 -1.22980374e+01 -4.72029267e+01 14 1.01251282e+01 1.22350863e+01 -8.51658290e+00 15 4.25372140e+01 -4.70119289e+00 9.45721947e+00 16 5.22697258e+00 3.49368768e+01 1.45391206e+01 17 -1.41262819e+01 -6.95219389e+00 -4.70820881e+00 18 -7.54726748e+00 8.77790527e+00 7.16956949e+00 19 5.75540254e+00 -1.21001259e+01 9.62424797e+00 20 -6.54965329e+00 8.42370613e+00 7.70139805e+00 21 -1.01320665e+01 -1.56307770e+01 9.78330049e+00 22 2.33823676e+01 2.29073532e+01 2.21855065e+01 23 5.29880225e+00 -2.61635627e+00 8.70123543e+00 24 3.01259248e+00 4.72517822e-01 8.99203352e+00 25 -1.37287183e+01 -3.89849531e+00 9.31415099e+00 26 -8.49150008e+00 2.25904886e+01 -9.54713106e+00 27 8.71155304e+00 -3.24380741e+01 1.30571744e+01 28 -2.87728128e+01 2.33864800e+01 5.56035338e+00 29 -7.04949196e+00 -1.05578885e+01 8.90721390e+00 30 1.16353694e+01 1.68335416e+01 1.51979044e+00 31 1.81855979e+01 -1.00661351e+01 1.56631929e+01 32 9.73413345e+00 1.72772414e+01 1.88037303e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==43724== Memcheck, a memory error detector ==43724== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==43724== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==43724== Command: python runner2.py Sim_LAMMPS_SMTBQ_SallesPolitanoAmzallag_2016_Al__SM_404097633924_000 ==43724== ==45602== Warning: invalid file descriptor 1048564 in syscall close() ==45602== Warning: invalid file descriptor 1048565 in syscall close() ==45602== Warning: invalid file descriptor 1048566 in syscall close() ==45602== Warning: invalid file descriptor 1048567 in syscall close() ==45602== Use --log-fd= to select an alternative log fd. ==45602== Warning: invalid file descriptor 1048568 in syscall close() ==45602== Warning: invalid file descriptor 1048569 in syscall close() ==45603== Warning: invalid file descriptor 1048564 in syscall close() ==45603== Warning: invalid file descriptor 1048565 in syscall close() ==45603== Warning: invalid file descriptor 1048566 in syscall close() ==45603== Warning: invalid file descriptor 1048567 in syscall close() ==45603== Use --log-fd= to select an alternative log fd. ==45603== Warning: invalid file descriptor 1048568 in syscall close() ==45603== Warning: invalid file descriptor 1048569 in syscall close() ==45604== Warning: invalid file descriptor 1048564 in syscall close() ==45604== Warning: invalid file descriptor 1048565 in syscall close() ==45604== Warning: invalid file descriptor 1048566 in syscall close() ==45604== Warning: invalid file descriptor 1048567 in syscall close() ==45604== Use --log-fd= to select an alternative log fd. ==45604== Warning: invalid file descriptor 1048568 in syscall close() ==45604== Warning: invalid file descriptor 1048569 in syscall close() ==45605== Warning: invalid file descriptor 1048564 in syscall close() ==45605== Warning: invalid file descriptor 1048565 in syscall close() ==45605== Warning: invalid file descriptor 1048566 in syscall close() ==45605== Warning: invalid file descriptor 1048567 in syscall close() ==45605== Use --log-fd= to select an alternative log fd. ==45605== Warning: invalid file descriptor 1048568 in syscall close() ==45605== Warning: invalid file descriptor 1048569 in syscall close() ==45610== Warning: invalid file descriptor 1048564 in syscall close() ==45610== Warning: invalid file descriptor 1048565 in syscall close() ==45610== Warning: invalid file descriptor 1048566 in syscall close() ==45610== Warning: invalid file descriptor 1048567 in syscall close() ==45610== Use --log-fd= to select an alternative log fd. ==45610== Warning: invalid file descriptor 1048568 in syscall close() ==45610== Warning: invalid file descriptor 1048569 in syscall close() ==45612== Warning: invalid file descriptor 1048564 in syscall close() ==45612== Warning: invalid file descriptor 1048565 in syscall close() ==45612== Warning: invalid file descriptor 1048566 in syscall close() ==45612== Warning: invalid file descriptor 1048567 in syscall close() ==45612== Use --log-fd= to select an alternative log fd. ==45612== Warning: invalid file descriptor 1048568 in syscall close() ==45612== Warning: invalid file descriptor 1048569 in syscall close() ==45614== Warning: invalid file descriptor 1048564 in syscall close() ==45614== Warning: invalid file descriptor 1048565 in syscall close() ==45614== Warning: invalid file descriptor 1048566 in syscall close() ==45614== Warning: invalid file descriptor 1048567 in syscall close() ==45614== Use --log-fd= to select an alternative log fd. ==45614== Warning: invalid file descriptor 1048568 in syscall close() ==45614== Warning: invalid file descriptor 1048569 in syscall close() ==45615== Warning: invalid file descriptor 1048564 in syscall close() ==45615== Warning: invalid file descriptor 1048565 in syscall close() ==45615== Warning: invalid file descriptor 1048566 in syscall close() ==45615== Warning: invalid file descriptor 1048567 in syscall close() ==45615== Use --log-fd= to select an alternative log fd. ==45615== Warning: invalid file descriptor 1048568 in syscall close() ==45615== Warning: invalid file descriptor 1048569 in syscall close() ==43724== ==43724== HEAP SUMMARY: ==43724== in use at exit: 1,780,767 bytes in 1,488 blocks ==43724== total heap usage: 766,190 allocs, 764,702 frees, 241,091,526 bytes allocated ==43724== ==43724== LEAK SUMMARY: ==43724== definitely lost: 0 bytes in 0 blocks ==43724== indirectly lost: 0 bytes in 0 blocks ==43724== possibly lost: 178,423 bytes in 96 blocks ==43724== still reachable: 1,602,344 bytes in 1,392 blocks ==43724== suppressed: 0 bytes in 0 blocks ==43724== Rerun with --leak-check=full to see details of leaked memory ==43724== ==43724== For counts of detected and suppressed errors, rerun with: -v ==43724== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16432 from 619) ================================================================================ 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.