!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_Dynamo_WilsonMendelev_2016_Mg__MO_574574915905_000 Supported species : Mg random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mg (Configuration in file "config-F-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 93.42141188130542 Forces: 1 -4.25335801e+00 -1.06225377e+01 -1.08903102e+01 2 -4.53589811e+00 6.61587652e+00 -9.26632711e+00 3 2.07677340e+00 -8.59727467e+00 -3.37886324e+00 4 -7.29100102e+00 8.44264636e+00 5.57123461e+00 5 5.44834930e+00 -1.28361244e+01 -1.84017702e+00 6 5.58839846e+00 -1.78175227e+00 -6.78054011e+00 7 3.18267578e+00 -1.78990947e+01 -1.51561954e+01 8 -1.31353955e+01 -1.44600885e+01 4.35912711e-01 9 -5.63763659e+00 -5.72692617e-02 -8.54479519e+00 10 -4.37148288e+00 9.35946668e+00 -1.13513252e+01 11 -3.36080610e+00 -6.23589202e+00 1.08418970e+00 12 -6.95416634e+00 8.08646633e+00 -1.38020223e+00 13 -3.04390016e+00 1.59654560e-01 -2.52186614e+01 14 5.01058105e+00 4.77586163e+00 -3.37697127e+00 15 3.00397333e+01 8.63740363e+00 3.27330378e+00 16 3.77134842e+00 1.73369696e+01 7.83416345e+00 17 -8.21012831e+00 -2.90336548e+00 3.40106638e+00 18 1.07919250e+00 5.04413289e+00 6.65415056e-01 19 -7.01638837e-05 -6.06966061e+00 7.34737222e+00 20 -3.94224963e+00 -4.00832252e-03 3.31141846e+00 21 -2.02754547e+00 -8.42990700e+00 4.61173990e+00 22 1.34205438e+01 9.30249760e+00 1.22943884e+01 23 2.86818789e+00 -2.44194649e+00 4.34048612e+00 24 -5.62253376e-01 -7.76522573e-01 5.67771956e+00 25 -7.63650980e+00 -3.54748379e+00 5.92609647e+00 26 -2.61183640e+00 8.88392869e+00 -1.81763802e+00 27 6.73169214e+00 -1.47175047e+01 6.62087354e+00 28 -1.60593330e+01 1.36205366e+01 2.81357799e+00 29 -7.97414013e+00 -1.71404491e+00 2.86690609e+00 30 7.38909816e+00 7.82364239e+00 7.21041034e-02 31 1.02384142e+01 -2.15016628e+00 1.24311109e+01 32 4.76272249e+00 7.15556017e+00 8.42292683e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mg (Configuration in file "config-T-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 93.42141188130542 Forces: 1 -4.25335801e+00 -1.06225377e+01 -1.08903102e+01 2 -4.53589811e+00 6.61587652e+00 -9.26632711e+00 3 2.07677340e+00 -8.59727467e+00 -3.37886324e+00 4 -7.29100102e+00 8.44264636e+00 5.57123461e+00 5 5.44834930e+00 -1.28361244e+01 -1.84017702e+00 6 5.58839846e+00 -1.78175227e+00 -6.78054011e+00 7 3.18267578e+00 -1.78990947e+01 -1.51561954e+01 8 -1.31353955e+01 -1.44600885e+01 4.35912711e-01 9 -5.63763659e+00 -5.72692617e-02 -8.54479519e+00 10 -4.37148288e+00 9.35946668e+00 -1.13513252e+01 11 -3.36080610e+00 -6.23589202e+00 1.08418970e+00 12 -6.95416634e+00 8.08646633e+00 -1.38020223e+00 13 -3.04390016e+00 1.59654560e-01 -2.52186614e+01 14 5.01058105e+00 4.77586163e+00 -3.37697127e+00 15 3.00397333e+01 8.63740363e+00 3.27330378e+00 16 3.77134842e+00 1.73369696e+01 7.83416345e+00 17 -8.21012831e+00 -2.90336548e+00 3.40106638e+00 18 1.07919250e+00 5.04413289e+00 6.65415056e-01 19 -7.01638837e-05 -6.06966061e+00 7.34737222e+00 20 -3.94224963e+00 -4.00832252e-03 3.31141846e+00 21 -2.02754547e+00 -8.42990700e+00 4.61173990e+00 22 1.34205438e+01 9.30249760e+00 1.22943884e+01 23 2.86818789e+00 -2.44194649e+00 4.34048612e+00 24 -5.62253376e-01 -7.76522573e-01 5.67771956e+00 25 -7.63650980e+00 -3.54748379e+00 5.92609647e+00 26 -2.61183640e+00 8.88392869e+00 -1.81763802e+00 27 6.73169214e+00 -1.47175047e+01 6.62087354e+00 28 -1.60593330e+01 1.36205366e+01 2.81357799e+00 29 -7.97414013e+00 -1.71404491e+00 2.86690609e+00 30 7.38909816e+00 7.82364239e+00 7.21041034e-02 31 1.02384142e+01 -2.15016628e+00 1.24311109e+01 32 4.76272249e+00 7.15556017e+00 8.42292683e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==73251== Memcheck, a memory error detector ==73251== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==73251== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==73251== Command: python runner2.py EAM_Dynamo_WilsonMendelev_2016_Mg__MO_574574915905_000 ==73251== ==74979== Warning: invalid file descriptor 1048564 in syscall close() ==74979== Warning: invalid file descriptor 1048565 in syscall close() ==74979== Warning: invalid file descriptor 1048566 in syscall close() ==74979== Warning: invalid file descriptor 1048567 in syscall close() ==74979== Use --log-fd= to select an alternative log fd. ==74979== Warning: invalid file descriptor 1048568 in syscall close() ==74979== Warning: invalid file descriptor 1048569 in syscall close() ==74981== Warning: invalid file descriptor 1048564 in syscall close() ==74981== Warning: invalid file descriptor 1048565 in syscall close() ==74981== Warning: invalid file descriptor 1048566 in syscall close() ==74981== Warning: invalid file descriptor 1048567 in syscall close() ==74981== Use --log-fd= to select an alternative log fd. ==74981== Warning: invalid file descriptor 1048568 in syscall close() ==74981== Warning: invalid file descriptor 1048569 in syscall close() ==75049== Warning: invalid file descriptor 1048564 in syscall close() ==75049== Warning: invalid file descriptor 1048565 in syscall close() ==75049== Warning: invalid file descriptor 1048566 in syscall close() ==75049== Warning: invalid file descriptor 1048567 in syscall close() ==75049== Use --log-fd= to select an alternative log fd. ==75049== Warning: invalid file descriptor 1048568 in syscall close() ==75049== Warning: invalid file descriptor 1048569 in syscall close() ==75067== Warning: invalid file descriptor 1048564 in syscall close() ==75067== Warning: invalid file descriptor 1048565 in syscall close() ==75067== Warning: invalid file descriptor 1048566 in syscall close() ==75067== Warning: invalid file descriptor 1048567 in syscall close() ==75067== Use --log-fd= to select an alternative log fd. ==75067== Warning: invalid file descriptor 1048568 in syscall close() ==75067== Warning: invalid file descriptor 1048569 in syscall close() ==75070== Warning: invalid file descriptor 1048564 in syscall close() ==75070== Warning: invalid file descriptor 1048565 in syscall close() ==75070== Warning: invalid file descriptor 1048566 in syscall close() ==75070== Warning: invalid file descriptor 1048567 in syscall close() ==75070== Use --log-fd= to select an alternative log fd. ==75070== Warning: invalid file descriptor 1048568 in syscall close() ==75070== Warning: invalid file descriptor 1048569 in syscall close() ==75071== Warning: invalid file descriptor 1048564 in syscall close() ==75071== Warning: invalid file descriptor 1048565 in syscall close() ==75071== Warning: invalid file descriptor 1048566 in syscall close() ==75071== Warning: invalid file descriptor 1048567 in syscall close() ==75071== Use --log-fd= to select an alternative log fd. ==75071== Warning: invalid file descriptor 1048568 in syscall close() ==75071== Warning: invalid file descriptor 1048569 in syscall close() ==73251== ==73251== HEAP SUMMARY: ==73251== in use at exit: 1,718,292 bytes in 1,321 blocks ==73251== total heap usage: 31,120 allocs, 29,799 frees, 47,288,315 bytes allocated ==73251== ==73251== LEAK SUMMARY: ==73251== definitely lost: 0 bytes in 0 blocks ==73251== indirectly lost: 0 bytes in 0 blocks ==73251== possibly lost: 178,943 bytes in 97 blocks ==73251== still reachable: 1,539,349 bytes in 1,224 blocks ==73251== suppressed: 0 bytes in 0 blocks ==73251== Rerun with --leak-check=full to see details of leaked memory ==73251== ==73251== For counts of detected and suppressed errors, rerun with: -v ==73251== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11274 from 613) ================================================================================ 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.