!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Wagner_2007_Cu__SM_521856783904_000 Supported species : Cu random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 13.352587812624312 Forces: 1 -9.82935828e+00 -7.25531531e+00 -1.72434691e+01 2 -3.71964206e+00 3.05366274e+00 -2.34738693e+00 3 1.43877175e+01 -9.32681116e+00 5.46534870e+00 4 -3.43899147e+00 8.54103533e+00 8.01587407e+00 5 -1.63803957e+00 -8.33892104e+00 -1.32972442e+00 6 5.57879176e+00 6.12873664e+00 -2.34120585e+00 7 -4.53847606e+00 -5.34625432e+01 -4.68072688e+01 8 -2.69901386e+00 -1.26393906e+01 7.05717552e+00 9 -1.75821774e+00 -1.70487093e+01 -1.73070721e+01 10 -4.03239218e+01 2.76059868e+01 -4.33245640e+01 11 -2.89535822e+01 -1.49120151e+00 -4.63839971e+00 12 1.71700975e+00 1.39240359e+01 1.35447501e+01 13 6.41649143e+00 -1.34104529e+01 -3.61814427e+01 14 2.21451095e+00 6.00841885e+00 -5.36616694e+00 15 2.18393595e+01 -2.73488275e+00 2.04338012e+01 16 3.55123475e+01 -6.41404942e+00 3.73911885e+01 17 -1.04012364e+01 -2.47443133e+00 -7.91577472e+00 18 1.15944869e+00 3.32389187e+00 -3.01287827e+00 19 9.53142147e+00 -1.07997543e+01 4.36038596e+00 20 -8.07057892e+00 1.18164554e+01 8.01044045e+00 21 -8.34990785e+00 -8.24218747e+00 -4.63163797e+00 22 1.69053396e+01 5.39874936e+01 5.03193691e+01 23 4.48641470e+00 9.77247935e-01 2.93107957e+00 24 3.96182772e+00 -9.60059139e-01 1.71946119e+00 25 -5.60350903e+00 5.20377136e-01 1.60603389e+00 26 -7.38565139e+00 8.96112067e+00 -3.46276066e+00 27 3.04436507e+01 -4.22152826e+01 9.59947079e+00 28 -3.95553330e+01 3.63567089e+01 -1.45602921e+00 29 -7.66848284e+00 -2.51921195e-01 -4.36729392e+00 30 7.53627870e+00 1.87386744e+01 -2.32980068e+00 31 3.04798785e+01 -2.30219188e+01 1.74731880e+01 32 -8.23654599e+00 2.01439860e+01 1.61353089e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 13.352587812624312 Forces: 1 -9.82935828e+00 -7.25531531e+00 -1.72434691e+01 2 -3.71964206e+00 3.05366274e+00 -2.34738693e+00 3 1.43877175e+01 -9.32681116e+00 5.46534870e+00 4 -3.43899147e+00 8.54103533e+00 8.01587407e+00 5 -1.63803957e+00 -8.33892104e+00 -1.32972442e+00 6 5.57879176e+00 6.12873664e+00 -2.34120585e+00 7 -4.53847606e+00 -5.34625432e+01 -4.68072688e+01 8 -2.69901386e+00 -1.26393906e+01 7.05717552e+00 9 -1.75821774e+00 -1.70487093e+01 -1.73070721e+01 10 -4.03239218e+01 2.76059868e+01 -4.33245640e+01 11 -2.89535822e+01 -1.49120151e+00 -4.63839971e+00 12 1.71700975e+00 1.39240359e+01 1.35447501e+01 13 6.41649143e+00 -1.34104529e+01 -3.61814427e+01 14 2.21451095e+00 6.00841885e+00 -5.36616694e+00 15 2.18393595e+01 -2.73488275e+00 2.04338012e+01 16 3.55123475e+01 -6.41404942e+00 3.73911885e+01 17 -1.04012364e+01 -2.47443133e+00 -7.91577472e+00 18 1.15944869e+00 3.32389187e+00 -3.01287827e+00 19 9.53142147e+00 -1.07997543e+01 4.36038596e+00 20 -8.07057892e+00 1.18164554e+01 8.01044045e+00 21 -8.34990785e+00 -8.24218747e+00 -4.63163797e+00 22 1.69053396e+01 5.39874936e+01 5.03193691e+01 23 4.48641470e+00 9.77247935e-01 2.93107957e+00 24 3.96182772e+00 -9.60059139e-01 1.71946119e+00 25 -5.60350903e+00 5.20377136e-01 1.60603389e+00 26 -7.38565139e+00 8.96112067e+00 -3.46276066e+00 27 3.04436507e+01 -4.22152826e+01 9.59947079e+00 28 -3.95553330e+01 3.63567089e+01 -1.45602921e+00 29 -7.66848284e+00 -2.51921195e-01 -4.36729392e+00 30 7.53627870e+00 1.87386744e+01 -2.32980068e+00 31 3.04798785e+01 -2.30219188e+01 1.74731880e+01 32 -8.23654599e+00 2.01439860e+01 1.61353089e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==56717== Memcheck, a memory error detector ==56717== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==56717== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==56717== Command: python runner2.py Sim_LAMMPS_MEAM_Wagner_2007_Cu__SM_521856783904_000 ==56717== ==57168== Warning: invalid file descriptor 1048564 in syscall close() ==57168== Warning: invalid file descriptor 1048565 in syscall close() ==57168== Warning: invalid file descriptor 1048566 in syscall close() ==57168== Warning: invalid file descriptor 1048567 in syscall close() ==57168== Use --log-fd= to select an alternative log fd. ==57168== Warning: invalid file descriptor 1048568 in syscall close() ==57168== Warning: invalid file descriptor 1048569 in syscall close() ==57176== Warning: invalid file descriptor 1048564 in syscall close() ==57176== Warning: invalid file descriptor 1048565 in syscall close() ==57176== Warning: invalid file descriptor 1048566 in syscall close() ==57176== Warning: invalid file descriptor 1048567 in syscall close() ==57176== Use --log-fd= to select an alternative log fd. ==57176== Warning: invalid file descriptor 1048568 in syscall close() ==57176== Warning: invalid file descriptor 1048569 in syscall close() ==57177== Warning: invalid file descriptor 1048564 in syscall close() ==57177== Warning: invalid file descriptor 1048565 in syscall close() ==57177== Warning: invalid file descriptor 1048566 in syscall close() ==57177== Warning: invalid file descriptor 1048567 in syscall close() ==57177== Use --log-fd= to select an alternative log fd. ==57177== Warning: invalid file descriptor 1048568 in syscall close() ==57177== Warning: invalid file descriptor 1048569 in syscall close() ==57196== Warning: invalid file descriptor 1048564 in syscall close() ==57196== Warning: invalid file descriptor 1048565 in syscall close() ==57196== Warning: invalid file descriptor 1048566 in syscall close() ==57196== Warning: invalid file descriptor 1048567 in syscall close() ==57196== Use --log-fd= to select an alternative log fd. ==57196== Warning: invalid file descriptor 1048568 in syscall close() ==57196== Warning: invalid file descriptor 1048569 in syscall close() ==57213== Warning: invalid file descriptor 1048564 in syscall close() ==57213== Warning: invalid file descriptor 1048565 in syscall close() ==57213== Warning: invalid file descriptor 1048566 in syscall close() ==57213== Warning: invalid file descriptor 1048567 in syscall close() ==57213== Use --log-fd= to select an alternative log fd. ==57213== Warning: invalid file descriptor 1048568 in syscall close() ==57213== Warning: invalid file descriptor 1048569 in syscall close() ==57218== Warning: invalid file descriptor 1048564 in syscall close() ==57218== Warning: invalid file descriptor 1048565 in syscall close() ==57218== Warning: invalid file descriptor 1048566 in syscall close() ==57218== Warning: invalid file descriptor 1048567 in syscall close() ==57218== Use --log-fd= to select an alternative log fd. ==57218== Warning: invalid file descriptor 1048568 in syscall close() ==57218== Warning: invalid file descriptor 1048569 in syscall close() ==57224== Warning: invalid file descriptor 1048564 in syscall close() ==57224== Warning: invalid file descriptor 1048565 in syscall close() ==57224== Warning: invalid file descriptor 1048566 in syscall close() ==57224== Warning: invalid file descriptor 1048567 in syscall close() ==57224== Use --log-fd= to select an alternative log fd. ==57224== Warning: invalid file descriptor 1048568 in syscall close() ==57224== Warning: invalid file descriptor 1048569 in syscall close() ==57227== Warning: invalid file descriptor 1048564 in syscall close() ==57227== Warning: invalid file descriptor 1048565 in syscall close() ==57227== Warning: invalid file descriptor 1048566 in syscall close() ==57227== Warning: invalid file descriptor 1048567 in syscall close() ==57227== Use --log-fd= to select an alternative log fd. ==57227== Warning: invalid file descriptor 1048568 in syscall close() ==57227== Warning: invalid file descriptor 1048569 in syscall close() ==56717== ==56717== HEAP SUMMARY: ==56717== in use at exit: 1,780,563 bytes in 1,488 blocks ==56717== total heap usage: 28,785 allocs, 27,297 frees, 48,638,703 bytes allocated ==56717== ==56717== LEAK SUMMARY: ==56717== definitely lost: 0 bytes in 0 blocks ==56717== indirectly lost: 0 bytes in 0 blocks ==56717== possibly lost: 178,423 bytes in 96 blocks ==56717== still reachable: 1,602,140 bytes in 1,392 blocks ==56717== suppressed: 0 bytes in 0 blocks ==56717== Rerun with --leak-check=full to see details of leaked memory ==56717== ==56717== For counts of detected and suppressed errors, rerun with: -v ==56717== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11328 from 596) ================================================================================ 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.