!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : MFF_MistriotisFlytzanisFarantos_1989_Si__MO_080526771943_001 Supported species : Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1054.7750110921359 Forces: 1 -3.12091109e+01 -2.99539225e+01 -3.35660591e+01 2 -3.12681178e+01 -4.23720668e+01 -1.38223538e+02 3 -5.63112017e+01 -1.51101875e+02 -2.76344187e+01 4 -1.13231299e+02 -2.31355525e+01 -2.67651123e+01 5 1.43150346e+01 -8.00818442e+01 -6.91628958e+01 6 6.25703704e+01 -3.32330438e+01 -7.98569502e+01 7 7.41304047e+01 -1.05690158e+02 -4.20119164e+01 8 5.14482464e+01 -7.99848149e+01 -5.82147358e+01 9 -7.11496077e+01 1.19505388e+01 -8.55990420e+01 10 -3.61349991e+01 8.90636999e+01 -9.46253362e+01 11 -1.19697798e+02 -5.22971545e+00 -7.65497929e+01 12 -8.57031678e+01 6.92517620e+01 -1.77692301e+01 13 4.68983987e+01 3.83727126e+01 -1.94061909e+02 14 4.97356226e+01 3.84751694e+01 -4.11560403e+01 15 1.98206149e+02 5.28085543e+01 -4.22738258e+01 16 3.24128519e+01 2.04778858e+02 -3.78227657e+01 17 -5.67396598e+01 -4.74894906e+01 8.08288001e+00 18 -6.92119148e+01 -8.22244711e+01 6.87521326e+01 19 -1.94624064e+00 -5.76047913e+01 5.64900205e+01 20 -5.09502914e+01 -7.98513075e+00 5.41834908e+01 21 2.81503513e+01 -1.29172035e+02 5.68543353e+01 22 1.40905393e+02 -4.35810020e+01 4.40055885e+01 23 2.07065986e+01 -2.13914342e+01 3.14646431e+01 24 2.52560671e+01 -4.17120783e+01 1.36537740e+02 25 -1.59860325e+02 3.29891540e+01 4.02412546e+01 26 -4.99855917e+01 1.59771730e+02 6.27143842e+01 27 -5.63345085e+01 1.10194013e+01 1.32848216e+02 28 -4.36580465e+01 3.04458456e+01 2.91126171e+01 29 7.83930296e+01 8.23652540e+01 1.06181161e+02 30 1.01720494e+02 8.24994607e+01 3.71423356e+01 31 8.79638159e+01 1.48180819e+01 1.06610070e+02 32 2.05790518e+01 6.33332031e+01 9.40726990e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1054.7750110921359 Forces: 1 -3.12091109e+01 -2.99539225e+01 -3.35660591e+01 2 -3.12681178e+01 -4.23720668e+01 -1.38223538e+02 3 -5.63112017e+01 -1.51101875e+02 -2.76344187e+01 4 -1.13231299e+02 -2.31355525e+01 -2.67651123e+01 5 1.43150346e+01 -8.00818442e+01 -6.91628958e+01 6 6.25703704e+01 -3.32330438e+01 -7.98569502e+01 7 7.41304047e+01 -1.05690158e+02 -4.20119164e+01 8 5.14482464e+01 -7.99848149e+01 -5.82147358e+01 9 -7.11496077e+01 1.19505388e+01 -8.55990420e+01 10 -3.61349991e+01 8.90636999e+01 -9.46253362e+01 11 -1.19697798e+02 -5.22971545e+00 -7.65497929e+01 12 -8.57031678e+01 6.92517620e+01 -1.77692301e+01 13 4.68983987e+01 3.83727126e+01 -1.94061909e+02 14 4.97356226e+01 3.84751694e+01 -4.11560403e+01 15 1.98206149e+02 5.28085543e+01 -4.22738258e+01 16 3.24128519e+01 2.04778858e+02 -3.78227657e+01 17 -5.67396598e+01 -4.74894906e+01 8.08288001e+00 18 -6.92119148e+01 -8.22244711e+01 6.87521326e+01 19 -1.94624064e+00 -5.76047913e+01 5.64900205e+01 20 -5.09502914e+01 -7.98513075e+00 5.41834908e+01 21 2.81503513e+01 -1.29172035e+02 5.68543353e+01 22 1.40905393e+02 -4.35810020e+01 4.40055885e+01 23 2.07065986e+01 -2.13914342e+01 3.14646431e+01 24 2.52560671e+01 -4.17120783e+01 1.36537740e+02 25 -1.59860325e+02 3.29891540e+01 4.02412546e+01 26 -4.99855917e+01 1.59771730e+02 6.27143842e+01 27 -5.63345085e+01 1.10194013e+01 1.32848216e+02 28 -4.36580465e+01 3.04458456e+01 2.91126171e+01 29 7.83930296e+01 8.23652540e+01 1.06181161e+02 30 1.01720494e+02 8.24994607e+01 3.71423356e+01 31 8.79638159e+01 1.48180819e+01 1.06610070e+02 32 2.05790518e+01 6.33332031e+01 9.40726990e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==38122== Memcheck, a memory error detector ==38122== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==38122== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==38122== Command: python runner2.py MFF_MistriotisFlytzanisFarantos_1989_Si__MO_080526771943_001 ==38122== ==40243== Warning: invalid file descriptor 1048564 in syscall close() ==40243== Warning: invalid file descriptor 1048565 in syscall close() ==40243== Warning: invalid file descriptor 1048566 in syscall close() ==40243== Warning: invalid file descriptor 1048567 in syscall close() ==40243== Use --log-fd= to select an alternative log fd. ==40243== Warning: invalid file descriptor 1048568 in syscall close() ==40243== Warning: invalid file descriptor 1048569 in syscall close() ==40244== Warning: invalid file descriptor 1048564 in syscall close() ==40244== Warning: invalid file descriptor 1048565 in syscall close() ==40244== Warning: invalid file descriptor 1048566 in syscall close() ==40244== Warning: invalid file descriptor 1048567 in syscall close() ==40244== Use --log-fd= to select an alternative log fd. ==40244== Warning: invalid file descriptor 1048568 in syscall close() ==40244== Warning: invalid file descriptor 1048569 in syscall close() ==40293== Warning: invalid file descriptor 1048564 in syscall close() ==40293== Warning: invalid file descriptor 1048565 in syscall close() ==40293== Warning: invalid file descriptor 1048566 in syscall close() ==40293== Warning: invalid file descriptor 1048567 in syscall close() ==40293== Use --log-fd= to select an alternative log fd. ==40293== Warning: invalid file descriptor 1048568 in syscall close() ==40293== Warning: invalid file descriptor 1048569 in syscall close() ==40298== Warning: invalid file descriptor 1048564 in syscall close() ==40298== Warning: invalid file descriptor 1048565 in syscall close() ==40298== Warning: invalid file descriptor 1048566 in syscall close() ==40298== Warning: invalid file descriptor 1048567 in syscall close() ==40298== Use --log-fd= to select an alternative log fd. ==40298== Warning: invalid file descriptor 1048568 in syscall close() ==40298== Warning: invalid file descriptor 1048569 in syscall close() ==40302== Warning: invalid file descriptor 1048564 in syscall close() ==40302== Warning: invalid file descriptor 1048565 in syscall close() ==40302== Warning: invalid file descriptor 1048566 in syscall close() ==40302== Warning: invalid file descriptor 1048567 in syscall close() ==40302== Use --log-fd= to select an alternative log fd. ==40302== Warning: invalid file descriptor 1048568 in syscall close() ==40302== Warning: invalid file descriptor 1048569 in syscall close() ==40309== Warning: invalid file descriptor 1048564 in syscall close() ==40309== Warning: invalid file descriptor 1048565 in syscall close() ==40309== Warning: invalid file descriptor 1048566 in syscall close() ==40309== Warning: invalid file descriptor 1048567 in syscall close() ==40309== Use --log-fd= to select an alternative log fd. ==40309== Warning: invalid file descriptor 1048568 in syscall close() ==40309== Warning: invalid file descriptor 1048569 in syscall close() ==38122== ==38122== HEAP SUMMARY: ==38122== in use at exit: 1,718,308 bytes in 1,321 blocks ==38122== total heap usage: 247,426 allocs, 246,105 frees, 43,358,003 bytes allocated ==38122== ==38122== LEAK SUMMARY: ==38122== definitely lost: 0 bytes in 0 blocks ==38122== indirectly lost: 0 bytes in 0 blocks ==38122== possibly lost: 178,943 bytes in 97 blocks ==38122== still reachable: 1,539,365 bytes in 1,224 blocks ==38122== suppressed: 0 bytes in 0 blocks ==38122== Rerun with --leak-check=full to see details of leaked memory ==38122== ==38122== For counts of detected and suppressed errors, rerun with: -v ==38122== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16370 from 603) ================================================================================ 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.