!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : ThreeBodyCluster_Gong_Gong_1993_Si__MO_407755720412_000 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 = 90.63696652254755 Forces: 1 -8.30700142e+00 -1.10913007e+01 -1.98524263e+01 2 -7.76838006e+00 1.24767855e+01 -1.90652021e+01 3 1.40435724e+01 -2.81961922e+01 -1.38800460e+01 4 -1.95466436e+01 8.13399318e+00 4.77980916e+00 5 9.37298739e+00 -2.55753335e+01 -5.37689430e+00 6 6.98442502e+00 3.21895130e+00 -1.49622520e+01 7 1.48796046e+01 -4.45830239e+01 -2.98704159e+01 8 -2.07930756e+01 -2.82149008e+01 -1.09545750e+01 9 -8.15238866e+00 -1.21480361e+01 -2.65133014e+01 10 -6.64757527e+00 1.89571947e+01 -2.50717549e+01 11 -1.53126503e+01 -9.35824735e+00 -1.08633821e+01 12 -1.68909341e+01 2.07018271e+01 1.19308176e+01 13 -1.04485448e+01 -1.32452779e+01 -5.73853061e+01 14 1.35062637e+01 1.24109101e+01 -8.80956127e+00 15 5.95019632e+01 9.85881779e+00 6.85489466e+00 16 6.92850656e+00 5.07682764e+01 1.39124995e+01 17 -3.25379647e+01 -8.39659713e+00 9.26010035e+00 18 -1.08251493e+00 1.48721476e+01 -5.65686845e+00 19 1.16533593e+00 -2.54897213e+01 2.04831772e+01 20 -1.00440611e+01 8.77409057e+00 7.61521774e+00 21 -5.79681642e+00 -2.35253460e+01 1.28668421e+01 22 3.42892843e+01 2.16974676e+01 2.42545640e+01 23 3.61110165e+00 -7.83504039e-01 1.45082030e+01 24 7.79346544e+00 -8.72826663e-02 1.97713328e+01 25 -3.28878165e+01 -2.11245654e+00 1.36417954e+01 26 -1.05259802e+01 4.66779350e+01 -3.09958955e+01 27 9.77206253e+00 -4.08114340e+01 3.11658165e+01 28 -4.05814747e+01 2.55834403e+01 1.01321105e+01 29 2.36473429e+00 -7.14591163e+00 1.96488251e+01 30 1.56232568e+01 1.88024902e+01 5.55026959e-01 31 2.36130772e+01 -9.44560887e+00 2.22548059e+01 32 2.38741811e+01 1.72758472e+01 3.56220429e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 90.63696652254755 Forces: 1 -8.30700142e+00 -1.10913007e+01 -1.98524263e+01 2 -7.76838006e+00 1.24767855e+01 -1.90652021e+01 3 1.40435724e+01 -2.81961922e+01 -1.38800460e+01 4 -1.95466436e+01 8.13399318e+00 4.77980916e+00 5 9.37298739e+00 -2.55753335e+01 -5.37689430e+00 6 6.98442502e+00 3.21895130e+00 -1.49622520e+01 7 1.48796046e+01 -4.45830239e+01 -2.98704159e+01 8 -2.07930756e+01 -2.82149008e+01 -1.09545750e+01 9 -8.15238866e+00 -1.21480361e+01 -2.65133014e+01 10 -6.64757527e+00 1.89571947e+01 -2.50717549e+01 11 -1.53126503e+01 -9.35824735e+00 -1.08633821e+01 12 -1.68909341e+01 2.07018271e+01 1.19308176e+01 13 -1.04485448e+01 -1.32452779e+01 -5.73853061e+01 14 1.35062637e+01 1.24109101e+01 -8.80956127e+00 15 5.95019632e+01 9.85881779e+00 6.85489466e+00 16 6.92850656e+00 5.07682764e+01 1.39124995e+01 17 -3.25379647e+01 -8.39659713e+00 9.26010035e+00 18 -1.08251493e+00 1.48721476e+01 -5.65686845e+00 19 1.16533593e+00 -2.54897213e+01 2.04831772e+01 20 -1.00440611e+01 8.77409057e+00 7.61521774e+00 21 -5.79681642e+00 -2.35253460e+01 1.28668421e+01 22 3.42892843e+01 2.16974676e+01 2.42545640e+01 23 3.61110165e+00 -7.83504039e-01 1.45082030e+01 24 7.79346544e+00 -8.72826663e-02 1.97713328e+01 25 -3.28878165e+01 -2.11245654e+00 1.36417954e+01 26 -1.05259802e+01 4.66779350e+01 -3.09958955e+01 27 9.77206253e+00 -4.08114340e+01 3.11658165e+01 28 -4.05814747e+01 2.55834403e+01 1.01321105e+01 29 2.36473429e+00 -7.14591163e+00 1.96488251e+01 30 1.56232568e+01 1.88024902e+01 5.55026959e-01 31 2.36130772e+01 -9.44560887e+00 2.22548059e+01 32 2.38741811e+01 1.72758472e+01 3.56220429e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==20451== Memcheck, a memory error detector ==20451== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==20451== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==20451== Command: python runner2.py ThreeBodyCluster_Gong_Gong_1993_Si__MO_407755720412_000 ==20451== ==22601== Warning: invalid file descriptor 1048564 in syscall close() ==22601== Warning: invalid file descriptor 1048565 in syscall close() ==22601== Warning: invalid file descriptor 1048566 in syscall close() ==22601== Warning: invalid file descriptor 1048567 in syscall close() ==22601== Use --log-fd= to select an alternative log fd. ==22601== Warning: invalid file descriptor 1048568 in syscall close() ==22601== Warning: invalid file descriptor 1048569 in syscall close() ==22608== Warning: invalid file descriptor 1048564 in syscall close() ==22608== Warning: invalid file descriptor 1048565 in syscall close() ==22608== Warning: invalid file descriptor 1048566 in syscall close() ==22608== Warning: invalid file descriptor 1048567 in syscall close() ==22608== Use --log-fd= to select an alternative log fd. ==22608== Warning: invalid file descriptor 1048568 in syscall close() ==22608== Warning: invalid file descriptor 1048569 in syscall close() ==22697== Warning: invalid file descriptor 1048564 in syscall close() ==22697== Warning: invalid file descriptor 1048565 in syscall close() ==22697== Warning: invalid file descriptor 1048566 in syscall close() ==22697== Warning: invalid file descriptor 1048567 in syscall close() ==22697== Use --log-fd= to select an alternative log fd. ==22697== Warning: invalid file descriptor 1048568 in syscall close() ==22697== Warning: invalid file descriptor 1048569 in syscall close() ==22716== Warning: invalid file descriptor 1048564 in syscall close() ==22716== Warning: invalid file descriptor 1048565 in syscall close() ==22716== Warning: invalid file descriptor 1048566 in syscall close() ==22716== Warning: invalid file descriptor 1048567 in syscall close() ==22716== Use --log-fd= to select an alternative log fd. ==22716== Warning: invalid file descriptor 1048568 in syscall close() ==22716== Warning: invalid file descriptor 1048569 in syscall close() ==22729== Warning: invalid file descriptor 1048564 in syscall close() ==22729== Warning: invalid file descriptor 1048565 in syscall close() ==22729== Warning: invalid file descriptor 1048566 in syscall close() ==22729== Warning: invalid file descriptor 1048567 in syscall close() ==22729== Use --log-fd= to select an alternative log fd. ==22729== Warning: invalid file descriptor 1048568 in syscall close() ==22729== Warning: invalid file descriptor 1048569 in syscall close() ==22745== Warning: invalid file descriptor 1048564 in syscall close() ==22745== Warning: invalid file descriptor 1048565 in syscall close() ==22745== Warning: invalid file descriptor 1048566 in syscall close() ==22745== Warning: invalid file descriptor 1048567 in syscall close() ==22745== Use --log-fd= to select an alternative log fd. ==22745== Warning: invalid file descriptor 1048568 in syscall close() ==22745== Warning: invalid file descriptor 1048569 in syscall close() ==20451== ==20451== HEAP SUMMARY: ==20451== in use at exit: 1,718,308 bytes in 1,321 blocks ==20451== total heap usage: 31,100 allocs, 29,779 frees, 38,088,869 bytes allocated ==20451== ==20451== LEAK SUMMARY: ==20451== definitely lost: 0 bytes in 0 blocks ==20451== indirectly lost: 0 bytes in 0 blocks ==20451== possibly lost: 178,943 bytes in 97 blocks ==20451== still reachable: 1,539,365 bytes in 1,224 blocks ==20451== suppressed: 0 bytes in 0 blocks ==20451== Rerun with --leak-check=full to see details of leaked memory ==20451== ==20451== For counts of detected and suppressed errors, rerun with: -v ==20451== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16349 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.