!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001NISTretabulation_Co__MO_247800397145_000 Supported species : Co random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Co (Configuration in file "config-F-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = -6.803405889729705 Forces: 1 -7.71646631e+00 -6.43725128e+00 -1.00888572e+01 2 -9.59248103e+00 1.77829550e+01 -9.22148396e+00 3 3.99408773e-01 -1.04884274e+01 9.14357712e+00 4 -8.36758048e+00 6.06022419e+00 4.63561295e+00 5 1.62757845e+01 -1.88621508e+01 -4.98270373e+00 6 5.09733789e+00 7.04418648e-01 -6.93552074e+00 7 3.72388110e+00 -2.73932108e+01 -2.76452540e+01 8 -1.08634135e+01 -1.21222270e+01 3.07491994e+00 9 -5.80495534e+00 -8.95959503e+00 -1.36236423e+01 10 -4.74401171e+00 1.38512419e+01 -1.68983917e+01 11 -5.70371583e+00 -7.98556085e+00 2.95660884e+00 12 -7.85848378e+00 1.01720085e+01 7.81533854e+00 13 -1.05120654e+01 -8.45194920e+00 -4.13430079e+01 14 5.90930478e+00 8.10516310e+00 -4.93074012e+00 15 3.57069618e+01 -5.80665399e+00 1.14216927e+01 16 5.43662626e+00 2.79880349e+01 1.35081289e+01 17 -7.17398728e+00 -4.04314311e+00 -6.31456460e+00 18 2.65407103e-01 3.05382416e+00 7.50359353e+00 19 6.56342878e+00 -5.13001209e+00 5.34073672e+00 20 -2.78350050e+00 6.71238082e+00 4.32659691e+00 21 -1.23118069e+01 -9.42251236e+00 5.63941024e+00 22 1.64238397e+01 2.42675578e+01 2.01843026e+01 23 7.53926866e+00 -4.31308310e+00 6.48671245e+00 24 -6.48351055e+00 2.74607701e+00 3.11528393e+00 25 -1.17126882e+01 -7.76417812e+00 -3.96109384e+00 26 -5.34598511e+00 1.77689158e+01 -9.09328733e+00 27 1.61571797e+01 -3.33878927e+01 1.24776902e+01 28 -2.64601994e+01 2.45271836e+01 5.99034926e+00 29 -6.04988193e+00 -1.20088068e+01 5.64126153e+00 30 6.77612898e+00 1.19557655e+01 3.62010185e+00 31 1.49631958e+01 -5.68406182e+00 9.11140059e+00 32 8.24697936e+00 1.25649656e+01 1.30452286e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Co (Configuration in file "config-T-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = -6.803405889729705 Forces: 1 -7.71646631e+00 -6.43725128e+00 -1.00888572e+01 2 -9.59248103e+00 1.77829550e+01 -9.22148396e+00 3 3.99408773e-01 -1.04884274e+01 9.14357712e+00 4 -8.36758048e+00 6.06022419e+00 4.63561295e+00 5 1.62757845e+01 -1.88621508e+01 -4.98270373e+00 6 5.09733789e+00 7.04418648e-01 -6.93552074e+00 7 3.72388110e+00 -2.73932108e+01 -2.76452540e+01 8 -1.08634135e+01 -1.21222270e+01 3.07491994e+00 9 -5.80495534e+00 -8.95959503e+00 -1.36236423e+01 10 -4.74401171e+00 1.38512419e+01 -1.68983917e+01 11 -5.70371583e+00 -7.98556085e+00 2.95660884e+00 12 -7.85848378e+00 1.01720085e+01 7.81533854e+00 13 -1.05120654e+01 -8.45194920e+00 -4.13430079e+01 14 5.90930478e+00 8.10516310e+00 -4.93074012e+00 15 3.57069618e+01 -5.80665399e+00 1.14216927e+01 16 5.43662626e+00 2.79880349e+01 1.35081289e+01 17 -7.17398728e+00 -4.04314311e+00 -6.31456460e+00 18 2.65407103e-01 3.05382416e+00 7.50359353e+00 19 6.56342878e+00 -5.13001209e+00 5.34073672e+00 20 -2.78350050e+00 6.71238082e+00 4.32659691e+00 21 -1.23118069e+01 -9.42251236e+00 5.63941024e+00 22 1.64238397e+01 2.42675578e+01 2.01843026e+01 23 7.53926866e+00 -4.31308310e+00 6.48671245e+00 24 -6.48351055e+00 2.74607701e+00 3.11528393e+00 25 -1.17126882e+01 -7.76417812e+00 -3.96109384e+00 26 -5.34598511e+00 1.77689158e+01 -9.09328733e+00 27 1.61571797e+01 -3.33878927e+01 1.24776902e+01 28 -2.64601994e+01 2.45271836e+01 5.99034926e+00 29 -6.04988193e+00 -1.20088068e+01 5.64126153e+00 30 6.77612898e+00 1.19557655e+01 3.62010185e+00 31 1.49631958e+01 -5.68406182e+00 9.11140059e+00 32 8.24697936e+00 1.25649656e+01 1.30452286e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==88099== Memcheck, a memory error detector ==88099== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==88099== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==88099== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Co__MO_247800397145_000 ==88099== ==89978== Warning: invalid file descriptor 1048564 in syscall close() ==89978== Warning: invalid file descriptor 1048565 in syscall close() ==89978== Warning: invalid file descriptor 1048566 in syscall close() ==89978== Warning: invalid file descriptor 1048567 in syscall close() ==89978== Use --log-fd= to select an alternative log fd. ==89978== Warning: invalid file descriptor 1048568 in syscall close() ==89978== Warning: invalid file descriptor 1048569 in syscall close() ==89989== Warning: invalid file descriptor 1048564 in syscall close() ==89989== Warning: invalid file descriptor 1048565 in syscall close() ==89989== Warning: invalid file descriptor 1048566 in syscall close() ==89989== Warning: invalid file descriptor 1048567 in syscall close() ==89989== Use --log-fd= to select an alternative log fd. ==89989== Warning: invalid file descriptor 1048568 in syscall close() ==89989== Warning: invalid file descriptor 1048569 in syscall close() ==90109== Warning: invalid file descriptor 1048564 in syscall close() ==90109== Warning: invalid file descriptor 1048565 in syscall close() ==90109== Warning: invalid file descriptor 1048566 in syscall close() ==90109== Warning: invalid file descriptor 1048567 in syscall close() ==90109== Use --log-fd= to select an alternative log fd. ==90109== Warning: invalid file descriptor 1048568 in syscall close() ==90109== Warning: invalid file descriptor 1048569 in syscall close() ==90113== Warning: invalid file descriptor 1048564 in syscall close() ==90113== Warning: invalid file descriptor 1048565 in syscall close() ==90113== Warning: invalid file descriptor 1048566 in syscall close() ==90113== Warning: invalid file descriptor 1048567 in syscall close() ==90113== Use --log-fd= to select an alternative log fd. ==90113== Warning: invalid file descriptor 1048568 in syscall close() ==90113== Warning: invalid file descriptor 1048569 in syscall close() ==90121== Warning: invalid file descriptor 1048564 in syscall close() ==90121== Warning: invalid file descriptor 1048565 in syscall close() ==90121== Warning: invalid file descriptor 1048566 in syscall close() ==90121== Warning: invalid file descriptor 1048567 in syscall close() ==90121== Use --log-fd= to select an alternative log fd. ==90121== Warning: invalid file descriptor 1048568 in syscall close() ==90121== Warning: invalid file descriptor 1048569 in syscall close() ==90126== Warning: invalid file descriptor 1048564 in syscall close() ==90126== Warning: invalid file descriptor 1048565 in syscall close() ==90126== Warning: invalid file descriptor 1048566 in syscall close() ==90126== Warning: invalid file descriptor 1048567 in syscall close() ==90126== Use --log-fd= to select an alternative log fd. ==90126== Warning: invalid file descriptor 1048568 in syscall close() ==90126== Warning: invalid file descriptor 1048569 in syscall close() ==88099== ==88099== HEAP SUMMARY: ==88099== in use at exit: 1,718,292 bytes in 1,321 blocks ==88099== total heap usage: 31,120 allocs, 29,799 frees, 40,378,391 bytes allocated ==88099== ==88099== LEAK SUMMARY: ==88099== definitely lost: 0 bytes in 0 blocks ==88099== indirectly lost: 0 bytes in 0 blocks ==88099== possibly lost: 178,943 bytes in 97 blocks ==88099== still reachable: 1,539,349 bytes in 1,224 blocks ==88099== suppressed: 0 bytes in 0 blocks ==88099== Rerun with --leak-check=full to see details of leaked memory ==88099== ==88099== For counts of detected and suppressed errors, rerun with: -v ==88099== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 13369 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.