!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AcklandTichyVitek_1987_Ni__MO_977363131043_005 Supported species : Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -69.5378601467148 Forces: 1 -1.18945546e+00 -2.81076452e+00 -3.17033844e+00 2 -1.83389818e+00 4.40844108e+00 -2.97553374e+00 3 1.42917281e+00 -3.15382631e+00 5.79645225e-01 4 -2.01850629e+00 1.80238651e+00 1.55305912e+00 5 3.37362328e+00 -5.17228295e+00 -1.22901339e+00 6 9.01113370e-01 1.25215377e+00 -2.16469487e+00 7 2.64427186e+00 -7.20845495e+00 -5.76030570e+00 8 -5.34822112e+00 -3.05435639e+00 -3.87416710e-01 9 -4.34024019e+00 -3.55711179e+00 -6.21582046e+00 10 7.81096818e-01 7.17517136e+00 -6.08150001e+00 11 -4.18314881e-01 -5.85406632e+00 3.62134587e+00 12 -4.08579013e+00 5.78506348e+00 1.76943731e+00 13 -8.66569618e-01 -4.20257285e+00 -1.10070265e+01 14 2.78624734e+00 3.57748396e+00 -2.18583819e+00 15 9.90291574e+00 -3.68468539e+00 1.27004438e+00 16 4.28892700e-01 9.31573729e+00 2.90019886e+00 17 -5.84908463e+00 -3.04473777e+00 -2.10176335e+00 18 2.62619662e+00 5.78065251e+00 -7.88270288e-01 19 3.45043284e+00 -4.07881906e+00 3.75082164e+00 20 -2.36422455e+00 3.92653717e+00 2.82669886e+00 21 -4.77306126e+00 -4.01012443e+00 1.22911135e+00 22 5.99045274e+00 6.01578268e+00 4.94300326e+00 23 2.01513330e+00 -1.05289162e+00 2.12543758e+00 24 -1.81736722e+00 7.02261555e-01 1.53327519e+00 25 -3.29995928e+00 -3.40351018e+00 3.64780759e+00 26 -1.90698976e+00 6.46382303e+00 -3.92300991e+00 27 1.71066833e+00 -9.77056727e+00 3.34583818e+00 28 -6.24371257e+00 4.86754298e+00 1.36317991e+00 29 -3.34391744e+00 -4.44066501e+00 2.16131154e+00 30 3.29014636e+00 5.31925299e+00 9.88538166e-01 31 5.90209448e+00 -2.77187094e+00 3.30333811e+00 32 2.46685401e+00 4.87901742e+00 5.07843943e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -69.5378601467148 Forces: 1 -1.18945546e+00 -2.81076452e+00 -3.17033844e+00 2 -1.83389818e+00 4.40844108e+00 -2.97553374e+00 3 1.42917281e+00 -3.15382631e+00 5.79645225e-01 4 -2.01850629e+00 1.80238651e+00 1.55305912e+00 5 3.37362328e+00 -5.17228295e+00 -1.22901339e+00 6 9.01113370e-01 1.25215377e+00 -2.16469487e+00 7 2.64427186e+00 -7.20845495e+00 -5.76030570e+00 8 -5.34822112e+00 -3.05435639e+00 -3.87416710e-01 9 -4.34024019e+00 -3.55711179e+00 -6.21582046e+00 10 7.81096818e-01 7.17517136e+00 -6.08150001e+00 11 -4.18314881e-01 -5.85406632e+00 3.62134587e+00 12 -4.08579013e+00 5.78506348e+00 1.76943731e+00 13 -8.66569618e-01 -4.20257285e+00 -1.10070265e+01 14 2.78624734e+00 3.57748396e+00 -2.18583819e+00 15 9.90291574e+00 -3.68468539e+00 1.27004438e+00 16 4.28892700e-01 9.31573729e+00 2.90019886e+00 17 -5.84908463e+00 -3.04473777e+00 -2.10176335e+00 18 2.62619662e+00 5.78065251e+00 -7.88270288e-01 19 3.45043284e+00 -4.07881906e+00 3.75082164e+00 20 -2.36422455e+00 3.92653717e+00 2.82669886e+00 21 -4.77306126e+00 -4.01012443e+00 1.22911135e+00 22 5.99045274e+00 6.01578268e+00 4.94300326e+00 23 2.01513330e+00 -1.05289162e+00 2.12543758e+00 24 -1.81736722e+00 7.02261555e-01 1.53327519e+00 25 -3.29995928e+00 -3.40351018e+00 3.64780759e+00 26 -1.90698976e+00 6.46382303e+00 -3.92300991e+00 27 1.71066833e+00 -9.77056727e+00 3.34583818e+00 28 -6.24371257e+00 4.86754298e+00 1.36317991e+00 29 -3.34391744e+00 -4.44066501e+00 2.16131154e+00 30 3.29014636e+00 5.31925299e+00 9.88538166e-01 31 5.90209448e+00 -2.77187094e+00 3.30333811e+00 32 2.46685401e+00 4.87901742e+00 5.07843943e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==6813== Memcheck, a memory error detector ==6813== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==6813== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==6813== Command: python runner2.py EAM_Dynamo_AcklandTichyVitek_1987_Ni__MO_977363131043_005 ==6813== ==7964== Warning: invalid file descriptor 1048564 in syscall close() ==7964== Warning: invalid file descriptor 1048565 in syscall close() ==7964== Warning: invalid file descriptor 1048566 in syscall close() ==7964== Warning: invalid file descriptor 1048567 in syscall close() ==7964== Use --log-fd= to select an alternative log fd. ==7964== Warning: invalid file descriptor 1048568 in syscall close() ==7964== Warning: invalid file descriptor 1048569 in syscall close() ==7965== Warning: invalid file descriptor 1048564 in syscall close() ==7965== Warning: invalid file descriptor 1048565 in syscall close() ==7965== Warning: invalid file descriptor 1048566 in syscall close() ==7965== Warning: invalid file descriptor 1048567 in syscall close() ==7965== Use --log-fd= to select an alternative log fd. ==7965== Warning: invalid file descriptor 1048568 in syscall close() ==7965== Warning: invalid file descriptor 1048569 in syscall close() ==7977== Warning: invalid file descriptor 1048564 in syscall close() ==7977== Warning: invalid file descriptor 1048565 in syscall close() ==7977== Warning: invalid file descriptor 1048566 in syscall close() ==7977== Warning: invalid file descriptor 1048567 in syscall close() ==7977== Use --log-fd= to select an alternative log fd. ==7977== Warning: invalid file descriptor 1048568 in syscall close() ==7977== Warning: invalid file descriptor 1048569 in syscall close() ==7979== Warning: invalid file descriptor 1048564 in syscall close() ==7979== Warning: invalid file descriptor 1048565 in syscall close() ==7979== Warning: invalid file descriptor 1048566 in syscall close() ==7979== Warning: invalid file descriptor 1048567 in syscall close() ==7979== Use --log-fd= to select an alternative log fd. ==7979== Warning: invalid file descriptor 1048568 in syscall close() ==7979== Warning: invalid file descriptor 1048569 in syscall close() ==7980== Warning: invalid file descriptor 1048564 in syscall close() ==7980== Warning: invalid file descriptor 1048565 in syscall close() ==7980== Warning: invalid file descriptor 1048566 in syscall close() ==7980== Warning: invalid file descriptor 1048567 in syscall close() ==7980== Use --log-fd= to select an alternative log fd. ==7980== Warning: invalid file descriptor 1048568 in syscall close() ==7980== Warning: invalid file descriptor 1048569 in syscall close() ==7981== Warning: invalid file descriptor 1048564 in syscall close() ==7981== Warning: invalid file descriptor 1048565 in syscall close() ==7981== Warning: invalid file descriptor 1048566 in syscall close() ==7981== Warning: invalid file descriptor 1048567 in syscall close() ==7981== Use --log-fd= to select an alternative log fd. ==7981== Warning: invalid file descriptor 1048568 in syscall close() ==7981== Warning: invalid file descriptor 1048569 in syscall close() ==6813== ==6813== HEAP SUMMARY: ==6813== in use at exit: 1,718,308 bytes in 1,321 blocks ==6813== total heap usage: 31,217 allocs, 29,896 frees, 47,299,896 bytes allocated ==6813== ==6813== LEAK SUMMARY: ==6813== definitely lost: 0 bytes in 0 blocks ==6813== indirectly lost: 0 bytes in 0 blocks ==6813== possibly lost: 178,943 bytes in 97 blocks ==6813== still reachable: 1,539,365 bytes in 1,224 blocks ==6813== suppressed: 0 bytes in 0 blocks ==6813== Rerun with --leak-check=full to see details of leaked memory ==6813== ==6813== For counts of detected and suppressed errors, rerun with: -v ==6813== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16326 from 599) ================================================================================ 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.