!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouJohnsonWadley_2004_Zr__MO_103270551167_005 Supported species : Zr random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Zr (Configuration in file "config-F-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 30.614660913355216 Forces: 1 -5.89565254e+00 -1.03833165e+01 -1.11081681e+01 2 -5.03116556e+00 6.74313625e+00 -1.06859856e+01 3 6.76901363e+00 -1.89492711e+01 -8.04432243e+00 4 -1.43402490e+01 6.33074407e+00 2.29035516e-01 5 -1.32009595e+00 -1.80707080e+01 -6.64668516e+00 6 1.11393336e+01 7.48453416e+00 -1.23718618e+01 7 1.33924420e+01 -3.24938471e+01 -2.08183632e+01 8 -1.53778484e+01 -1.18677356e+01 -2.49779354e+00 9 -1.19464811e+01 -8.41083264e+00 -1.90807637e+01 10 -4.93790313e+00 2.12405750e+01 -2.25432735e+01 11 -4.49182627e+00 -1.34519634e+01 3.57611025e+00 12 -1.31888481e+01 1.86705970e+01 2.50808154e+00 13 -5.94546529e+00 -1.50469764e+01 -4.43099195e+01 14 1.00449623e+01 1.24752191e+01 -8.49471656e+00 15 4.14370208e+01 -5.11383178e+00 8.43800989e+00 16 7.02875495e+00 3.55192577e+01 1.31422167e+01 17 -2.07040222e+01 -1.37216378e+01 -3.09783971e+00 18 1.16291874e+01 1.43682624e+01 1.03056619e+01 19 4.43331952e+00 -1.56907590e+01 9.39063061e+00 20 -8.29307870e+00 9.17028132e+00 9.97973621e+00 21 -1.31409830e+01 -1.42639140e+01 7.99087127e+00 22 2.24765184e+01 2.46838244e+01 1.69516783e+01 23 6.46877447e+00 -4.54444568e+00 1.30507071e+01 24 3.00379438e+00 7.02871846e+00 7.33179612e+00 25 -1.75944857e+01 -6.49492104e+00 9.94766476e+00 26 -7.31451579e+00 2.43613845e+01 -9.54334615e+00 27 9.30366552e+00 -3.25173490e+01 1.48855827e+01 28 -2.67832614e+01 2.27786826e+01 6.85862425e+00 29 -8.28278538e+00 -1.32133174e+01 1.01328506e+01 30 1.13027473e+01 1.77321884e+01 -1.31642912e+00 31 1.70564680e+01 -1.26377265e+01 1.70914416e+01 32 9.10266501e+00 1.82851477e+01 1.87487688e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zr (Configuration in file "config-T-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 30.614660913355216 Forces: 1 -5.89565254e+00 -1.03833165e+01 -1.11081681e+01 2 -5.03116556e+00 6.74313625e+00 -1.06859856e+01 3 6.76901363e+00 -1.89492711e+01 -8.04432243e+00 4 -1.43402490e+01 6.33074407e+00 2.29035516e-01 5 -1.32009595e+00 -1.80707080e+01 -6.64668516e+00 6 1.11393336e+01 7.48453416e+00 -1.23718618e+01 7 1.33924420e+01 -3.24938471e+01 -2.08183632e+01 8 -1.53778484e+01 -1.18677356e+01 -2.49779354e+00 9 -1.19464811e+01 -8.41083264e+00 -1.90807637e+01 10 -4.93790313e+00 2.12405750e+01 -2.25432735e+01 11 -4.49182627e+00 -1.34519634e+01 3.57611025e+00 12 -1.31888481e+01 1.86705970e+01 2.50808154e+00 13 -5.94546529e+00 -1.50469764e+01 -4.43099195e+01 14 1.00449623e+01 1.24752191e+01 -8.49471656e+00 15 4.14370208e+01 -5.11383178e+00 8.43800989e+00 16 7.02875495e+00 3.55192577e+01 1.31422167e+01 17 -2.07040222e+01 -1.37216378e+01 -3.09783971e+00 18 1.16291874e+01 1.43682624e+01 1.03056619e+01 19 4.43331952e+00 -1.56907590e+01 9.39063061e+00 20 -8.29307870e+00 9.17028132e+00 9.97973621e+00 21 -1.31409830e+01 -1.42639140e+01 7.99087127e+00 22 2.24765184e+01 2.46838244e+01 1.69516783e+01 23 6.46877447e+00 -4.54444568e+00 1.30507071e+01 24 3.00379438e+00 7.02871846e+00 7.33179612e+00 25 -1.75944857e+01 -6.49492104e+00 9.94766476e+00 26 -7.31451579e+00 2.43613845e+01 -9.54334615e+00 27 9.30366552e+00 -3.25173490e+01 1.48855827e+01 28 -2.67832614e+01 2.27786826e+01 6.85862425e+00 29 -8.28278538e+00 -1.32133174e+01 1.01328506e+01 30 1.13027473e+01 1.77321884e+01 -1.31642912e+00 31 1.70564680e+01 -1.26377265e+01 1.70914416e+01 32 9.10266501e+00 1.82851477e+01 1.87487688e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==85631== Memcheck, a memory error detector ==85631== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==85631== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==85631== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004_Zr__MO_103270551167_005 ==85631== ==86801== Warning: invalid file descriptor 1048564 in syscall close() ==86801== Warning: invalid file descriptor 1048565 in syscall close() ==86801== Warning: invalid file descriptor 1048566 in syscall close() ==86801== Warning: invalid file descriptor 1048567 in syscall close() ==86801== Use --log-fd= to select an alternative log fd. ==86801== Warning: invalid file descriptor 1048568 in syscall close() ==86801== Warning: invalid file descriptor 1048569 in syscall close() ==86802== Warning: invalid file descriptor 1048564 in syscall close() ==86802== Warning: invalid file descriptor 1048565 in syscall close() ==86802== Warning: invalid file descriptor 1048566 in syscall close() ==86802== Warning: invalid file descriptor 1048567 in syscall close() ==86802== Use --log-fd= to select an alternative log fd. ==86802== Warning: invalid file descriptor 1048568 in syscall close() ==86802== Warning: invalid file descriptor 1048569 in syscall close() ==86805== Warning: invalid file descriptor 1048564 in syscall close() ==86805== Warning: invalid file descriptor 1048565 in syscall close() ==86805== Warning: invalid file descriptor 1048566 in syscall close() ==86805== Warning: invalid file descriptor 1048567 in syscall close() ==86805== Use --log-fd= to select an alternative log fd. ==86805== Warning: invalid file descriptor 1048568 in syscall close() ==86805== Warning: invalid file descriptor 1048569 in syscall close() ==86806== Warning: invalid file descriptor 1048564 in syscall close() ==86806== Warning: invalid file descriptor 1048565 in syscall close() ==86806== Warning: invalid file descriptor 1048566 in syscall close() ==86806== Warning: invalid file descriptor 1048567 in syscall close() ==86806== Use --log-fd= to select an alternative log fd. ==86806== Warning: invalid file descriptor 1048568 in syscall close() ==86806== Warning: invalid file descriptor 1048569 in syscall close() ==86807== Warning: invalid file descriptor 1048564 in syscall close() ==86807== Warning: invalid file descriptor 1048565 in syscall close() ==86807== Warning: invalid file descriptor 1048566 in syscall close() ==86807== Warning: invalid file descriptor 1048567 in syscall close() ==86807== Use --log-fd= to select an alternative log fd. ==86807== Warning: invalid file descriptor 1048568 in syscall close() ==86807== Warning: invalid file descriptor 1048569 in syscall close() ==86808== Warning: invalid file descriptor 1048564 in syscall close() ==86808== Warning: invalid file descriptor 1048565 in syscall close() ==86808== Warning: invalid file descriptor 1048566 in syscall close() ==86808== Warning: invalid file descriptor 1048567 in syscall close() ==86808== Use --log-fd= to select an alternative log fd. ==86808== Warning: invalid file descriptor 1048568 in syscall close() ==86808== Warning: invalid file descriptor 1048569 in syscall close() ==85631== ==85631== HEAP SUMMARY: ==85631== in use at exit: 1,718,292 bytes in 1,321 blocks ==85631== total heap usage: 33,153 allocs, 31,832 frees, 44,915,363 bytes allocated ==85631== ==85631== LEAK SUMMARY: ==85631== definitely lost: 0 bytes in 0 blocks ==85631== indirectly lost: 0 bytes in 0 blocks ==85631== possibly lost: 178,943 bytes in 97 blocks ==85631== still reachable: 1,539,349 bytes in 1,224 blocks ==85631== suppressed: 0 bytes in 0 blocks ==85631== Rerun with --leak-check=full to see details of leaked memory ==85631== ==85631== For counts of detected and suppressed errors, rerun with: -v ==85631== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16355 from 601) ================================================================================ 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.