!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EDIP_JustoBazantKaxiras_1998_Si__MO_958932894036_002 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 = 116.62318225847696 Forces: 1 8.49108234e-02 4.75334141e-01 9.62950201e-01 2 -5.77099396e+00 8.14177978e-01 -1.24050300e+01 3 5.71830505e-01 -1.57169189e+01 -6.32666593e+00 4 -1.47359106e+01 -4.48036177e+00 9.03752107e-01 5 -5.99405936e+00 -9.39262467e+00 -1.30717538e+01 6 1.76640260e+01 -1.96093421e+00 -2.01752108e+01 7 6.29911452e+00 -2.24097181e+01 -1.95489295e-01 8 -3.32287739e+00 -3.57388111e+00 -6.68640865e+00 9 -1.65437251e+01 -8.85539660e+00 -1.82999198e+01 10 9.21929393e+00 1.27556434e+01 -1.16526709e+01 11 -1.52276966e+01 -4.10097213e+00 -1.12745930e+00 12 -2.25139924e+01 1.73647603e+01 -4.51460361e+00 13 1.05346487e+01 -5.34856313e+00 -2.06688932e+01 14 -1.47629556e+00 7.97568638e+00 -4.89224449e+00 15 2.82361538e+01 8.69912158e+00 -8.33783856e+00 16 7.31240928e+00 2.22644244e+01 5.15601540e+00 17 -1.15846736e+01 -8.31558210e+00 -8.18814523e+00 18 -1.96715331e+00 1.52098034e+00 2.32963290e-01 19 9.89842501e-01 -9.76509773e+00 1.39553697e+01 20 -1.55387737e+01 2.89688307e+00 8.19064754e+00 21 3.32973046e-01 -1.32621587e+01 6.98795569e+00 22 2.09945856e+01 4.18926556e+00 5.37058201e+00 23 4.27269686e+00 1.43916679e-01 4.12385855e+00 24 3.72408749e+00 -6.44816631e+00 3.10136347e+01 25 -2.76542935e+01 1.37227098e-01 4.14067912e+00 26 -3.96142344e+00 1.80237305e+01 -1.84622120e+00 27 -2.99551610e+00 -1.03292195e+01 1.54023830e+01 28 -1.17496633e+01 8.46214526e+00 6.91349747e+00 29 1.65996015e+01 -1.82617412e+00 7.54408015e+00 30 1.52730368e+01 1.07021437e+01 -1.46479999e+00 31 1.33404647e+01 -7.79464927e+00 1.66563791e+01 32 5.58737190e+00 1.71549779e+01 1.22986066e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 116.62318225847696 Forces: 1 8.49108234e-02 4.75334141e-01 9.62950201e-01 2 -5.77099396e+00 8.14177978e-01 -1.24050300e+01 3 5.71830505e-01 -1.57169189e+01 -6.32666593e+00 4 -1.47359106e+01 -4.48036177e+00 9.03752107e-01 5 -5.99405936e+00 -9.39262467e+00 -1.30717538e+01 6 1.76640260e+01 -1.96093421e+00 -2.01752108e+01 7 6.29911452e+00 -2.24097181e+01 -1.95489295e-01 8 -3.32287739e+00 -3.57388111e+00 -6.68640865e+00 9 -1.65437251e+01 -8.85539660e+00 -1.82999198e+01 10 9.21929393e+00 1.27556434e+01 -1.16526709e+01 11 -1.52276966e+01 -4.10097213e+00 -1.12745930e+00 12 -2.25139924e+01 1.73647603e+01 -4.51460361e+00 13 1.05346487e+01 -5.34856313e+00 -2.06688932e+01 14 -1.47629556e+00 7.97568638e+00 -4.89224449e+00 15 2.82361538e+01 8.69912158e+00 -8.33783856e+00 16 7.31240928e+00 2.22644244e+01 5.15601540e+00 17 -1.15846736e+01 -8.31558210e+00 -8.18814523e+00 18 -1.96715331e+00 1.52098034e+00 2.32963290e-01 19 9.89842501e-01 -9.76509773e+00 1.39553697e+01 20 -1.55387737e+01 2.89688307e+00 8.19064754e+00 21 3.32973046e-01 -1.32621587e+01 6.98795569e+00 22 2.09945856e+01 4.18926556e+00 5.37058201e+00 23 4.27269686e+00 1.43916679e-01 4.12385855e+00 24 3.72408749e+00 -6.44816631e+00 3.10136347e+01 25 -2.76542935e+01 1.37227098e-01 4.14067912e+00 26 -3.96142344e+00 1.80237305e+01 -1.84622120e+00 27 -2.99551610e+00 -1.03292195e+01 1.54023830e+01 28 -1.17496633e+01 8.46214526e+00 6.91349747e+00 29 1.65996015e+01 -1.82617412e+00 7.54408015e+00 30 1.52730368e+01 1.07021437e+01 -1.46479999e+00 31 1.33404647e+01 -7.79464927e+00 1.66563791e+01 32 5.58737190e+00 1.71549779e+01 1.22986066e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==16363== Memcheck, a memory error detector ==16363== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==16363== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==16363== Command: python runner2.py EDIP_JustoBazantKaxiras_1998_Si__MO_958932894036_002 ==16363== ==18202== Warning: invalid file descriptor 1048564 in syscall close() ==18202== Warning: invalid file descriptor 1048565 in syscall close() ==18202== Warning: invalid file descriptor 1048566 in syscall close() ==18202== Warning: invalid file descriptor 1048567 in syscall close() ==18202== Use --log-fd= to select an alternative log fd. ==18202== Warning: invalid file descriptor 1048568 in syscall close() ==18202== Warning: invalid file descriptor 1048569 in syscall close() ==18212== Warning: invalid file descriptor 1048564 in syscall close() ==18212== Warning: invalid file descriptor 1048565 in syscall close() ==18212== Warning: invalid file descriptor 1048566 in syscall close() ==18212== Warning: invalid file descriptor 1048567 in syscall close() ==18212== Use --log-fd= to select an alternative log fd. ==18212== Warning: invalid file descriptor 1048568 in syscall close() ==18212== Warning: invalid file descriptor 1048569 in syscall close() ==18284== Warning: invalid file descriptor 1048564 in syscall close() ==18284== Warning: invalid file descriptor 1048565 in syscall close() ==18284== Warning: invalid file descriptor 1048566 in syscall close() ==18284== Warning: invalid file descriptor 1048567 in syscall close() ==18284== Use --log-fd= to select an alternative log fd. ==18284== Warning: invalid file descriptor 1048568 in syscall close() ==18284== Warning: invalid file descriptor 1048569 in syscall close() ==18285== Warning: invalid file descriptor 1048564 in syscall close() ==18285== Warning: invalid file descriptor 1048565 in syscall close() ==18285== Warning: invalid file descriptor 1048566 in syscall close() ==18285== Warning: invalid file descriptor 1048567 in syscall close() ==18285== Use --log-fd= to select an alternative log fd. ==18285== Warning: invalid file descriptor 1048568 in syscall close() ==18285== Warning: invalid file descriptor 1048569 in syscall close() ==18287== Warning: invalid file descriptor 1048564 in syscall close() ==18287== Warning: invalid file descriptor 1048565 in syscall close() ==18287== Warning: invalid file descriptor 1048566 in syscall close() ==18287== Warning: invalid file descriptor 1048567 in syscall close() ==18287== Use --log-fd= to select an alternative log fd. ==18287== Warning: invalid file descriptor 1048568 in syscall close() ==18287== Warning: invalid file descriptor 1048569 in syscall close() ==18301== Warning: invalid file descriptor 1048564 in syscall close() ==18301== Warning: invalid file descriptor 1048565 in syscall close() ==18301== Warning: invalid file descriptor 1048566 in syscall close() ==18301== Warning: invalid file descriptor 1048567 in syscall close() ==18301== Use --log-fd= to select an alternative log fd. ==18301== Warning: invalid file descriptor 1048568 in syscall close() ==18301== Warning: invalid file descriptor 1048569 in syscall close() ==16363== ==16363== HEAP SUMMARY: ==16363== in use at exit: 1,718,292 bytes in 1,321 blocks ==16363== total heap usage: 31,782 allocs, 30,461 frees, 38,311,513 bytes allocated ==16363== ==16363== LEAK SUMMARY: ==16363== definitely lost: 0 bytes in 0 blocks ==16363== indirectly lost: 0 bytes in 0 blocks ==16363== possibly lost: 178,943 bytes in 97 blocks ==16363== still reachable: 1,539,349 bytes in 1,224 blocks ==16363== suppressed: 0 bytes in 0 blocks ==16363== Rerun with --leak-check=full to see details of leaked memory ==16363== ==16363== For counts of detected and suppressed errors, rerun with: -v ==16363== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11290 from 614) ================================================================================ 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.