!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Morse_Shifted_GirifalcoWeizer_1959LowCutoff_Rb__MO_754498969542_003 Supported species : Rb random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Rb (Configuration in file "config-F-Rb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 449.37713590891605 Forces: 1 -7.75830433e+00 -7.13153750e+00 -7.82280170e+00 2 -2.38180999e+00 -3.05124342e+00 -1.34746145e+01 3 -2.54364629e+00 -1.29376053e+01 -2.77054014e+00 4 -1.30639161e+01 -1.50435282e+00 -2.82978186e+00 5 2.00894953e+00 -1.14524266e+01 -9.29526210e+00 6 9.53357689e+00 -2.90581118e+00 -1.07193290e+01 7 9.91134701e+00 -1.20062508e+01 -4.05258840e+00 8 2.59195097e+00 -4.94945652e+00 -3.24734099e+00 9 -9.09621807e+00 1.74377292e+00 -1.22116913e+01 10 -2.52531231e+00 1.21798133e+01 -1.16570323e+01 11 -5.58837228e+00 7.45456976e-01 -4.05468241e+00 12 -1.15660772e+01 1.04298066e+01 -2.26486609e+00 13 3.70727797e+00 1.84518385e+00 -1.55545180e+01 14 8.83511162e+00 8.44941087e+00 -7.95473801e+00 15 1.51958517e+01 2.50179050e+00 -3.22913908e+00 16 2.35576627e+00 1.56825546e+01 -2.09368606e+00 17 -1.12997468e+01 -8.96156014e+00 8.70586536e-01 18 -3.23170795e+00 -3.71601529e+00 3.39864079e+00 19 -9.16247088e-01 -1.10459851e+01 9.49581941e+00 20 -9.84490741e+00 -5.81940217e-01 9.92143525e+00 21 1.83158618e+00 -1.32247060e+01 4.60762017e+00 22 1.46992424e+01 -1.97834185e+00 3.78455977e+00 23 7.46977125e+00 -5.95284073e+00 8.50969788e+00 24 1.97948615e+00 -3.32072055e+00 1.34681095e+01 25 -1.34831300e+01 2.66524600e+00 2.70497642e+00 26 -3.30697196e+00 1.48221730e+01 3.14693525e+00 27 -3.69049518e+00 4.21886274e-01 1.29906800e+01 28 -9.54848776e+00 8.34315525e+00 7.95772965e+00 29 3.38826839e+00 1.92863388e+00 5.69056714e+00 30 1.17059137e+01 1.10001013e+01 3.12563700e+00 31 1.11667928e+01 1.80895095e+00 1.11495154e+01 32 3.46445784e+00 1.01528578e+01 1.24101017e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Rb (Configuration in file "config-T-Rb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 449.37713590891605 Forces: 1 -7.75830433e+00 -7.13153750e+00 -7.82280170e+00 2 -2.38180999e+00 -3.05124342e+00 -1.34746145e+01 3 -2.54364629e+00 -1.29376053e+01 -2.77054014e+00 4 -1.30639161e+01 -1.50435282e+00 -2.82978186e+00 5 2.00894953e+00 -1.14524266e+01 -9.29526210e+00 6 9.53357689e+00 -2.90581118e+00 -1.07193290e+01 7 9.91134701e+00 -1.20062508e+01 -4.05258840e+00 8 2.59195097e+00 -4.94945652e+00 -3.24734099e+00 9 -9.09621807e+00 1.74377292e+00 -1.22116913e+01 10 -2.52531231e+00 1.21798133e+01 -1.16570323e+01 11 -5.58837228e+00 7.45456976e-01 -4.05468241e+00 12 -1.15660772e+01 1.04298066e+01 -2.26486609e+00 13 3.70727797e+00 1.84518385e+00 -1.55545180e+01 14 8.83511162e+00 8.44941087e+00 -7.95473801e+00 15 1.51958517e+01 2.50179050e+00 -3.22913908e+00 16 2.35576627e+00 1.56825546e+01 -2.09368606e+00 17 -1.12997468e+01 -8.96156014e+00 8.70586536e-01 18 -3.23170795e+00 -3.71601529e+00 3.39864079e+00 19 -9.16247088e-01 -1.10459851e+01 9.49581941e+00 20 -9.84490741e+00 -5.81940217e-01 9.92143525e+00 21 1.83158618e+00 -1.32247060e+01 4.60762017e+00 22 1.46992424e+01 -1.97834185e+00 3.78455977e+00 23 7.46977125e+00 -5.95284073e+00 8.50969788e+00 24 1.97948615e+00 -3.32072055e+00 1.34681095e+01 25 -1.34831300e+01 2.66524600e+00 2.70497642e+00 26 -3.30697196e+00 1.48221730e+01 3.14693525e+00 27 -3.69049518e+00 4.21886274e-01 1.29906800e+01 28 -9.54848776e+00 8.34315525e+00 7.95772965e+00 29 3.38826839e+00 1.92863388e+00 5.69056714e+00 30 1.17059137e+01 1.10001013e+01 3.12563700e+00 31 1.11667928e+01 1.80895095e+00 1.11495154e+01 32 3.46445784e+00 1.01528578e+01 1.24101017e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==60060== Memcheck, a memory error detector ==60060== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==60060== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==60060== Command: python runner2.py Morse_Shifted_GirifalcoWeizer_1959LowCutoff_Rb__MO_754498969542_003 ==60060== ==61885== Warning: invalid file descriptor 1048564 in syscall close() ==61885== Warning: invalid file descriptor 1048565 in syscall close() ==61885== Warning: invalid file descriptor 1048566 in syscall close() ==61885== Warning: invalid file descriptor 1048567 in syscall close() ==61885== Use --log-fd= to select an alternative log fd. ==61885== Warning: invalid file descriptor 1048568 in syscall close() ==61885== Warning: invalid file descriptor 1048569 in syscall close() ==61894== Warning: invalid file descriptor 1048564 in syscall close() ==61894== Warning: invalid file descriptor 1048565 in syscall close() ==61894== Warning: invalid file descriptor 1048566 in syscall close() ==61894== Warning: invalid file descriptor 1048567 in syscall close() ==61894== Use --log-fd= to select an alternative log fd. ==61894== Warning: invalid file descriptor 1048568 in syscall close() ==61894== Warning: invalid file descriptor 1048569 in syscall close() ==61965== Warning: invalid file descriptor 1048564 in syscall close() ==61965== Warning: invalid file descriptor 1048565 in syscall close() ==61965== Warning: invalid file descriptor 1048566 in syscall close() ==61965== Warning: invalid file descriptor 1048567 in syscall close() ==61965== Use --log-fd= to select an alternative log fd. ==61965== Warning: invalid file descriptor 1048568 in syscall close() ==61965== Warning: invalid file descriptor 1048569 in syscall close() ==61973== Warning: invalid file descriptor 1048564 in syscall close() ==61973== Warning: invalid file descriptor 1048565 in syscall close() ==61973== Warning: invalid file descriptor 1048566 in syscall close() ==61973== Warning: invalid file descriptor 1048567 in syscall close() ==61973== Use --log-fd= to select an alternative log fd. ==61973== Warning: invalid file descriptor 1048568 in syscall close() ==61973== Warning: invalid file descriptor 1048569 in syscall close() ==61980== Warning: invalid file descriptor 1048564 in syscall close() ==61980== Warning: invalid file descriptor 1048565 in syscall close() ==61980== Warning: invalid file descriptor 1048566 in syscall close() ==61980== Warning: invalid file descriptor 1048567 in syscall close() ==61980== Use --log-fd= to select an alternative log fd. ==61980== Warning: invalid file descriptor 1048568 in syscall close() ==61980== Warning: invalid file descriptor 1048569 in syscall close() ==61987== Warning: invalid file descriptor 1048564 in syscall close() ==61987== Warning: invalid file descriptor 1048565 in syscall close() ==61987== Warning: invalid file descriptor 1048566 in syscall close() ==61987== Warning: invalid file descriptor 1048567 in syscall close() ==61987== Use --log-fd= to select an alternative log fd. ==61987== Warning: invalid file descriptor 1048568 in syscall close() ==61987== Warning: invalid file descriptor 1048569 in syscall close() ==60060== ==60060== HEAP SUMMARY: ==60060== in use at exit: 1,718,292 bytes in 1,321 blocks ==60060== total heap usage: 31,396 allocs, 30,075 frees, 38,295,244 bytes allocated ==60060== ==60060== LEAK SUMMARY: ==60060== definitely lost: 0 bytes in 0 blocks ==60060== indirectly lost: 0 bytes in 0 blocks ==60060== possibly lost: 178,423 bytes in 96 blocks ==60060== still reachable: 1,539,869 bytes in 1,225 blocks ==60060== suppressed: 0 bytes in 0 blocks ==60060== Rerun with --leak-check=full to see details of leaked memory ==60060== ==60060== For counts of detected and suppressed errors, rerun with: -v ==60060== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16378 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.