!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : LJ_Shifted_Bernardes_1958LowCutoff_Ne__MO_466741694288_003 Supported species : Ne random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ne (Configuration in file "config-F-Ne.xyz") ----------------------------------------------------------------------------------------------------- Energy = 138.47044318813616 Forces: 1 -1.46475282e+01 -4.29443283e+01 -5.77193888e+01 2 -1.54363398e-01 7.56773256e+00 -7.02042987e+00 3 2.57037788e+01 -2.25890183e+01 8.64920569e+00 4 -1.35373659e+01 6.17850255e+01 4.50029444e+01 5 2.67273353e-01 -8.29859232e+00 -5.36478444e+00 6 2.12902820e+00 1.45254384e+00 -3.99314972e+00 7 -6.94669128e+00 -5.65649754e+01 -5.84429716e+01 8 -1.94875927e+01 -2.02836719e+01 4.38046359e+00 9 -5.14222386e-01 -2.71551329e+00 -3.54858072e+00 10 -1.20899397e+01 5.68038461e+00 -1.48263789e+01 11 -1.72404067e+01 -1.86483483e+01 -4.64197952e-01 12 -4.63924462e+00 1.33077767e+01 -6.50500556e+00 13 -3.02176791e+01 -1.35438265e+01 -5.87670920e+01 14 7.83311157e+00 8.39398426e+00 -3.26135587e+00 15 5.58162644e+01 1.07197185e+01 3.49046800e+01 16 1.74098162e+01 3.72792984e+01 2.43552317e+01 17 -1.08663763e+01 -4.67787216e+00 5.24425638e+00 18 -1.95482782e-01 2.04012036e+02 -1.92743897e+02 19 6.43810224e+00 -2.03814258e+02 1.93576559e+02 20 -4.59208892e+00 2.70107981e+00 3.17466285e+00 21 -1.59291563e+01 -1.01454520e+01 -8.92022131e-01 22 2.99669217e+01 5.82459994e+01 4.51921560e+01 23 2.51962348e+01 -1.28580156e+01 1.82876660e+01 24 -1.70691854e+01 1.27302308e+01 5.99810169e+00 25 -7.95595026e+00 -1.36448087e+01 1.21995579e+01 26 6.34445162e-01 1.41107400e+01 -9.26905762e+00 27 5.27131019e+01 -6.76862628e+01 1.18802101e+01 28 -6.64569392e+01 5.70241447e+01 -7.07494633e-02 29 -2.62850707e+01 -2.58746638e+01 -3.67223441e+01 30 1.24260283e+01 1.52137721e+01 -4.64200482e+00 31 3.02757739e+01 -1.15067870e+01 2.40468790e+01 32 2.01540331e+00 2.55719274e+01 2.73608364e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ne (Configuration in file "config-T-Ne.xyz") ----------------------------------------------------------------------------------------------------- Energy = 138.47044318813616 Forces: 1 -1.46475282e+01 -4.29443283e+01 -5.77193888e+01 2 -1.54363398e-01 7.56773256e+00 -7.02042987e+00 3 2.57037788e+01 -2.25890183e+01 8.64920569e+00 4 -1.35373659e+01 6.17850255e+01 4.50029444e+01 5 2.67273353e-01 -8.29859232e+00 -5.36478444e+00 6 2.12902820e+00 1.45254384e+00 -3.99314972e+00 7 -6.94669128e+00 -5.65649754e+01 -5.84429716e+01 8 -1.94875927e+01 -2.02836719e+01 4.38046359e+00 9 -5.14222386e-01 -2.71551329e+00 -3.54858072e+00 10 -1.20899397e+01 5.68038461e+00 -1.48263789e+01 11 -1.72404067e+01 -1.86483483e+01 -4.64197952e-01 12 -4.63924462e+00 1.33077767e+01 -6.50500556e+00 13 -3.02176791e+01 -1.35438265e+01 -5.87670920e+01 14 7.83311157e+00 8.39398426e+00 -3.26135587e+00 15 5.58162644e+01 1.07197185e+01 3.49046800e+01 16 1.74098162e+01 3.72792984e+01 2.43552317e+01 17 -1.08663763e+01 -4.67787216e+00 5.24425638e+00 18 -1.95482782e-01 2.04012036e+02 -1.92743897e+02 19 6.43810224e+00 -2.03814258e+02 1.93576559e+02 20 -4.59208892e+00 2.70107981e+00 3.17466285e+00 21 -1.59291563e+01 -1.01454520e+01 -8.92022131e-01 22 2.99669217e+01 5.82459994e+01 4.51921560e+01 23 2.51962348e+01 -1.28580156e+01 1.82876660e+01 24 -1.70691854e+01 1.27302308e+01 5.99810169e+00 25 -7.95595026e+00 -1.36448087e+01 1.21995579e+01 26 6.34445162e-01 1.41107400e+01 -9.26905762e+00 27 5.27131019e+01 -6.76862628e+01 1.18802101e+01 28 -6.64569392e+01 5.70241447e+01 -7.07494633e-02 29 -2.62850707e+01 -2.58746638e+01 -3.67223441e+01 30 1.24260283e+01 1.52137721e+01 -4.64200482e+00 31 3.02757739e+01 -1.15067870e+01 2.40468790e+01 32 2.01540331e+00 2.55719274e+01 2.73608364e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==30886== Memcheck, a memory error detector ==30886== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==30886== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==30886== Command: python runner2.py LJ_Shifted_Bernardes_1958LowCutoff_Ne__MO_466741694288_003 ==30886== ==32051== Warning: invalid file descriptor 1048564 in syscall close() ==32051== Warning: invalid file descriptor 1048565 in syscall close() ==32051== Warning: invalid file descriptor 1048566 in syscall close() ==32051== Warning: invalid file descriptor 1048567 in syscall close() ==32051== Use --log-fd= to select an alternative log fd. ==32051== Warning: invalid file descriptor 1048568 in syscall close() ==32051== Warning: invalid file descriptor 1048569 in syscall close() ==32052== Warning: invalid file descriptor 1048564 in syscall close() ==32052== Warning: invalid file descriptor 1048565 in syscall close() ==32052== Warning: invalid file descriptor 1048566 in syscall close() ==32052== Warning: invalid file descriptor 1048567 in syscall close() ==32052== Use --log-fd= to select an alternative log fd. ==32052== Warning: invalid file descriptor 1048568 in syscall close() ==32052== Warning: invalid file descriptor 1048569 in syscall close() ==32057== Warning: invalid file descriptor 1048564 in syscall close() ==32057== Warning: invalid file descriptor 1048565 in syscall close() ==32057== Warning: invalid file descriptor 1048566 in syscall close() ==32057== Warning: invalid file descriptor 1048567 in syscall close() ==32057== Use --log-fd= to select an alternative log fd. ==32057== Warning: invalid file descriptor 1048568 in syscall close() ==32057== Warning: invalid file descriptor 1048569 in syscall close() ==32058== Warning: invalid file descriptor 1048564 in syscall close() ==32058== Warning: invalid file descriptor 1048565 in syscall close() ==32058== Warning: invalid file descriptor 1048566 in syscall close() ==32058== Warning: invalid file descriptor 1048567 in syscall close() ==32058== Use --log-fd= to select an alternative log fd. ==32058== Warning: invalid file descriptor 1048568 in syscall close() ==32058== Warning: invalid file descriptor 1048569 in syscall close() ==32059== Warning: invalid file descriptor 1048564 in syscall close() ==32059== Warning: invalid file descriptor 1048565 in syscall close() ==32059== Warning: invalid file descriptor 1048566 in syscall close() ==32059== Warning: invalid file descriptor 1048567 in syscall close() ==32059== Use --log-fd= to select an alternative log fd. ==32059== Warning: invalid file descriptor 1048568 in syscall close() ==32059== Warning: invalid file descriptor 1048569 in syscall close() ==32060== Warning: invalid file descriptor 1048564 in syscall close() ==32060== Warning: invalid file descriptor 1048565 in syscall close() ==32060== Warning: invalid file descriptor 1048566 in syscall close() ==32060== Warning: invalid file descriptor 1048567 in syscall close() ==32060== Use --log-fd= to select an alternative log fd. ==32060== Warning: invalid file descriptor 1048568 in syscall close() ==32060== Warning: invalid file descriptor 1048569 in syscall close() ==30886== ==30886== HEAP SUMMARY: ==30886== in use at exit: 1,718,292 bytes in 1,321 blocks ==30886== total heap usage: 30,945 allocs, 29,624 frees, 38,087,104 bytes allocated ==30886== ==30886== LEAK SUMMARY: ==30886== definitely lost: 0 bytes in 0 blocks ==30886== indirectly lost: 0 bytes in 0 blocks ==30886== possibly lost: 178,943 bytes in 97 blocks ==30886== still reachable: 1,539,349 bytes in 1,224 blocks ==30886== suppressed: 0 bytes in 0 blocks ==30886== Rerun with --leak-check=full to see details of leaked memory ==30886== ==30886== For counts of detected and suppressed errors, rerun with: -v ==30886== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16342 from 602) ================================================================================ 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.