!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Sim_LAMMPS_ModifiedTersoff_KumagaiIzumiHara_2007_Si__SM_773333226968_000 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 = 120.68774869352806 Forces: 1 -1.28018960e+01 -1.31564448e+01 -1.93779045e+01 2 -1.31189907e+01 2.09294645e+01 -1.99795272e+01 3 1.00575968e-01 -2.12353277e+01 1.12355842e+01 4 -1.49666818e+01 1.11651439e+01 5.59780859e+00 5 1.60611905e+01 -2.87008690e+01 -1.36707925e+01 6 1.25341422e+01 3.22067937e+00 -1.66812240e+01 7 1.18722861e+01 -4.91571474e+01 -3.98627257e+01 8 -2.46242077e+01 -2.83914280e+01 3.46594328e+00 9 -7.01876788e+00 -2.31237545e+01 -2.79395467e+01 10 -6.59907819e+00 2.32725934e+01 -3.01202854e+01 11 -2.56180641e-02 -1.79063964e+01 -2.71599730e+01 12 -2.15440745e+01 2.70460691e+01 1.69400745e+01 13 -1.68471905e+01 -1.02690663e+01 -7.52795437e+01 14 1.34267288e+01 1.44173531e+01 -8.88419314e+00 15 7.29587916e+01 3.62970916e+00 1.96807928e+01 16 1.14400351e+01 5.53504969e+01 1.83619188e+01 17 -1.63642532e+01 -9.85846364e+00 -2.56077484e+00 18 4.92270572e+00 3.80251141e-01 9.60933863e+00 19 4.95227532e+00 -1.36049468e+01 1.15436365e+01 20 -7.61576609e+00 8.82912472e+00 8.01443412e+00 21 -2.11536386e+01 -2.34774710e+01 7.75721823e+00 22 3.49646911e+01 3.85413067e+01 3.64180545e+01 23 1.45638976e+01 -7.00145123e+00 1.18180206e+01 24 -6.46460705e+00 1.17476900e+01 1.32062687e+01 25 -4.51173229e+01 -2.53037822e+00 1.80173311e+01 26 -9.85888791e+00 4.16296737e+01 -1.03921835e+01 27 1.93017019e+01 -5.54296421e+01 2.48173644e+01 28 -4.63629783e+01 3.81726228e+01 9.36997240e+00 29 -1.81618668e+00 -2.38345190e+01 1.72293179e+01 30 1.58925532e+01 2.02840056e+01 -1.74509671e+00 31 2.42188931e+01 -1.40644905e+01 2.24696699e+01 32 1.50896783e+01 2.31256124e+01 2.81010218e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 120.68774869352806 Forces: 1 -1.28018960e+01 -1.31564448e+01 -1.93779045e+01 2 -1.31189907e+01 2.09294645e+01 -1.99795272e+01 3 1.00575968e-01 -2.12353277e+01 1.12355842e+01 4 -1.49666818e+01 1.11651439e+01 5.59780859e+00 5 1.60611905e+01 -2.87008690e+01 -1.36707925e+01 6 1.25341422e+01 3.22067937e+00 -1.66812240e+01 7 1.18722861e+01 -4.91571474e+01 -3.98627257e+01 8 -2.46242077e+01 -2.83914280e+01 3.46594328e+00 9 -7.01876788e+00 -2.31237545e+01 -2.79395467e+01 10 -6.59907819e+00 2.32725934e+01 -3.01202854e+01 11 -2.56180641e-02 -1.79063964e+01 -2.71599730e+01 12 -2.15440745e+01 2.70460691e+01 1.69400745e+01 13 -1.68471905e+01 -1.02690663e+01 -7.52795437e+01 14 1.34267288e+01 1.44173531e+01 -8.88419314e+00 15 7.29587916e+01 3.62970916e+00 1.96807928e+01 16 1.14400351e+01 5.53504969e+01 1.83619188e+01 17 -1.63642532e+01 -9.85846364e+00 -2.56077484e+00 18 4.92270572e+00 3.80251141e-01 9.60933863e+00 19 4.95227532e+00 -1.36049468e+01 1.15436365e+01 20 -7.61576609e+00 8.82912472e+00 8.01443412e+00 21 -2.11536386e+01 -2.34774710e+01 7.75721823e+00 22 3.49646911e+01 3.85413067e+01 3.64180545e+01 23 1.45638976e+01 -7.00145123e+00 1.18180206e+01 24 -6.46460705e+00 1.17476900e+01 1.32062687e+01 25 -4.51173229e+01 -2.53037822e+00 1.80173311e+01 26 -9.85888791e+00 4.16296737e+01 -1.03921835e+01 27 1.93017019e+01 -5.54296421e+01 2.48173644e+01 28 -4.63629783e+01 3.81726228e+01 9.36997240e+00 29 -1.81618668e+00 -2.38345190e+01 1.72293179e+01 30 1.58925532e+01 2.02840056e+01 -1.74509671e+00 31 2.42188931e+01 -1.40644905e+01 2.24696699e+01 32 1.50896783e+01 2.31256124e+01 2.81010218e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==69862== Memcheck, a memory error detector ==69862== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==69862== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==69862== Command: python runner2.py Sim_LAMMPS_ModifiedTersoff_KumagaiIzumiHara_2007_Si__SM_773333226968_000 ==69862== ==71088== Warning: invalid file descriptor 1048564 in syscall close() ==71088== Warning: invalid file descriptor 1048565 in syscall close() ==71088== Warning: invalid file descriptor 1048566 in syscall close() ==71088== Warning: invalid file descriptor 1048567 in syscall close() ==71088== Use --log-fd= to select an alternative log fd. ==71088== Warning: invalid file descriptor 1048568 in syscall close() ==71088== Warning: invalid file descriptor 1048569 in syscall close() ==71101== Warning: invalid file descriptor 1048564 in syscall close() ==71101== Warning: invalid file descriptor 1048565 in syscall close() ==71101== Warning: invalid file descriptor 1048566 in syscall close() ==71101== Warning: invalid file descriptor 1048567 in syscall close() ==71101== Use --log-fd= to select an alternative log fd. ==71101== Warning: invalid file descriptor 1048568 in syscall close() ==71101== Warning: invalid file descriptor 1048569 in syscall close() ==71108== Warning: invalid file descriptor 1048564 in syscall close() ==71108== Warning: invalid file descriptor 1048565 in syscall close() ==71108== Warning: invalid file descriptor 1048566 in syscall close() ==71108== Warning: invalid file descriptor 1048567 in syscall close() ==71108== Use --log-fd= to select an alternative log fd. ==71108== Warning: invalid file descriptor 1048568 in syscall close() ==71108== Warning: invalid file descriptor 1048569 in syscall close() ==71125== Warning: invalid file descriptor 1048564 in syscall close() ==71125== Warning: invalid file descriptor 1048565 in syscall close() ==71125== Warning: invalid file descriptor 1048566 in syscall close() ==71125== Warning: invalid file descriptor 1048567 in syscall close() ==71125== Use --log-fd= to select an alternative log fd. ==71125== Warning: invalid file descriptor 1048568 in syscall close() ==71125== Warning: invalid file descriptor 1048569 in syscall close() ==71140== Warning: invalid file descriptor 1048564 in syscall close() ==71140== Warning: invalid file descriptor 1048565 in syscall close() ==71140== Warning: invalid file descriptor 1048566 in syscall close() ==71140== Warning: invalid file descriptor 1048567 in syscall close() ==71140== Use --log-fd= to select an alternative log fd. ==71140== Warning: invalid file descriptor 1048568 in syscall close() ==71140== Warning: invalid file descriptor 1048569 in syscall close() ==71149== Warning: invalid file descriptor 1048564 in syscall close() ==71149== Warning: invalid file descriptor 1048565 in syscall close() ==71149== Warning: invalid file descriptor 1048566 in syscall close() ==71149== Warning: invalid file descriptor 1048567 in syscall close() ==71149== Use --log-fd= to select an alternative log fd. ==71149== Warning: invalid file descriptor 1048568 in syscall close() ==71149== Warning: invalid file descriptor 1048569 in syscall close() ==71161== Warning: invalid file descriptor 1048564 in syscall close() ==71161== Warning: invalid file descriptor 1048565 in syscall close() ==71161== Warning: invalid file descriptor 1048566 in syscall close() ==71161== Warning: invalid file descriptor 1048567 in syscall close() ==71161== Use --log-fd= to select an alternative log fd. ==71161== Warning: invalid file descriptor 1048568 in syscall close() ==71161== Warning: invalid file descriptor 1048569 in syscall close() ==71167== Warning: invalid file descriptor 1048564 in syscall close() ==71167== Warning: invalid file descriptor 1048565 in syscall close() ==71167== Warning: invalid file descriptor 1048566 in syscall close() ==71167== Warning: invalid file descriptor 1048567 in syscall close() ==71167== Use --log-fd= to select an alternative log fd. ==71167== Warning: invalid file descriptor 1048568 in syscall close() ==71167== Warning: invalid file descriptor 1048569 in syscall close() ==69862== ==69862== HEAP SUMMARY: ==69862== in use at exit: 1,779,759 bytes in 1,487 blocks ==69862== total heap usage: 28,423 allocs, 26,936 frees, 41,956,661 bytes allocated ==69862== ==69862== LEAK SUMMARY: ==69862== definitely lost: 0 bytes in 0 blocks ==69862== indirectly lost: 0 bytes in 0 blocks ==69862== possibly lost: 178,423 bytes in 96 blocks ==69862== still reachable: 1,601,336 bytes in 1,391 blocks ==69862== suppressed: 0 bytes in 0 blocks ==69862== Rerun with --leak-check=full to see details of leaked memory ==69862== ==69862== For counts of detected and suppressed errors, rerun with: -v ==69862== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 13464 from 610) ================================================================================ 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.