!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_LCBOP_LosFasolino_2003_C__SM_469631949122_000 Supported species : C random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = C (Configuration in file "config-F-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -29.186724734800034 Forces: 1 -1.11632219e+00 5.51662023e+00 6.14636808e+00 2 2.44583591e+00 -5.43963700e+00 -4.26779791e+00 3 5.72486177e+00 8.70791532e-01 -3.19261748e+00 4 -2.04615823e+00 -7.00124304e+00 -5.27456364e+00 5 -9.88178548e+00 3.06851102e+00 3.98390609e+00 6 -4.33167284e+00 1.86717943e+00 5.22841459e+00 7 -3.51918918e+00 5.87596737e+00 4.39912135e+00 8 6.85823720e+00 -3.41043081e+00 7.27119159e-01 9 -4.26127727e-01 3.05545761e+00 4.88815421e+00 10 3.99365007e+00 5.87112280e-01 1.10801101e+00 11 7.97024602e+00 -7.61042960e+00 -9.32256621e-01 12 -6.52834449e+00 1.13184357e-01 -6.77532605e-01 13 -9.59646494e+00 -3.33128392e+00 -4.54977674e+00 14 4.72344293e+00 5.24792797e-01 3.79850728e+00 15 2.69244904e+00 1.24550924e+01 2.17158023e+00 16 -5.30920511e+00 2.45659894e+00 2.54649448e+00 17 -1.00563569e+00 2.65337431e+00 2.50181744e+00 18 1.75023880e+00 -4.76426765e+00 -2.56652874e-01 19 3.42220418e+00 4.21293362e+00 2.23288865e+00 20 -1.96333650e+00 -2.31190455e+00 -1.38812258e+00 21 3.30034952e+00 -8.68315084e+00 8.57685971e+00 22 9.86186071e+00 5.55067469e+00 -3.88379618e+00 23 -8.58347513e+00 -1.77320050e+00 -7.89016180e+00 24 -5.39616250e+00 -4.75420126e+00 -2.93660921e+00 25 -1.05516977e+00 4.42946391e+00 -1.30222097e+01 26 5.97743229e+00 3.54430485e-01 -1.19356770e+01 27 -2.00302350e+00 1.76872849e+00 9.62487497e+00 28 -2.39540573e+00 -2.04039146e+00 6.91990328e+00 29 -3.69605151e+00 -1.01326499e+01 -7.51629255e+00 30 6.52519488e+00 -1.49013782e+00 3.05646941e-01 31 -9.42904944e-01 6.27481652e+00 -2.86594177e+00 32 4.55043212e+00 1.10719835e+00 5.43034120e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -29.186724734800034 Forces: 1 -1.11632219e+00 5.51662023e+00 6.14636808e+00 2 2.44583591e+00 -5.43963700e+00 -4.26779791e+00 3 5.72486177e+00 8.70791532e-01 -3.19261748e+00 4 -2.04615823e+00 -7.00124304e+00 -5.27456364e+00 5 -9.88178548e+00 3.06851102e+00 3.98390609e+00 6 -4.33167284e+00 1.86717943e+00 5.22841459e+00 7 -3.51918918e+00 5.87596737e+00 4.39912135e+00 8 6.85823720e+00 -3.41043081e+00 7.27119159e-01 9 -4.26127727e-01 3.05545761e+00 4.88815421e+00 10 3.99365007e+00 5.87112280e-01 1.10801101e+00 11 7.97024602e+00 -7.61042960e+00 -9.32256621e-01 12 -6.52834449e+00 1.13184357e-01 -6.77532605e-01 13 -9.59646494e+00 -3.33128392e+00 -4.54977674e+00 14 4.72344293e+00 5.24792797e-01 3.79850728e+00 15 2.69244904e+00 1.24550924e+01 2.17158023e+00 16 -5.30920511e+00 2.45659894e+00 2.54649448e+00 17 -1.00563569e+00 2.65337431e+00 2.50181744e+00 18 1.75023880e+00 -4.76426765e+00 -2.56652874e-01 19 3.42220418e+00 4.21293362e+00 2.23288865e+00 20 -1.96333650e+00 -2.31190455e+00 -1.38812258e+00 21 3.30034952e+00 -8.68315084e+00 8.57685971e+00 22 9.86186071e+00 5.55067469e+00 -3.88379618e+00 23 -8.58347513e+00 -1.77320050e+00 -7.89016180e+00 24 -5.39616250e+00 -4.75420126e+00 -2.93660921e+00 25 -1.05516977e+00 4.42946391e+00 -1.30222097e+01 26 5.97743229e+00 3.54430485e-01 -1.19356770e+01 27 -2.00302350e+00 1.76872849e+00 9.62487497e+00 28 -2.39540573e+00 -2.04039146e+00 6.91990328e+00 29 -3.69605151e+00 -1.01326499e+01 -7.51629255e+00 30 6.52519488e+00 -1.49013782e+00 3.05646941e-01 31 -9.42904944e-01 6.27481652e+00 -2.86594177e+00 32 4.55043212e+00 1.10719835e+00 5.43034120e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==50450== Memcheck, a memory error detector ==50450== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==50450== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==50450== Command: python runner2.py Sim_LAMMPS_LCBOP_LosFasolino_2003_C__SM_469631949122_000 ==50450== ==51720== Warning: invalid file descriptor 1048564 in syscall close() ==51720== Warning: invalid file descriptor 1048565 in syscall close() ==51720== Warning: invalid file descriptor 1048566 in syscall close() ==51720== Warning: invalid file descriptor 1048567 in syscall close() ==51720== Use --log-fd= to select an alternative log fd. ==51720== Warning: invalid file descriptor 1048568 in syscall close() ==51720== Warning: invalid file descriptor 1048569 in syscall close() ==51721== Warning: invalid file descriptor 1048564 in syscall close() ==51721== Warning: invalid file descriptor 1048565 in syscall close() ==51721== Warning: invalid file descriptor 1048566 in syscall close() ==51721== Warning: invalid file descriptor 1048567 in syscall close() ==51721== Use --log-fd= to select an alternative log fd. ==51721== Warning: invalid file descriptor 1048568 in syscall close() ==51721== Warning: invalid file descriptor 1048569 in syscall close() ==51722== Warning: invalid file descriptor 1048564 in syscall close() ==51722== Warning: invalid file descriptor 1048565 in syscall close() ==51722== Warning: invalid file descriptor 1048566 in syscall close() ==51722== Warning: invalid file descriptor 1048567 in syscall close() ==51722== Use --log-fd= to select an alternative log fd. ==51722== Warning: invalid file descriptor 1048568 in syscall close() ==51722== Warning: invalid file descriptor 1048569 in syscall close() ==51723== Warning: invalid file descriptor 1048564 in syscall close() ==51723== Warning: invalid file descriptor 1048565 in syscall close() ==51723== Warning: invalid file descriptor 1048566 in syscall close() ==51723== Warning: invalid file descriptor 1048567 in syscall close() ==51723== Use --log-fd= to select an alternative log fd. ==51723== Warning: invalid file descriptor 1048568 in syscall close() ==51723== Warning: invalid file descriptor 1048569 in syscall close() ==51724== Warning: invalid file descriptor 1048564 in syscall close() ==51724== Warning: invalid file descriptor 1048565 in syscall close() ==51724== Warning: invalid file descriptor 1048566 in syscall close() ==51724== Warning: invalid file descriptor 1048567 in syscall close() ==51724== Use --log-fd= to select an alternative log fd. ==51724== Warning: invalid file descriptor 1048568 in syscall close() ==51724== Warning: invalid file descriptor 1048569 in syscall close() ==51725== Warning: invalid file descriptor 1048564 in syscall close() ==51725== Warning: invalid file descriptor 1048565 in syscall close() ==51725== Warning: invalid file descriptor 1048566 in syscall close() ==51725== Warning: invalid file descriptor 1048567 in syscall close() ==51725== Use --log-fd= to select an alternative log fd. ==51725== Warning: invalid file descriptor 1048568 in syscall close() ==51725== Warning: invalid file descriptor 1048569 in syscall close() ==51726== Warning: invalid file descriptor 1048564 in syscall close() ==51726== Warning: invalid file descriptor 1048565 in syscall close() ==51726== Warning: invalid file descriptor 1048566 in syscall close() ==51726== Warning: invalid file descriptor 1048567 in syscall close() ==51726== Use --log-fd= to select an alternative log fd. ==51726== Warning: invalid file descriptor 1048568 in syscall close() ==51726== Warning: invalid file descriptor 1048569 in syscall close() ==51727== Warning: invalid file descriptor 1048564 in syscall close() ==51727== Warning: invalid file descriptor 1048565 in syscall close() ==51727== Warning: invalid file descriptor 1048566 in syscall close() ==51727== Warning: invalid file descriptor 1048567 in syscall close() ==51727== Use --log-fd= to select an alternative log fd. ==51727== Warning: invalid file descriptor 1048568 in syscall close() ==51727== Warning: invalid file descriptor 1048569 in syscall close() ==50450== ==50450== HEAP SUMMARY: ==50450== in use at exit: 1,780,623 bytes in 1,488 blocks ==50450== total heap usage: 28,394 allocs, 26,906 frees, 42,788,872 bytes allocated ==50450== ==50450== LEAK SUMMARY: ==50450== definitely lost: 0 bytes in 0 blocks ==50450== indirectly lost: 0 bytes in 0 blocks ==50450== possibly lost: 178,423 bytes in 96 blocks ==50450== still reachable: 1,602,200 bytes in 1,392 blocks ==50450== suppressed: 0 bytes in 0 blocks ==50450== Rerun with --leak-check=full to see details of leaked memory ==50450== ==50450== For counts of detected and suppressed errors, rerun with: -v ==50450== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16418 from 609) ================================================================================ 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.