!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_SNAP_ChenDengTran_2017_Mo__SM_003882782678_000 Supported species : Mo random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mo (Configuration in file "config-F-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = -317.7139788669854 Forces: 1 -1.45667737e+01 -1.08086934e+01 -2.04102144e+01 2 -9.99613669e+00 2.15785207e+01 -1.70787701e+01 3 9.76224231e+00 -2.26797783e+01 1.62303263e+01 4 -1.89471422e+01 1.67770514e+01 7.82379539e+00 5 1.90847035e+01 -2.38324512e+01 -6.98784841e+00 6 8.37459036e+00 -5.63675164e+00 -1.51119275e+01 7 1.40308697e+01 -4.36845742e+01 -5.09824751e+01 8 -1.33351336e+01 -3.66303285e+01 -9.03190007e+00 9 -2.58702165e+01 -2.77631123e+01 -3.12728361e+01 10 2.76658357e+00 4.83226898e+01 -4.43383967e+01 11 -5.20264240e+01 -5.60304503e+01 3.23339709e+00 12 -3.07154760e+01 2.03798506e+01 1.95382147e+01 13 1.13653307e+01 -1.28410999e+01 -8.90940830e+01 14 1.41720392e+01 1.44232415e+01 -1.21514183e+01 15 6.75536012e+01 -6.05905751e+00 4.09507779e+00 16 1.94736898e+01 8.95195945e+01 1.91996565e+01 17 -2.26106290e+01 -1.32177068e+01 -1.74200047e+01 18 -8.45895501e-01 2.59559453e+00 1.12243840e+00 19 2.07102653e+01 -1.86542496e+01 1.81694293e+01 20 -1.07272926e+01 2.01528196e+01 1.73624813e+01 21 -3.57276765e+01 -2.99854843e+01 1.40959114e+01 22 4.31782875e+01 3.85327261e+01 3.43093884e+01 23 9.04490085e+00 -7.16976125e-01 2.08652976e+01 24 2.14513642e-01 -1.24775179e+01 1.33832817e+01 25 -3.01861765e+01 -1.43485638e+01 -4.65361290e+00 26 -1.38460528e+01 5.34768507e+01 -1.73217858e+01 27 -8.27158947e+00 -4.85612491e+01 3.92588970e+01 28 -3.77912832e+01 2.48079414e+01 1.53382194e+01 29 1.30687154e+01 -1.40362400e+01 3.17843430e+01 30 1.59370343e+01 2.47757929e+01 1.63280195e+01 31 3.03650212e+01 -7.66690676e+00 1.16548846e+01 32 2.63615097e+01 3.02885180e+01 3.20622138e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mo (Configuration in file "config-T-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = -317.7139788669854 Forces: 1 -1.45667737e+01 -1.08086934e+01 -2.04102144e+01 2 -9.99613669e+00 2.15785207e+01 -1.70787701e+01 3 9.76224231e+00 -2.26797783e+01 1.62303263e+01 4 -1.89471422e+01 1.67770514e+01 7.82379539e+00 5 1.90847035e+01 -2.38324512e+01 -6.98784841e+00 6 8.37459036e+00 -5.63675164e+00 -1.51119275e+01 7 1.40308697e+01 -4.36845742e+01 -5.09824751e+01 8 -1.33351336e+01 -3.66303285e+01 -9.03190007e+00 9 -2.58702165e+01 -2.77631123e+01 -3.12728361e+01 10 2.76658357e+00 4.83226898e+01 -4.43383967e+01 11 -5.20264240e+01 -5.60304503e+01 3.23339709e+00 12 -3.07154760e+01 2.03798506e+01 1.95382147e+01 13 1.13653307e+01 -1.28410999e+01 -8.90940830e+01 14 1.41720392e+01 1.44232415e+01 -1.21514183e+01 15 6.75536012e+01 -6.05905751e+00 4.09507779e+00 16 1.94736898e+01 8.95195945e+01 1.91996565e+01 17 -2.26106290e+01 -1.32177068e+01 -1.74200047e+01 18 -8.45895501e-01 2.59559453e+00 1.12243840e+00 19 2.07102653e+01 -1.86542496e+01 1.81694293e+01 20 -1.07272926e+01 2.01528196e+01 1.73624813e+01 21 -3.57276765e+01 -2.99854843e+01 1.40959114e+01 22 4.31782875e+01 3.85327261e+01 3.43093884e+01 23 9.04490085e+00 -7.16976125e-01 2.08652976e+01 24 2.14513642e-01 -1.24775179e+01 1.33832817e+01 25 -3.01861765e+01 -1.43485638e+01 -4.65361290e+00 26 -1.38460528e+01 5.34768507e+01 -1.73217858e+01 27 -8.27158947e+00 -4.85612491e+01 3.92588970e+01 28 -3.77912832e+01 2.48079414e+01 1.53382194e+01 29 1.30687154e+01 -1.40362400e+01 3.17843430e+01 30 1.59370343e+01 2.47757929e+01 1.63280195e+01 31 3.03650212e+01 -7.66690676e+00 1.16548846e+01 32 2.63615097e+01 3.02885180e+01 3.20622138e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==25045== Memcheck, a memory error detector ==25045== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==25045== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==25045== Command: python runner2.py Sim_LAMMPS_SNAP_ChenDengTran_2017_Mo__SM_003882782678_000 ==25045== ==25055== Warning: invalid file descriptor 1048564 in syscall close() ==25055== Warning: invalid file descriptor 1048565 in syscall close() ==25055== Warning: invalid file descriptor 1048566 in syscall close() ==25055== Warning: invalid file descriptor 1048567 in syscall close() ==25055== Use --log-fd= to select an alternative log fd. ==25055== Warning: invalid file descriptor 1048568 in syscall close() ==25055== Warning: invalid file descriptor 1048569 in syscall close() ==25056== Warning: invalid file descriptor 1048564 in syscall close() ==25056== Warning: invalid file descriptor 1048565 in syscall close() ==25056== Warning: invalid file descriptor 1048566 in syscall close() ==25056== Warning: invalid file descriptor 1048567 in syscall close() ==25056== Use --log-fd= to select an alternative log fd. ==25056== Warning: invalid file descriptor 1048568 in syscall close() ==25056== Warning: invalid file descriptor 1048569 in syscall close() ==25057== Warning: invalid file descriptor 1048564 in syscall close() ==25057== Warning: invalid file descriptor 1048565 in syscall close() ==25057== Warning: invalid file descriptor 1048566 in syscall close() ==25057== Warning: invalid file descriptor 1048567 in syscall close() ==25057== Use --log-fd= to select an alternative log fd. ==25057== Warning: invalid file descriptor 1048568 in syscall close() ==25057== Warning: invalid file descriptor 1048569 in syscall close() ==25058== Warning: invalid file descriptor 1048564 in syscall close() ==25058== Warning: invalid file descriptor 1048565 in syscall close() ==25058== Warning: invalid file descriptor 1048566 in syscall close() ==25058== Warning: invalid file descriptor 1048567 in syscall close() ==25058== Use --log-fd= to select an alternative log fd. ==25058== Warning: invalid file descriptor 1048568 in syscall close() ==25058== Warning: invalid file descriptor 1048569 in syscall close() ==25059== Warning: invalid file descriptor 1048564 in syscall close() ==25059== Warning: invalid file descriptor 1048565 in syscall close() ==25059== Warning: invalid file descriptor 1048566 in syscall close() ==25059== Warning: invalid file descriptor 1048567 in syscall close() ==25059== Use --log-fd= to select an alternative log fd. ==25059== Warning: invalid file descriptor 1048568 in syscall close() ==25059== Warning: invalid file descriptor 1048569 in syscall close() ==25060== Warning: invalid file descriptor 1048564 in syscall close() ==25060== Warning: invalid file descriptor 1048565 in syscall close() ==25060== Warning: invalid file descriptor 1048566 in syscall close() ==25060== Warning: invalid file descriptor 1048567 in syscall close() ==25060== Use --log-fd= to select an alternative log fd. ==25060== Warning: invalid file descriptor 1048568 in syscall close() ==25060== Warning: invalid file descriptor 1048569 in syscall close() ==25061== Warning: invalid file descriptor 1048564 in syscall close() ==25061== Warning: invalid file descriptor 1048565 in syscall close() ==25061== Warning: invalid file descriptor 1048566 in syscall close() ==25061== Warning: invalid file descriptor 1048567 in syscall close() ==25061== Use --log-fd= to select an alternative log fd. ==25061== Warning: invalid file descriptor 1048568 in syscall close() ==25061== Warning: invalid file descriptor 1048569 in syscall close() ==25062== Warning: invalid file descriptor 1048564 in syscall close() ==25062== Warning: invalid file descriptor 1048565 in syscall close() ==25062== Warning: invalid file descriptor 1048566 in syscall close() ==25062== Warning: invalid file descriptor 1048567 in syscall close() ==25062== Use --log-fd= to select an alternative log fd. ==25062== Warning: invalid file descriptor 1048568 in syscall close() ==25062== Warning: invalid file descriptor 1048569 in syscall close() ==25045== ==25045== HEAP SUMMARY: ==25045== in use at exit: 1,780,635 bytes in 1,488 blocks ==25045== total heap usage: 28,552 allocs, 27,064 frees, 42,188,009 bytes allocated ==25045== ==25045== LEAK SUMMARY: ==25045== definitely lost: 0 bytes in 0 blocks ==25045== indirectly lost: 0 bytes in 0 blocks ==25045== possibly lost: 178,423 bytes in 96 blocks ==25045== still reachable: 1,602,212 bytes in 1,392 blocks ==25045== suppressed: 0 bytes in 0 blocks ==25045== Rerun with --leak-check=full to see details of leaked memory ==25045== ==25045== For counts of detected and suppressed errors, rerun with: -v ==25045== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16421 from 608) ================================================================================ 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.