!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MEAM_EtesamiAsadi_2018_Ni__SM_333792531460_000 Supported species : Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -11.200163993579036 Forces: 1 -1.32537934e+01 -1.90145506e+01 -3.67550387e+01 2 -7.30716491e+00 9.34054753e+00 -3.43234838e+00 3 3.82138435e+01 -2.41201326e+01 1.76837710e+01 4 -2.66496508e+01 4.02668163e+01 1.66901633e+01 5 1.00646527e+00 -1.49644652e+01 1.54544378e+00 6 6.54076258e+00 7.35160003e+00 -2.22850167e+00 7 -2.33128749e+00 -5.66926914e+01 -5.81553275e+01 8 -9.57937518e+00 -1.20736176e+01 6.09467699e-01 9 -4.55443391e+00 -3.22154865e+00 -2.81680966e+00 10 -1.10064512e+01 1.32405777e+01 -1.55605546e+01 11 -8.47301197e+00 -1.30915384e+01 5.12759088e+00 12 -6.27552903e+00 2.31128723e+01 -1.65345871e+01 13 -1.12072355e+01 -1.17093184e+01 -4.36979950e+01 14 5.21351720e+00 7.88120391e+00 -5.50543861e+00 15 3.15521478e+01 -1.57245214e+01 1.55110177e+01 16 8.47820475e+00 2.11939001e+01 1.89000002e+01 17 -8.63252185e+00 -9.68908560e+00 -6.89870675e+00 18 3.05388262e+00 1.11299927e+01 -1.11031156e+01 19 -3.56614511e+00 -1.57809928e+01 8.57894489e+00 20 -3.65973281e+00 7.41596831e+00 8.90813162e+00 21 -7.30950691e+00 -7.44268328e+00 -3.62613522e+00 22 1.60586869e+01 5.67986506e+01 5.55279993e+01 23 3.84373103e+00 -3.31660763e-01 5.85836284e+00 24 1.17082686e+01 7.02036912e+00 7.17760374e+00 25 9.23356751e-01 -1.69277854e+01 2.20733511e+01 26 -7.42993020e+00 8.99466775e+00 -8.78461978e+00 27 3.43270029e+01 -4.85130121e+01 6.26127685e+00 28 -4.53327512e+01 3.97686633e+01 1.08013179e+00 29 -1.09286864e+01 -8.25779823e+00 -1.19862849e+01 30 3.82165804e+00 1.23942072e+01 1.16713885e+01 31 1.78036138e+01 -2.50568296e+00 9.48185683e+00 32 4.95206618e+00 1.41510486e+01 1.43989618e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -11.200163993579036 Forces: 1 -1.32537934e+01 -1.90145506e+01 -3.67550387e+01 2 -7.30716491e+00 9.34054753e+00 -3.43234838e+00 3 3.82138435e+01 -2.41201326e+01 1.76837710e+01 4 -2.66496508e+01 4.02668163e+01 1.66901633e+01 5 1.00646527e+00 -1.49644652e+01 1.54544378e+00 6 6.54076258e+00 7.35160003e+00 -2.22850167e+00 7 -2.33128749e+00 -5.66926914e+01 -5.81553275e+01 8 -9.57937518e+00 -1.20736176e+01 6.09467699e-01 9 -4.55443391e+00 -3.22154865e+00 -2.81680966e+00 10 -1.10064512e+01 1.32405777e+01 -1.55605546e+01 11 -8.47301197e+00 -1.30915384e+01 5.12759088e+00 12 -6.27552903e+00 2.31128723e+01 -1.65345871e+01 13 -1.12072355e+01 -1.17093184e+01 -4.36979950e+01 14 5.21351720e+00 7.88120391e+00 -5.50543861e+00 15 3.15521478e+01 -1.57245214e+01 1.55110177e+01 16 8.47820475e+00 2.11939001e+01 1.89000002e+01 17 -8.63252185e+00 -9.68908560e+00 -6.89870675e+00 18 3.05388262e+00 1.11299927e+01 -1.11031156e+01 19 -3.56614511e+00 -1.57809928e+01 8.57894489e+00 20 -3.65973281e+00 7.41596831e+00 8.90813162e+00 21 -7.30950691e+00 -7.44268328e+00 -3.62613522e+00 22 1.60586869e+01 5.67986506e+01 5.55279993e+01 23 3.84373103e+00 -3.31660763e-01 5.85836284e+00 24 1.17082686e+01 7.02036912e+00 7.17760374e+00 25 9.23356751e-01 -1.69277854e+01 2.20733511e+01 26 -7.42993020e+00 8.99466775e+00 -8.78461978e+00 27 3.43270029e+01 -4.85130121e+01 6.26127685e+00 28 -4.53327512e+01 3.97686633e+01 1.08013179e+00 29 -1.09286864e+01 -8.25779823e+00 -1.19862849e+01 30 3.82165804e+00 1.23942072e+01 1.16713885e+01 31 1.78036138e+01 -2.50568296e+00 9.48185683e+00 32 4.95206618e+00 1.41510486e+01 1.43989618e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==41935== Memcheck, a memory error detector ==41935== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==41935== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==41935== Command: python runner2.py Sim_LAMMPS_MEAM_EtesamiAsadi_2018_Ni__SM_333792531460_000 ==41935== ==43136== Warning: invalid file descriptor 1048564 in syscall close() ==43136== Warning: invalid file descriptor 1048565 in syscall close() ==43136== Warning: invalid file descriptor 1048566 in syscall close() ==43136== Warning: invalid file descriptor 1048567 in syscall close() ==43136== Use --log-fd= to select an alternative log fd. ==43136== Warning: invalid file descriptor 1048568 in syscall close() ==43136== Warning: invalid file descriptor 1048569 in syscall close() ==43141== Warning: invalid file descriptor 1048564 in syscall close() ==43141== Warning: invalid file descriptor 1048565 in syscall close() ==43141== Warning: invalid file descriptor 1048566 in syscall close() ==43141== Warning: invalid file descriptor 1048567 in syscall close() ==43141== Use --log-fd= to select an alternative log fd. ==43141== Warning: invalid file descriptor 1048568 in syscall close() ==43141== Warning: invalid file descriptor 1048569 in syscall close() ==43146== Warning: invalid file descriptor 1048564 in syscall close() ==43146== Warning: invalid file descriptor 1048565 in syscall close() ==43146== Warning: invalid file descriptor 1048566 in syscall close() ==43146== Warning: invalid file descriptor 1048567 in syscall close() ==43146== Use --log-fd= to select an alternative log fd. ==43146== Warning: invalid file descriptor 1048568 in syscall close() ==43146== Warning: invalid file descriptor 1048569 in syscall close() ==43156== Warning: invalid file descriptor 1048564 in syscall close() ==43156== Warning: invalid file descriptor 1048565 in syscall close() ==43156== Warning: invalid file descriptor 1048566 in syscall close() ==43156== Warning: invalid file descriptor 1048567 in syscall close() ==43156== Use --log-fd= to select an alternative log fd. ==43156== Warning: invalid file descriptor 1048568 in syscall close() ==43156== Warning: invalid file descriptor 1048569 in syscall close() ==43163== Warning: invalid file descriptor 1048564 in syscall close() ==43163== Warning: invalid file descriptor 1048565 in syscall close() ==43163== Warning: invalid file descriptor 1048566 in syscall close() ==43163== Warning: invalid file descriptor 1048567 in syscall close() ==43163== Use --log-fd= to select an alternative log fd. ==43163== Warning: invalid file descriptor 1048568 in syscall close() ==43163== Warning: invalid file descriptor 1048569 in syscall close() ==43171== Warning: invalid file descriptor 1048564 in syscall close() ==43171== Warning: invalid file descriptor 1048565 in syscall close() ==43171== Warning: invalid file descriptor 1048566 in syscall close() ==43171== Warning: invalid file descriptor 1048567 in syscall close() ==43171== Use --log-fd= to select an alternative log fd. ==43171== Warning: invalid file descriptor 1048568 in syscall close() ==43171== Warning: invalid file descriptor 1048569 in syscall close() ==43180== Warning: invalid file descriptor 1048564 in syscall close() ==43180== Warning: invalid file descriptor 1048565 in syscall close() ==43180== Warning: invalid file descriptor 1048566 in syscall close() ==43180== Warning: invalid file descriptor 1048567 in syscall close() ==43180== Use --log-fd= to select an alternative log fd. ==43180== Warning: invalid file descriptor 1048568 in syscall close() ==43180== Warning: invalid file descriptor 1048569 in syscall close() ==43182== Warning: invalid file descriptor 1048564 in syscall close() ==43182== Warning: invalid file descriptor 1048565 in syscall close() ==43182== Warning: invalid file descriptor 1048566 in syscall close() ==43182== Warning: invalid file descriptor 1048567 in syscall close() ==43182== Use --log-fd= to select an alternative log fd. ==43182== Warning: invalid file descriptor 1048568 in syscall close() ==43182== Warning: invalid file descriptor 1048569 in syscall close() ==41935== ==41935== HEAP SUMMARY: ==41935== in use at exit: 1,780,635 bytes in 1,488 blocks ==41935== total heap usage: 28,634 allocs, 27,146 frees, 48,624,468 bytes allocated ==41935== ==41935== LEAK SUMMARY: ==41935== definitely lost: 0 bytes in 0 blocks ==41935== indirectly lost: 0 bytes in 0 blocks ==41935== possibly lost: 178,423 bytes in 96 blocks ==41935== still reachable: 1,602,212 bytes in 1,392 blocks ==41935== suppressed: 0 bytes in 0 blocks ==41935== Rerun with --leak-check=full to see details of leaked memory ==41935== ==41935== For counts of detected and suppressed errors, rerun with: -v ==41935== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16419 from 606) ================================================================================ 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.