!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : ThreeBodyBondOrder_KDS_KhorDasSarma_1988_Ge__MO_216597146527_000 Supported species : Ge random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ge (Configuration in file "config-F-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1558.0651027874762 Forces: 1 -3.42029674e+01 -3.57285713e+01 -4.64973940e+01 2 -4.49697084e+00 2.23249063e+01 -8.49243951e+01 3 -1.89494483e+01 -8.24080365e+01 1.16500523e+01 4 -7.29977387e+01 9.46186706e+00 1.83786840e+01 5 3.63956319e+01 -6.24070552e+01 -4.00411879e+01 6 3.41553600e+01 7.07119121e-01 -5.21372710e+01 7 5.45902549e+01 -1.15022180e+02 -6.16235662e+01 8 -7.09097843e+01 -6.24893722e+01 -3.09972958e+01 9 -4.23506605e+01 2.36079057e+00 -7.62196144e+01 10 -2.22027061e+01 7.52231239e+01 -8.56589001e+01 11 -3.83106274e+01 -5.51080784e+01 2.89709928e+00 12 -5.95171171e+01 5.58793022e+01 3.63094451e-01 13 -2.73925002e+00 -3.36289999e+01 -1.62730951e+02 14 4.13422024e+01 4.65090651e+01 -3.42463703e+01 15 1.73956557e+02 1.34454203e+01 -2.13209528e+01 16 2.44805458e+01 1.52260260e+02 2.71530710e+01 17 -4.81565135e+01 -2.70046234e+01 4.46678784e+00 18 -3.33035139e+01 1.82775191e+01 8.19471497e+00 19 -4.74101275e+00 -4.47350057e+01 5.16748084e+01 20 -2.67904223e+01 2.88060447e+00 2.35316610e+01 21 -1.46745753e+01 -1.03087174e+02 3.83190948e+01 22 1.34016908e+02 3.32929705e+01 5.22774208e+01 23 2.48233693e+01 -1.20329217e+01 4.04847065e+01 24 -3.99243801e+00 -1.73923589e+01 7.85380217e+01 25 -6.60447882e+01 -6.00896068e+00 5.12718138e+01 26 -3.64126132e+01 1.03513076e+02 -1.43674824e+01 27 -4.41651096e+01 -5.90108870e+01 6.83372710e+01 28 -5.72835699e+01 3.14126588e+01 1.79181113e+01 29 -1.27981984e+01 1.72111186e+01 5.79819144e+01 30 6.04676130e+01 5.97079557e+01 1.04008983e+01 31 8.22072005e+01 -8.82848823e+00 7.16749369e+01 32 4.86043825e+01 8.04249557e+01 7.52512187e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ge (Configuration in file "config-T-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1558.0651027874762 Forces: 1 -3.42029674e+01 -3.57285713e+01 -4.64973940e+01 2 -4.49697084e+00 2.23249063e+01 -8.49243951e+01 3 -1.89494483e+01 -8.24080365e+01 1.16500523e+01 4 -7.29977387e+01 9.46186706e+00 1.83786840e+01 5 3.63956319e+01 -6.24070552e+01 -4.00411879e+01 6 3.41553600e+01 7.07119121e-01 -5.21372710e+01 7 5.45902549e+01 -1.15022180e+02 -6.16235662e+01 8 -7.09097843e+01 -6.24893722e+01 -3.09972958e+01 9 -4.23506605e+01 2.36079057e+00 -7.62196144e+01 10 -2.22027061e+01 7.52231239e+01 -8.56589001e+01 11 -3.83106274e+01 -5.51080784e+01 2.89709928e+00 12 -5.95171171e+01 5.58793022e+01 3.63094451e-01 13 -2.73925002e+00 -3.36289999e+01 -1.62730951e+02 14 4.13422024e+01 4.65090651e+01 -3.42463703e+01 15 1.73956557e+02 1.34454203e+01 -2.13209528e+01 16 2.44805458e+01 1.52260260e+02 2.71530710e+01 17 -4.81565135e+01 -2.70046234e+01 4.46678784e+00 18 -3.33035139e+01 1.82775191e+01 8.19471497e+00 19 -4.74101275e+00 -4.47350057e+01 5.16748084e+01 20 -2.67904223e+01 2.88060447e+00 2.35316610e+01 21 -1.46745753e+01 -1.03087174e+02 3.83190948e+01 22 1.34016908e+02 3.32929705e+01 5.22774208e+01 23 2.48233693e+01 -1.20329217e+01 4.04847065e+01 24 -3.99243801e+00 -1.73923589e+01 7.85380217e+01 25 -6.60447882e+01 -6.00896068e+00 5.12718138e+01 26 -3.64126132e+01 1.03513076e+02 -1.43674824e+01 27 -4.41651096e+01 -5.90108870e+01 6.83372710e+01 28 -5.72835699e+01 3.14126588e+01 1.79181113e+01 29 -1.27981984e+01 1.72111186e+01 5.79819144e+01 30 6.04676130e+01 5.97079557e+01 1.04008983e+01 31 8.22072005e+01 -8.82848823e+00 7.16749369e+01 32 4.86043825e+01 8.04249557e+01 7.52512187e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==15711== Memcheck, a memory error detector ==15711== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==15711== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==15711== Command: python runner2.py ThreeBodyBondOrder_KDS_KhorDasSarma_1988_Ge__MO_216597146527_000 ==15711== ==19459== Warning: invalid file descriptor 1048564 in syscall close() ==19459== Warning: invalid file descriptor 1048565 in syscall close() ==19459== Warning: invalid file descriptor 1048566 in syscall close() ==19459== Warning: invalid file descriptor 1048567 in syscall close() ==19459== Use --log-fd= to select an alternative log fd. ==19459== Warning: invalid file descriptor 1048568 in syscall close() ==19459== Warning: invalid file descriptor 1048569 in syscall close() ==19478== Warning: invalid file descriptor 1048564 in syscall close() ==19478== Warning: invalid file descriptor 1048565 in syscall close() ==19478== Warning: invalid file descriptor 1048566 in syscall close() ==19478== Warning: invalid file descriptor 1048567 in syscall close() ==19478== Use --log-fd= to select an alternative log fd. ==19478== Warning: invalid file descriptor 1048568 in syscall close() ==19478== Warning: invalid file descriptor 1048569 in syscall close() ==19640== Warning: invalid file descriptor 1048564 in syscall close() ==19640== Warning: invalid file descriptor 1048565 in syscall close() ==19640== Warning: invalid file descriptor 1048566 in syscall close() ==19640== Warning: invalid file descriptor 1048567 in syscall close() ==19640== Use --log-fd= to select an alternative log fd. ==19640== Warning: invalid file descriptor 1048568 in syscall close() ==19640== Warning: invalid file descriptor 1048569 in syscall close() ==19649== Warning: invalid file descriptor 1048564 in syscall close() ==19649== Warning: invalid file descriptor 1048565 in syscall close() ==19649== Warning: invalid file descriptor 1048566 in syscall close() ==19649== Warning: invalid file descriptor 1048567 in syscall close() ==19649== Use --log-fd= to select an alternative log fd. ==19649== Warning: invalid file descriptor 1048568 in syscall close() ==19649== Warning: invalid file descriptor 1048569 in syscall close() ==19668== Warning: invalid file descriptor 1048564 in syscall close() ==19668== Warning: invalid file descriptor 1048565 in syscall close() ==19668== Warning: invalid file descriptor 1048566 in syscall close() ==19668== Warning: invalid file descriptor 1048567 in syscall close() ==19668== Use --log-fd= to select an alternative log fd. ==19668== Warning: invalid file descriptor 1048568 in syscall close() ==19668== Warning: invalid file descriptor 1048569 in syscall close() ==19674== Warning: invalid file descriptor 1048564 in syscall close() ==19674== Warning: invalid file descriptor 1048565 in syscall close() ==19674== Warning: invalid file descriptor 1048566 in syscall close() ==19674== Warning: invalid file descriptor 1048567 in syscall close() ==19674== Use --log-fd= to select an alternative log fd. ==19674== Warning: invalid file descriptor 1048568 in syscall close() ==19674== Warning: invalid file descriptor 1048569 in syscall close() ==15711== ==15711== HEAP SUMMARY: ==15711== in use at exit: 1,718,308 bytes in 1,321 blocks ==15711== total heap usage: 31,107 allocs, 29,786 frees, 38,094,163 bytes allocated ==15711== ==15711== LEAK SUMMARY: ==15711== definitely lost: 0 bytes in 0 blocks ==15711== indirectly lost: 0 bytes in 0 blocks ==15711== possibly lost: 178,943 bytes in 97 blocks ==15711== still reachable: 1,539,365 bytes in 1,224 blocks ==15711== suppressed: 0 bytes in 0 blocks ==15711== Rerun with --leak-check=full to see details of leaked memory ==15711== ==15711== For counts of detected and suppressed errors, rerun with: -v ==15711== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16374 from 614) ================================================================================ 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.