!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Si__MO_722489435928_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 = 1084.754556147279 Forces: 1 -1.99048791e+01 -3.73031777e+01 -3.39671468e+01 2 -5.08052802e+01 8.85638545e+01 -7.87322581e+01 3 -4.58518768e+00 -4.63355356e+01 2.21637289e+01 4 -4.07239950e+01 2.48281641e+01 2.30094398e+01 5 6.98223971e+01 -1.02771046e+02 -5.70651672e+00 6 2.75988381e+01 -1.44859859e+01 -3.75563597e+01 7 3.01544841e+01 -7.92959796e+01 -5.86308402e+01 8 -5.94115433e+01 -5.34859429e+01 6.67869075e+00 9 -2.45649895e+01 -1.85576167e+01 -5.82098653e+01 10 -1.31092092e+01 6.33033681e+01 -6.68729067e+01 11 -2.92794876e+01 -6.03281599e+01 1.12348377e+01 12 -4.07881206e+01 4.40169522e+01 1.62904258e+01 13 -2.03934557e+01 -1.17914141e+01 -1.34612817e+02 14 3.01712297e+01 3.04990269e+01 -1.24770404e+01 15 1.34597146e+02 2.62305588e+01 3.27423554e+01 16 2.33709773e+01 1.09093846e+02 3.13429934e+01 17 -5.60494412e+01 -2.14970257e+01 -2.35799755e+01 18 1.57649649e+01 1.93617815e+01 -1.76221316e+01 19 3.01235689e+01 -5.16883629e+01 4.32905701e+01 20 -3.93881961e+01 2.18267750e+01 3.51214909e+01 21 -2.48551760e+01 -4.50163068e+01 2.86363348e+01 22 7.17807724e+01 3.67381443e+01 5.14091157e+01 23 1.18822705e+01 -6.08531284e+00 1.95918895e+01 24 3.56868042e+00 -2.29807244e+01 4.19144941e+01 25 -5.31284130e+01 -1.61490794e+01 -1.96871550e+00 26 -1.89812613e+01 8.46236386e+01 -1.50839015e+01 27 1.48167389e+01 -6.16601996e+01 5.36110114e+01 28 -6.17464689e+01 5.27060295e+01 1.94645754e+01 29 -2.00919667e+01 -3.31660594e+01 1.65480966e+01 30 3.90038579e+01 4.72862641e+01 -1.19234026e+01 31 5.45633034e+01 -2.00248467e+01 4.52629367e+01 32 2.05878407e+01 5.35443725e+01 5.86308904e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1084.754556147279 Forces: 1 -1.99048791e+01 -3.73031777e+01 -3.39671468e+01 2 -5.08052802e+01 8.85638545e+01 -7.87322581e+01 3 -4.58518768e+00 -4.63355356e+01 2.21637289e+01 4 -4.07239950e+01 2.48281641e+01 2.30094398e+01 5 6.98223971e+01 -1.02771046e+02 -5.70651672e+00 6 2.75988381e+01 -1.44859859e+01 -3.75563597e+01 7 3.01544841e+01 -7.92959796e+01 -5.86308402e+01 8 -5.94115433e+01 -5.34859429e+01 6.67869075e+00 9 -2.45649895e+01 -1.85576167e+01 -5.82098653e+01 10 -1.31092092e+01 6.33033681e+01 -6.68729067e+01 11 -2.92794876e+01 -6.03281599e+01 1.12348377e+01 12 -4.07881206e+01 4.40169522e+01 1.62904258e+01 13 -2.03934557e+01 -1.17914141e+01 -1.34612817e+02 14 3.01712297e+01 3.04990269e+01 -1.24770404e+01 15 1.34597146e+02 2.62305588e+01 3.27423554e+01 16 2.33709773e+01 1.09093846e+02 3.13429934e+01 17 -5.60494412e+01 -2.14970257e+01 -2.35799755e+01 18 1.57649649e+01 1.93617815e+01 -1.76221316e+01 19 3.01235689e+01 -5.16883629e+01 4.32905701e+01 20 -3.93881961e+01 2.18267750e+01 3.51214909e+01 21 -2.48551760e+01 -4.50163068e+01 2.86363348e+01 22 7.17807724e+01 3.67381443e+01 5.14091157e+01 23 1.18822705e+01 -6.08531284e+00 1.95918895e+01 24 3.56868042e+00 -2.29807244e+01 4.19144941e+01 25 -5.31284130e+01 -1.61490794e+01 -1.96871550e+00 26 -1.89812613e+01 8.46236386e+01 -1.50839015e+01 27 1.48167389e+01 -6.16601996e+01 5.36110114e+01 28 -6.17464689e+01 5.27060295e+01 1.94645754e+01 29 -2.00919667e+01 -3.31660594e+01 1.65480966e+01 30 3.90038579e+01 4.72862641e+01 -1.19234026e+01 31 5.45633034e+01 -2.00248467e+01 4.52629367e+01 32 2.05878407e+01 5.35443725e+01 5.86308904e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==17110== Memcheck, a memory error detector ==17110== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==17110== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==17110== Command: python runner2.py ThreeBodyBondOrder_KDS_KhorDasSarma_1988_Si__MO_722489435928_000 ==17110== ==20225== Warning: invalid file descriptor 1048564 in syscall close() ==20225== Warning: invalid file descriptor 1048565 in syscall close() ==20225== Warning: invalid file descriptor 1048566 in syscall close() ==20225== Warning: invalid file descriptor 1048567 in syscall close() ==20225== Use --log-fd= to select an alternative log fd. ==20225== Warning: invalid file descriptor 1048568 in syscall close() ==20225== Warning: invalid file descriptor 1048569 in syscall close() ==20230== Warning: invalid file descriptor 1048564 in syscall close() ==20230== Warning: invalid file descriptor 1048565 in syscall close() ==20230== Warning: invalid file descriptor 1048566 in syscall close() ==20230== Warning: invalid file descriptor 1048567 in syscall close() ==20230== Use --log-fd= to select an alternative log fd. ==20230== Warning: invalid file descriptor 1048568 in syscall close() ==20230== Warning: invalid file descriptor 1048569 in syscall close() ==20311== Warning: invalid file descriptor 1048564 in syscall close() ==20311== Warning: invalid file descriptor 1048565 in syscall close() ==20311== Warning: invalid file descriptor 1048566 in syscall close() ==20311== Warning: invalid file descriptor 1048567 in syscall close() ==20311== Use --log-fd= to select an alternative log fd. ==20311== Warning: invalid file descriptor 1048568 in syscall close() ==20311== Warning: invalid file descriptor 1048569 in syscall close() ==20316== Warning: invalid file descriptor 1048564 in syscall close() ==20316== Warning: invalid file descriptor 1048565 in syscall close() ==20316== Warning: invalid file descriptor 1048566 in syscall close() ==20316== Warning: invalid file descriptor 1048567 in syscall close() ==20316== Use --log-fd= to select an alternative log fd. ==20316== Warning: invalid file descriptor 1048568 in syscall close() ==20316== Warning: invalid file descriptor 1048569 in syscall close() ==20320== Warning: invalid file descriptor 1048564 in syscall close() ==20320== Warning: invalid file descriptor 1048565 in syscall close() ==20320== Warning: invalid file descriptor 1048566 in syscall close() ==20320== Warning: invalid file descriptor 1048567 in syscall close() ==20320== Use --log-fd= to select an alternative log fd. ==20320== Warning: invalid file descriptor 1048568 in syscall close() ==20320== Warning: invalid file descriptor 1048569 in syscall close() ==20325== Warning: invalid file descriptor 1048564 in syscall close() ==20325== Warning: invalid file descriptor 1048565 in syscall close() ==20325== Warning: invalid file descriptor 1048566 in syscall close() ==20325== Warning: invalid file descriptor 1048567 in syscall close() ==20325== Use --log-fd= to select an alternative log fd. ==20325== Warning: invalid file descriptor 1048568 in syscall close() ==20325== Warning: invalid file descriptor 1048569 in syscall close() ==17110== ==17110== HEAP SUMMARY: ==17110== in use at exit: 1,718,308 bytes in 1,321 blocks ==17110== total heap usage: 31,107 allocs, 29,786 frees, 38,093,235 bytes allocated ==17110== ==17110== LEAK SUMMARY: ==17110== definitely lost: 0 bytes in 0 blocks ==17110== indirectly lost: 0 bytes in 0 blocks ==17110== possibly lost: 178,943 bytes in 97 blocks ==17110== still reachable: 1,539,365 bytes in 1,224 blocks ==17110== suppressed: 0 bytes in 0 blocks ==17110== Rerun with --leak-check=full to see details of leaked memory ==17110== ==17110== For counts of detected and suppressed errors, rerun with: -v ==17110== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16368 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.