!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_Dynamo_ZhouJohnsonWadley_2004_Mo__MO_271256517527_005 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 = 183.5813045264053 Forces: 1 -1.01693475e+01 -1.97968503e+01 -2.07434201e+01 2 -2.02931963e+01 3.25542718e+01 -2.72139080e+01 3 -3.45496700e+00 -2.96883684e+01 -2.98447146e+00 4 -1.59494937e+01 9.26157016e+00 1.06583823e+01 5 2.97680031e+01 -4.53902228e+01 -9.64316145e+00 6 1.09081078e+01 3.39444269e+00 -1.74544699e+01 7 1.63221004e+01 -6.55356734e+01 -5.95807007e+01 8 -2.04710995e+01 -2.17160222e+01 -1.04899813e+01 9 -2.39137548e+01 -3.47776668e+01 -5.76915359e+01 10 -2.68762959e+00 4.83480651e+01 -4.96893970e+01 11 -9.45500974e+00 -3.56358092e+01 2.10897013e+01 12 -3.58223272e+01 4.80154177e+01 2.65540831e+01 13 -1.03372245e+01 -2.70622697e+01 -9.57545954e+01 14 1.92589220e+01 2.30206849e+01 -1.60737884e+01 15 8.60781921e+01 -9.90171766e+00 2.12931586e+01 16 1.08640201e+01 6.97574408e+01 3.17999887e+01 17 -2.71136505e+01 -1.28462541e+01 -9.94395958e+00 18 -1.43843318e+01 2.00449025e+01 1.40743681e+01 19 1.28353644e+01 -2.31644483e+01 1.88876484e+01 20 -1.24756292e+01 1.73577048e+01 1.42513835e+01 21 -2.21219600e+01 -2.98879243e+01 2.00887250e+01 22 4.67819871e+01 4.96627556e+01 4.65788593e+01 23 9.51340255e+00 -4.78895882e+00 1.71065794e+01 24 5.60142157e+00 1.56058392e+00 1.56553800e+01 25 -2.56101997e+01 -8.90567513e+00 1.89592672e+01 26 -1.63321188e+01 4.33759395e+01 -2.07969134e+01 27 2.03000446e+01 -6.95123972e+01 2.47859581e+01 28 -5.99230581e+01 4.89959717e+01 1.02498772e+01 29 -1.50253709e+01 -2.20878942e+01 1.68489742e+01 30 2.20823269e+01 3.26625708e+01 2.15738118e+00 31 3.55385428e+01 -2.18773952e+01 3.01410564e+01 32 1.96879333e+01 3.45632258e+01 3.68795309e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mo (Configuration in file "config-T-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 183.5813045264053 Forces: 1 -1.01693475e+01 -1.97968503e+01 -2.07434201e+01 2 -2.02931963e+01 3.25542718e+01 -2.72139080e+01 3 -3.45496700e+00 -2.96883684e+01 -2.98447146e+00 4 -1.59494937e+01 9.26157016e+00 1.06583823e+01 5 2.97680031e+01 -4.53902228e+01 -9.64316145e+00 6 1.09081078e+01 3.39444269e+00 -1.74544699e+01 7 1.63221004e+01 -6.55356734e+01 -5.95807007e+01 8 -2.04710995e+01 -2.17160222e+01 -1.04899813e+01 9 -2.39137548e+01 -3.47776668e+01 -5.76915359e+01 10 -2.68762959e+00 4.83480651e+01 -4.96893970e+01 11 -9.45500974e+00 -3.56358092e+01 2.10897013e+01 12 -3.58223272e+01 4.80154177e+01 2.65540831e+01 13 -1.03372245e+01 -2.70622697e+01 -9.57545954e+01 14 1.92589220e+01 2.30206849e+01 -1.60737884e+01 15 8.60781921e+01 -9.90171766e+00 2.12931586e+01 16 1.08640201e+01 6.97574408e+01 3.17999887e+01 17 -2.71136505e+01 -1.28462541e+01 -9.94395958e+00 18 -1.43843318e+01 2.00449025e+01 1.40743681e+01 19 1.28353644e+01 -2.31644483e+01 1.88876484e+01 20 -1.24756292e+01 1.73577048e+01 1.42513835e+01 21 -2.21219600e+01 -2.98879243e+01 2.00887250e+01 22 4.67819871e+01 4.96627556e+01 4.65788593e+01 23 9.51340255e+00 -4.78895882e+00 1.71065794e+01 24 5.60142157e+00 1.56058392e+00 1.56553800e+01 25 -2.56101997e+01 -8.90567513e+00 1.89592672e+01 26 -1.63321188e+01 4.33759395e+01 -2.07969134e+01 27 2.03000446e+01 -6.95123972e+01 2.47859581e+01 28 -5.99230581e+01 4.89959717e+01 1.02498772e+01 29 -1.50253709e+01 -2.20878942e+01 1.68489742e+01 30 2.20823269e+01 3.26625708e+01 2.15738118e+00 31 3.55385428e+01 -2.18773952e+01 3.01410564e+01 32 1.96879333e+01 3.45632258e+01 3.68795309e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==82032== Memcheck, a memory error detector ==82032== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==82032== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==82032== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004_Mo__MO_271256517527_005 ==82032== ==84011== Warning: invalid file descriptor 1048564 in syscall close() ==84011== Warning: invalid file descriptor 1048565 in syscall close() ==84011== Warning: invalid file descriptor 1048566 in syscall close() ==84011== Warning: invalid file descriptor 1048567 in syscall close() ==84011== Use --log-fd= to select an alternative log fd. ==84011== Warning: invalid file descriptor 1048568 in syscall close() ==84011== Warning: invalid file descriptor 1048569 in syscall close() ==84030== Warning: invalid file descriptor 1048564 in syscall close() ==84030== Warning: invalid file descriptor 1048565 in syscall close() ==84030== Warning: invalid file descriptor 1048566 in syscall close() ==84030== Warning: invalid file descriptor 1048567 in syscall close() ==84030== Use --log-fd= to select an alternative log fd. ==84030== Warning: invalid file descriptor 1048568 in syscall close() ==84030== Warning: invalid file descriptor 1048569 in syscall close() ==84142== Warning: invalid file descriptor 1048564 in syscall close() ==84142== Warning: invalid file descriptor 1048565 in syscall close() ==84142== Warning: invalid file descriptor 1048566 in syscall close() ==84142== Warning: invalid file descriptor 1048567 in syscall close() ==84142== Use --log-fd= to select an alternative log fd. ==84142== Warning: invalid file descriptor 1048568 in syscall close() ==84142== Warning: invalid file descriptor 1048569 in syscall close() ==84146== Warning: invalid file descriptor 1048564 in syscall close() ==84146== Warning: invalid file descriptor 1048565 in syscall close() ==84146== Warning: invalid file descriptor 1048566 in syscall close() ==84146== Warning: invalid file descriptor 1048567 in syscall close() ==84146== Use --log-fd= to select an alternative log fd. ==84146== Warning: invalid file descriptor 1048568 in syscall close() ==84146== Warning: invalid file descriptor 1048569 in syscall close() ==84155== Warning: invalid file descriptor 1048564 in syscall close() ==84155== Warning: invalid file descriptor 1048565 in syscall close() ==84155== Warning: invalid file descriptor 1048566 in syscall close() ==84155== Warning: invalid file descriptor 1048567 in syscall close() ==84155== Use --log-fd= to select an alternative log fd. ==84155== Warning: invalid file descriptor 1048568 in syscall close() ==84155== Warning: invalid file descriptor 1048569 in syscall close() ==84162== Warning: invalid file descriptor 1048564 in syscall close() ==84162== Warning: invalid file descriptor 1048565 in syscall close() ==84162== Warning: invalid file descriptor 1048566 in syscall close() ==84162== Warning: invalid file descriptor 1048567 in syscall close() ==84162== Use --log-fd= to select an alternative log fd. ==84162== Warning: invalid file descriptor 1048568 in syscall close() ==84162== Warning: invalid file descriptor 1048569 in syscall close() ==82032== ==82032== HEAP SUMMARY: ==82032== in use at exit: 1,718,292 bytes in 1,321 blocks ==82032== total heap usage: 31,120 allocs, 29,799 frees, 40,376,678 bytes allocated ==82032== ==82032== LEAK SUMMARY: ==82032== definitely lost: 0 bytes in 0 blocks ==82032== indirectly lost: 0 bytes in 0 blocks ==82032== possibly lost: 178,943 bytes in 97 blocks ==82032== still reachable: 1,539,349 bytes in 1,224 blocks ==82032== suppressed: 0 bytes in 0 blocks ==82032== Rerun with --leak-check=full to see details of leaked memory ==82032== ==82032== For counts of detected and suppressed errors, rerun with: -v ==82032== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16338 from 599) ================================================================================ 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.