!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001NISTretabulation_Zr__MO_380166217430_000 Supported species : Zr random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Zr (Configuration in file "config-F-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 30.614594807562142 Forces: 1 -5.89580110e+00 -1.03832577e+01 -1.11084422e+01 2 -5.03107669e+00 6.74282662e+00 -1.06860296e+01 3 6.76878902e+00 -1.89493950e+01 -8.04375143e+00 4 -1.43403963e+01 6.33081691e+00 2.28909988e-01 5 -1.31974983e+00 -1.80703745e+01 -6.64696983e+00 6 1.11389125e+01 7.48454638e+00 -1.23714571e+01 7 1.33924563e+01 -3.24940043e+01 -2.08170520e+01 8 -1.53784058e+01 -1.18663883e+01 -2.49770062e+00 9 -1.19465827e+01 -8.41084729e+00 -1.90804910e+01 10 -4.93728046e+00 2.12406380e+01 -2.25426098e+01 11 -4.49037696e+00 -1.34515070e+01 3.57443328e+00 12 -1.31887741e+01 1.86708100e+01 2.50739490e+00 13 -5.94608477e+00 -1.50468532e+01 -4.43106306e+01 14 1.00447191e+01 1.24752745e+01 -8.49499516e+00 15 4.14374813e+01 -5.11492424e+00 8.43911778e+00 16 7.02807371e+00 3.55194982e+01 1.31414465e+01 17 -2.07035610e+01 -1.37215278e+01 -3.09871241e+00 18 1.16285296e+01 1.43677675e+01 1.03055572e+01 19 4.43308718e+00 -1.56908409e+01 9.39113615e+00 20 -8.29290849e+00 9.17034185e+00 9.98025220e+00 21 -1.31394969e+01 -1.42638251e+01 7.99004233e+00 22 2.24761429e+01 2.46833689e+01 1.69516759e+01 23 6.46879418e+00 -4.54442389e+00 1.30502973e+01 24 3.00381017e+00 7.02900245e+00 7.33192376e+00 25 -1.75949989e+01 -6.49478474e+00 9.94869942e+00 26 -7.31470381e+00 2.43602915e+01 -9.54209072e+00 27 9.30416358e+00 -3.25164092e+01 1.48858161e+01 28 -2.67828005e+01 2.27782585e+01 6.85808744e+00 29 -8.28302369e+00 -1.32135018e+01 1.01330914e+01 30 1.13027640e+01 1.77321624e+01 -1.31679901e+00 31 1.70555727e+01 -1.26376465e+01 1.70908966e+01 32 9.10272571e+00 1.82849079e+01 1.87489532e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zr (Configuration in file "config-T-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 30.614594807562142 Forces: 1 -5.89580110e+00 -1.03832577e+01 -1.11084422e+01 2 -5.03107669e+00 6.74282662e+00 -1.06860296e+01 3 6.76878902e+00 -1.89493950e+01 -8.04375143e+00 4 -1.43403963e+01 6.33081691e+00 2.28909988e-01 5 -1.31974983e+00 -1.80703745e+01 -6.64696983e+00 6 1.11389125e+01 7.48454638e+00 -1.23714571e+01 7 1.33924563e+01 -3.24940043e+01 -2.08170520e+01 8 -1.53784058e+01 -1.18663883e+01 -2.49770062e+00 9 -1.19465827e+01 -8.41084729e+00 -1.90804910e+01 10 -4.93728046e+00 2.12406380e+01 -2.25426098e+01 11 -4.49037696e+00 -1.34515070e+01 3.57443328e+00 12 -1.31887741e+01 1.86708100e+01 2.50739490e+00 13 -5.94608477e+00 -1.50468532e+01 -4.43106306e+01 14 1.00447191e+01 1.24752745e+01 -8.49499516e+00 15 4.14374813e+01 -5.11492424e+00 8.43911778e+00 16 7.02807371e+00 3.55194982e+01 1.31414465e+01 17 -2.07035610e+01 -1.37215278e+01 -3.09871241e+00 18 1.16285296e+01 1.43677675e+01 1.03055572e+01 19 4.43308718e+00 -1.56908409e+01 9.39113615e+00 20 -8.29290849e+00 9.17034185e+00 9.98025220e+00 21 -1.31394969e+01 -1.42638251e+01 7.99004233e+00 22 2.24761429e+01 2.46833689e+01 1.69516759e+01 23 6.46879418e+00 -4.54442389e+00 1.30502973e+01 24 3.00381017e+00 7.02900245e+00 7.33192376e+00 25 -1.75949989e+01 -6.49478474e+00 9.94869942e+00 26 -7.31470381e+00 2.43602915e+01 -9.54209072e+00 27 9.30416358e+00 -3.25164092e+01 1.48858161e+01 28 -2.67828005e+01 2.27782585e+01 6.85808744e+00 29 -8.28302369e+00 -1.32135018e+01 1.01330914e+01 30 1.13027640e+01 1.77321624e+01 -1.31679901e+00 31 1.70555727e+01 -1.26376465e+01 1.70908966e+01 32 9.10272571e+00 1.82849079e+01 1.87489532e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==96108== Memcheck, a memory error detector ==96108== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==96108== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==96108== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Zr__MO_380166217430_000 ==96108== ==97779== Warning: invalid file descriptor 1048564 in syscall close() ==97779== Warning: invalid file descriptor 1048565 in syscall close() ==97779== Warning: invalid file descriptor 1048566 in syscall close() ==97779== Warning: invalid file descriptor 1048567 in syscall close() ==97779== Use --log-fd= to select an alternative log fd. ==97779== Warning: invalid file descriptor 1048568 in syscall close() ==97779== Warning: invalid file descriptor 1048569 in syscall close() ==97782== Warning: invalid file descriptor 1048564 in syscall close() ==97782== Warning: invalid file descriptor 1048565 in syscall close() ==97782== Warning: invalid file descriptor 1048566 in syscall close() ==97782== Warning: invalid file descriptor 1048567 in syscall close() ==97782== Use --log-fd= to select an alternative log fd. ==97782== Warning: invalid file descriptor 1048568 in syscall close() ==97782== Warning: invalid file descriptor 1048569 in syscall close() ==97820== Warning: invalid file descriptor 1048564 in syscall close() ==97820== Warning: invalid file descriptor 1048565 in syscall close() ==97820== Warning: invalid file descriptor 1048566 in syscall close() ==97820== Warning: invalid file descriptor 1048567 in syscall close() ==97820== Use --log-fd= to select an alternative log fd. ==97820== Warning: invalid file descriptor 1048568 in syscall close() ==97820== Warning: invalid file descriptor 1048569 in syscall close() ==97821== Warning: invalid file descriptor 1048564 in syscall close() ==97821== Warning: invalid file descriptor 1048565 in syscall close() ==97821== Warning: invalid file descriptor 1048566 in syscall close() ==97821== Warning: invalid file descriptor 1048567 in syscall close() ==97821== Use --log-fd= to select an alternative log fd. ==97821== Warning: invalid file descriptor 1048568 in syscall close() ==97821== Warning: invalid file descriptor 1048569 in syscall close() ==97822== Warning: invalid file descriptor 1048564 in syscall close() ==97822== Warning: invalid file descriptor 1048565 in syscall close() ==97822== Warning: invalid file descriptor 1048566 in syscall close() ==97822== Warning: invalid file descriptor 1048567 in syscall close() ==97822== Use --log-fd= to select an alternative log fd. ==97822== Warning: invalid file descriptor 1048568 in syscall close() ==97822== Warning: invalid file descriptor 1048569 in syscall close() ==97823== Warning: invalid file descriptor 1048564 in syscall close() ==97823== Warning: invalid file descriptor 1048565 in syscall close() ==97823== Warning: invalid file descriptor 1048566 in syscall close() ==97823== Warning: invalid file descriptor 1048567 in syscall close() ==97823== Use --log-fd= to select an alternative log fd. ==97823== Warning: invalid file descriptor 1048568 in syscall close() ==97823== Warning: invalid file descriptor 1048569 in syscall close() ==96108== ==96108== HEAP SUMMARY: ==96108== in use at exit: 1,718,292 bytes in 1,321 blocks ==96108== total heap usage: 33,153 allocs, 31,832 frees, 44,917,268 bytes allocated ==96108== ==96108== LEAK SUMMARY: ==96108== definitely lost: 0 bytes in 0 blocks ==96108== indirectly lost: 0 bytes in 0 blocks ==96108== possibly lost: 178,943 bytes in 97 blocks ==96108== still reachable: 1,539,349 bytes in 1,224 blocks ==96108== suppressed: 0 bytes in 0 blocks ==96108== Rerun with --leak-check=full to see details of leaked memory ==96108== ==96108== For counts of detected and suppressed errors, rerun with: -v ==96108== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 13389 from 597) ================================================================================ 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.