!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : LJ_Truncated_Nguyen_2005_Ar__MO_398194508715_001 Supported species : Ar random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ar (Configuration in file "config-F-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6451.2160039909 Forces: 1 -6.65411924e+02 -1.92169609e+03 -2.58819182e+03 2 -5.37656981e+00 3.44876359e+02 -3.29283254e+02 3 1.15674186e+03 -1.02636403e+03 3.89254529e+02 4 -6.19267569e+02 2.76665043e+03 2.00780429e+03 5 1.29526964e+01 -3.85396249e+02 -2.49512481e+02 6 1.03903208e+02 6.54630519e+01 -1.90483376e+02 7 -2.92879183e+02 -2.53386571e+03 -2.60629449e+03 8 -8.75590646e+02 -9.10647137e+02 2.00126982e+02 9 -2.82310589e+01 -1.24119990e+02 -1.68246871e+02 10 -5.46519292e+02 2.65848149e+02 -6.75798986e+02 11 -7.80083713e+02 -8.39315833e+02 -2.11589524e+01 12 -2.16345472e+02 6.07088936e+02 -2.91901279e+02 13 -1.34639943e+03 -6.11325421e+02 -2.64446654e+03 14 3.60081510e+02 3.85451266e+02 -1.53641841e+02 15 2.51017270e+03 4.78211907e+02 1.55731472e+03 16 7.79960670e+02 1.68672300e+03 1.09111790e+03 17 -5.01645757e+02 -2.19868356e+02 2.38297610e+02 18 -2.90342280e+00 9.06017207e+03 -8.55422209e+03 19 2.86888039e+02 -9.05649965e+03 8.59902939e+03 20 -2.16118072e+02 1.24872924e+02 1.51014272e+02 21 -7.18568247e+02 -4.69473315e+02 -4.08518812e+01 22 1.35101531e+03 2.60220687e+03 2.01155078e+03 23 1.13943129e+03 -5.81905998e+02 8.31775189e+02 24 -7.66446002e+02 5.75061654e+02 2.80447701e+02 25 -3.68894336e+02 -6.17831475e+02 5.50349859e+02 26 2.59278514e+01 6.50241527e+02 -4.19823064e+02 27 2.34140077e+03 -3.02721726e+03 5.43462657e+02 28 -2.97255614e+03 2.54660168e+03 5.28889880e+00 29 -1.17601450e+03 -1.16731051e+03 -1.63932532e+03 30 5.69551220e+02 6.96545426e+02 -2.08548589e+02 31 1.36748905e+03 -5.20370616e+02 1.08618722e+03 32 9.37351470e+01 1.15719240e+03 1.23872884e+03 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ar (Configuration in file "config-T-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6451.2160039909 Forces: 1 -6.65411924e+02 -1.92169609e+03 -2.58819182e+03 2 -5.37656981e+00 3.44876359e+02 -3.29283254e+02 3 1.15674186e+03 -1.02636403e+03 3.89254529e+02 4 -6.19267569e+02 2.76665043e+03 2.00780429e+03 5 1.29526964e+01 -3.85396249e+02 -2.49512481e+02 6 1.03903208e+02 6.54630519e+01 -1.90483376e+02 7 -2.92879183e+02 -2.53386571e+03 -2.60629449e+03 8 -8.75590646e+02 -9.10647137e+02 2.00126982e+02 9 -2.82310589e+01 -1.24119990e+02 -1.68246871e+02 10 -5.46519292e+02 2.65848149e+02 -6.75798986e+02 11 -7.80083713e+02 -8.39315833e+02 -2.11589524e+01 12 -2.16345472e+02 6.07088936e+02 -2.91901279e+02 13 -1.34639943e+03 -6.11325421e+02 -2.64446654e+03 14 3.60081510e+02 3.85451266e+02 -1.53641841e+02 15 2.51017270e+03 4.78211907e+02 1.55731472e+03 16 7.79960670e+02 1.68672300e+03 1.09111790e+03 17 -5.01645757e+02 -2.19868356e+02 2.38297610e+02 18 -2.90342280e+00 9.06017207e+03 -8.55422209e+03 19 2.86888039e+02 -9.05649965e+03 8.59902939e+03 20 -2.16118072e+02 1.24872924e+02 1.51014272e+02 21 -7.18568247e+02 -4.69473315e+02 -4.08518812e+01 22 1.35101531e+03 2.60220687e+03 2.01155078e+03 23 1.13943129e+03 -5.81905998e+02 8.31775189e+02 24 -7.66446002e+02 5.75061654e+02 2.80447701e+02 25 -3.68894336e+02 -6.17831475e+02 5.50349859e+02 26 2.59278514e+01 6.50241527e+02 -4.19823064e+02 27 2.34140077e+03 -3.02721726e+03 5.43462657e+02 28 -2.97255614e+03 2.54660168e+03 5.28889880e+00 29 -1.17601450e+03 -1.16731051e+03 -1.63932532e+03 30 5.69551220e+02 6.96545426e+02 -2.08548589e+02 31 1.36748905e+03 -5.20370616e+02 1.08618722e+03 32 9.37351470e+01 1.15719240e+03 1.23872884e+03 ================================================================================ VALGRIND OUTPUT ================================================================================ ==36916== Memcheck, a memory error detector ==36916== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==36916== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==36916== Command: python runner2.py LJ_Truncated_Nguyen_2005_Ar__MO_398194508715_001 ==36916== ==39802== Warning: invalid file descriptor 1048564 in syscall close() ==39802== Warning: invalid file descriptor 1048565 in syscall close() ==39802== Warning: invalid file descriptor 1048566 in syscall close() ==39802== Warning: invalid file descriptor 1048567 in syscall close() ==39802== Use --log-fd= to select an alternative log fd. ==39802== Warning: invalid file descriptor 1048568 in syscall close() ==39802== Warning: invalid file descriptor 1048569 in syscall close() ==39810== Warning: invalid file descriptor 1048564 in syscall close() ==39810== Warning: invalid file descriptor 1048565 in syscall close() ==39810== Warning: invalid file descriptor 1048566 in syscall close() ==39810== Warning: invalid file descriptor 1048567 in syscall close() ==39810== Use --log-fd= to select an alternative log fd. ==39810== Warning: invalid file descriptor 1048568 in syscall close() ==39810== Warning: invalid file descriptor 1048569 in syscall close() ==39900== Warning: invalid file descriptor 1048564 in syscall close() ==39900== Warning: invalid file descriptor 1048565 in syscall close() ==39900== Warning: invalid file descriptor 1048566 in syscall close() ==39900== Warning: invalid file descriptor 1048567 in syscall close() ==39900== Use --log-fd= to select an alternative log fd. ==39900== Warning: invalid file descriptor 1048568 in syscall close() ==39900== Warning: invalid file descriptor 1048569 in syscall close() ==39904== Warning: invalid file descriptor 1048564 in syscall close() ==39904== Warning: invalid file descriptor 1048565 in syscall close() ==39904== Warning: invalid file descriptor 1048566 in syscall close() ==39904== Warning: invalid file descriptor 1048567 in syscall close() ==39904== Use --log-fd= to select an alternative log fd. ==39904== Warning: invalid file descriptor 1048568 in syscall close() ==39904== Warning: invalid file descriptor 1048569 in syscall close() ==39911== Warning: invalid file descriptor 1048564 in syscall close() ==39911== Warning: invalid file descriptor 1048565 in syscall close() ==39911== Warning: invalid file descriptor 1048566 in syscall close() ==39911== Warning: invalid file descriptor 1048567 in syscall close() ==39911== Use --log-fd= to select an alternative log fd. ==39911== Warning: invalid file descriptor 1048568 in syscall close() ==39911== Warning: invalid file descriptor 1048569 in syscall close() ==39916== Warning: invalid file descriptor 1048564 in syscall close() ==39916== Warning: invalid file descriptor 1048565 in syscall close() ==39916== Warning: invalid file descriptor 1048566 in syscall close() ==39916== Warning: invalid file descriptor 1048567 in syscall close() ==39916== Use --log-fd= to select an alternative log fd. ==39916== Warning: invalid file descriptor 1048568 in syscall close() ==39916== Warning: invalid file descriptor 1048569 in syscall close() ==36916== ==36916== HEAP SUMMARY: ==36916== in use at exit: 1,718,292 bytes in 1,321 blocks ==36916== total heap usage: 30,945 allocs, 29,624 frees, 38,085,822 bytes allocated ==36916== ==36916== LEAK SUMMARY: ==36916== definitely lost: 0 bytes in 0 blocks ==36916== indirectly lost: 0 bytes in 0 blocks ==36916== possibly lost: 178,943 bytes in 97 blocks ==36916== still reachable: 1,539,349 bytes in 1,224 blocks ==36916== suppressed: 0 bytes in 0 blocks ==36916== Rerun with --leak-check=full to see details of leaked memory ==36916== ==36916== For counts of detected and suppressed errors, rerun with: -v ==36916== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11243 from 589) ================================================================================ 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.