!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Al__MO_131650261510_005 Supported species : Al random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 14.93505495162251 Forces: 1 -3.27320938e+00 -8.23322239e+00 -6.97875246e+00 2 -2.35835487e+00 1.71350726e+00 -8.35281944e+00 3 3.11507481e+00 -8.21616072e+00 -2.91622646e+00 4 -6.58474368e+00 5.10304748e+00 4.30554044e+00 5 1.39850167e+00 -9.60100278e+00 -4.37775818e+00 6 5.63186770e+00 1.12182310e+00 -6.59055231e+00 7 5.84009488e+00 -1.34612730e+01 -8.55704325e+00 8 -5.25686150e+00 -5.95239149e+00 1.97413940e+00 9 -8.15206838e+00 -7.90947431e-02 -9.96430187e+00 10 -3.13146484e+00 1.25888492e+01 -1.09970411e+01 11 -4.40113048e+00 -7.06108301e+00 5.55356005e+00 12 -6.68896446e+00 8.94158438e+00 -2.56090724e+00 13 1.77335480e-01 -3.69297349e+00 -2.16058178e+01 14 5.67480903e+00 6.39750294e+00 -4.97251101e+00 15 1.90275731e+01 -2.71071289e+00 2.83847149e+00 16 1.52986687e+00 1.68551000e+01 5.39454802e+00 17 -9.90089752e+00 -4.84163514e+00 7.78603949e-01 18 2.73557547e+00 6.00595891e+00 1.18035865e+00 19 8.58137117e-01 -7.56165388e+00 5.10838662e+00 20 -4.76932911e+00 2.77241727e+00 4.56408624e+00 21 -5.13549095e+00 -8.10275479e+00 2.33057237e+00 22 1.10025291e+01 8.91124698e+00 7.37968062e+00 23 4.91903954e+00 -2.63902804e+00 5.26129881e+00 24 -6.81308425e-01 3.64601585e+00 5.69494368e+00 25 -7.57310902e+00 -6.68583264e+00 2.07996094e+00 26 -2.26019300e+00 1.22003468e+01 -3.57094217e+00 27 3.69473844e+00 -1.34730032e+01 8.78872467e+00 28 -1.22293178e+01 1.02101506e+01 4.57010750e+00 29 -3.41652638e+00 -7.26996549e+00 4.24799244e+00 30 6.99151593e+00 8.85484328e+00 1.95633489e+00 31 8.68818572e+00 -4.04800088e+00 7.78168410e+00 32 4.52812498e+00 8.30739460e+00 9.65567842e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 14.93505495162251 Forces: 1 -3.27320938e+00 -8.23322239e+00 -6.97875246e+00 2 -2.35835487e+00 1.71350726e+00 -8.35281944e+00 3 3.11507481e+00 -8.21616072e+00 -2.91622646e+00 4 -6.58474368e+00 5.10304748e+00 4.30554044e+00 5 1.39850167e+00 -9.60100278e+00 -4.37775818e+00 6 5.63186770e+00 1.12182310e+00 -6.59055231e+00 7 5.84009488e+00 -1.34612730e+01 -8.55704325e+00 8 -5.25686150e+00 -5.95239149e+00 1.97413940e+00 9 -8.15206838e+00 -7.90947431e-02 -9.96430187e+00 10 -3.13146484e+00 1.25888492e+01 -1.09970411e+01 11 -4.40113048e+00 -7.06108301e+00 5.55356005e+00 12 -6.68896446e+00 8.94158438e+00 -2.56090724e+00 13 1.77335480e-01 -3.69297349e+00 -2.16058178e+01 14 5.67480903e+00 6.39750294e+00 -4.97251101e+00 15 1.90275731e+01 -2.71071289e+00 2.83847149e+00 16 1.52986687e+00 1.68551000e+01 5.39454802e+00 17 -9.90089752e+00 -4.84163514e+00 7.78603949e-01 18 2.73557547e+00 6.00595891e+00 1.18035865e+00 19 8.58137117e-01 -7.56165388e+00 5.10838662e+00 20 -4.76932911e+00 2.77241727e+00 4.56408624e+00 21 -5.13549095e+00 -8.10275479e+00 2.33057237e+00 22 1.10025291e+01 8.91124698e+00 7.37968062e+00 23 4.91903954e+00 -2.63902804e+00 5.26129881e+00 24 -6.81308425e-01 3.64601585e+00 5.69494368e+00 25 -7.57310902e+00 -6.68583264e+00 2.07996094e+00 26 -2.26019300e+00 1.22003468e+01 -3.57094217e+00 27 3.69473844e+00 -1.34730032e+01 8.78872467e+00 28 -1.22293178e+01 1.02101506e+01 4.57010750e+00 29 -3.41652638e+00 -7.26996549e+00 4.24799244e+00 30 6.99151593e+00 8.85484328e+00 1.95633489e+00 31 8.68818572e+00 -4.04800088e+00 7.78168410e+00 32 4.52812498e+00 8.30739460e+00 9.65567842e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==78218== Memcheck, a memory error detector ==78218== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==78218== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==78218== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004_Al__MO_131650261510_005 ==78218== ==80259== Warning: invalid file descriptor 1048564 in syscall close() ==80259== Warning: invalid file descriptor 1048565 in syscall close() ==80259== Warning: invalid file descriptor 1048566 in syscall close() ==80259== Warning: invalid file descriptor 1048567 in syscall close() ==80259== Use --log-fd= to select an alternative log fd. ==80259== Warning: invalid file descriptor 1048568 in syscall close() ==80259== Warning: invalid file descriptor 1048569 in syscall close() ==80264== Warning: invalid file descriptor 1048564 in syscall close() ==80264== Warning: invalid file descriptor 1048565 in syscall close() ==80264== Warning: invalid file descriptor 1048566 in syscall close() ==80264== Warning: invalid file descriptor 1048567 in syscall close() ==80264== Use --log-fd= to select an alternative log fd. ==80264== Warning: invalid file descriptor 1048568 in syscall close() ==80264== Warning: invalid file descriptor 1048569 in syscall close() ==80367== Warning: invalid file descriptor 1048564 in syscall close() ==80367== Warning: invalid file descriptor 1048565 in syscall close() ==80367== Warning: invalid file descriptor 1048566 in syscall close() ==80367== Warning: invalid file descriptor 1048567 in syscall close() ==80367== Use --log-fd= to select an alternative log fd. ==80367== Warning: invalid file descriptor 1048568 in syscall close() ==80367== Warning: invalid file descriptor 1048569 in syscall close() ==80374== Warning: invalid file descriptor 1048564 in syscall close() ==80374== Warning: invalid file descriptor 1048565 in syscall close() ==80374== Warning: invalid file descriptor 1048566 in syscall close() ==80374== Warning: invalid file descriptor 1048567 in syscall close() ==80374== Use --log-fd= to select an alternative log fd. ==80374== Warning: invalid file descriptor 1048568 in syscall close() ==80374== Warning: invalid file descriptor 1048569 in syscall close() ==80375== Warning: invalid file descriptor 1048564 in syscall close() ==80375== Warning: invalid file descriptor 1048565 in syscall close() ==80375== Warning: invalid file descriptor 1048566 in syscall close() ==80375== Warning: invalid file descriptor 1048567 in syscall close() ==80375== Use --log-fd= to select an alternative log fd. ==80375== Warning: invalid file descriptor 1048568 in syscall close() ==80375== Warning: invalid file descriptor 1048569 in syscall close() ==80382== Warning: invalid file descriptor 1048564 in syscall close() ==80382== Warning: invalid file descriptor 1048565 in syscall close() ==80382== Warning: invalid file descriptor 1048566 in syscall close() ==80382== Warning: invalid file descriptor 1048567 in syscall close() ==80382== Use --log-fd= to select an alternative log fd. ==80382== Warning: invalid file descriptor 1048568 in syscall close() ==80382== Warning: invalid file descriptor 1048569 in syscall close() ==78218== ==78218== HEAP SUMMARY: ==78218== in use at exit: 1,718,292 bytes in 1,321 blocks ==78218== total heap usage: 31,120 allocs, 29,799 frees, 40,376,686 bytes allocated ==78218== ==78218== LEAK SUMMARY: ==78218== definitely lost: 0 bytes in 0 blocks ==78218== indirectly lost: 0 bytes in 0 blocks ==78218== possibly lost: 178,943 bytes in 97 blocks ==78218== still reachable: 1,539,349 bytes in 1,224 blocks ==78218== suppressed: 0 bytes in 0 blocks ==78218== Rerun with --leak-check=full to see details of leaked memory ==78218== ==78218== For counts of detected and suppressed errors, rerun with: -v ==78218== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16333 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.