!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_JacobsenNorskovPuska_1987_Al__MO_411692133366_000 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 = -56.843277168347484 Forces: 1 -9.39911457e-01 -2.24824855e+00 -2.41204098e+00 2 -1.75852998e+00 3.38818858e+00 -5.37736993e-01 3 2.03400698e+00 -3.34070008e+00 -2.10446172e+00 4 -1.90075955e+00 1.66942597e+00 1.21461398e+00 5 1.36234488e+00 -3.67374684e+00 -2.95307248e-01 6 1.31493707e+00 1.37515258e+00 -1.31538846e+00 7 1.97369141e+00 -8.09243806e+00 -7.99737886e+00 8 -4.58679586e+00 -1.59094048e+00 -3.24707055e-01 9 -2.56635290e+00 -4.24743450e+00 -3.63785863e+00 10 3.01095231e+00 3.89889229e+00 -3.20463192e+00 11 7.08863529e+00 -2.35848235e+00 -5.78878255e+00 12 -3.97230018e+00 4.06250108e+00 2.34231487e+00 13 -4.37430220e+00 -3.33258680e+00 -8.85936042e+00 14 1.62110739e+00 2.21993539e+00 -1.21585274e+00 15 8.23768943e+00 -1.97974261e+00 2.65523267e+00 16 -2.86879476e-01 5.83701813e+00 2.14046328e+00 17 -3.90007886e+00 -1.87288990e+00 -1.23792517e+00 18 1.03809808e+00 3.12963967e+00 1.48360151e+00 19 1.73105123e+00 -2.68777585e+00 2.16504519e+00 20 -1.03091263e+00 2.47980822e+00 1.44034599e+00 21 -3.83662069e+00 -2.94270673e+00 1.78889916e+00 22 4.65912385e+00 7.43676014e+00 6.16272615e+00 23 7.83410785e-01 -2.29367451e-01 1.52822928e+00 24 8.65933040e-01 8.70942231e-01 1.63059718e+00 25 -7.64149875e+00 -1.73536927e+00 5.53753689e+00 26 -1.30661878e+00 5.27424806e+00 -2.97744776e+00 27 3.43443072e+00 -9.45191241e+00 3.02037926e+00 28 -7.06795592e+00 6.36390233e+00 1.47293618e+00 29 -2.14506205e+00 -2.97980462e+00 3.78868364e-01 30 1.67576573e+00 3.43415738e+00 2.78803767e-01 31 4.08335203e+00 -2.91159852e+00 2.83654206e+00 32 2.40004907e+00 4.23517298e+00 3.83174473e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -56.843277168347484 Forces: 1 -9.39911457e-01 -2.24824855e+00 -2.41204098e+00 2 -1.75852998e+00 3.38818858e+00 -5.37736993e-01 3 2.03400698e+00 -3.34070008e+00 -2.10446172e+00 4 -1.90075955e+00 1.66942597e+00 1.21461398e+00 5 1.36234488e+00 -3.67374684e+00 -2.95307248e-01 6 1.31493707e+00 1.37515258e+00 -1.31538846e+00 7 1.97369141e+00 -8.09243806e+00 -7.99737886e+00 8 -4.58679586e+00 -1.59094048e+00 -3.24707055e-01 9 -2.56635290e+00 -4.24743450e+00 -3.63785863e+00 10 3.01095231e+00 3.89889229e+00 -3.20463192e+00 11 7.08863529e+00 -2.35848235e+00 -5.78878255e+00 12 -3.97230018e+00 4.06250108e+00 2.34231487e+00 13 -4.37430220e+00 -3.33258680e+00 -8.85936042e+00 14 1.62110739e+00 2.21993539e+00 -1.21585274e+00 15 8.23768943e+00 -1.97974261e+00 2.65523267e+00 16 -2.86879476e-01 5.83701813e+00 2.14046328e+00 17 -3.90007886e+00 -1.87288990e+00 -1.23792517e+00 18 1.03809808e+00 3.12963967e+00 1.48360151e+00 19 1.73105123e+00 -2.68777585e+00 2.16504519e+00 20 -1.03091263e+00 2.47980822e+00 1.44034599e+00 21 -3.83662069e+00 -2.94270673e+00 1.78889916e+00 22 4.65912385e+00 7.43676014e+00 6.16272615e+00 23 7.83410785e-01 -2.29367451e-01 1.52822928e+00 24 8.65933040e-01 8.70942231e-01 1.63059718e+00 25 -7.64149875e+00 -1.73536927e+00 5.53753689e+00 26 -1.30661878e+00 5.27424806e+00 -2.97744776e+00 27 3.43443072e+00 -9.45191241e+00 3.02037926e+00 28 -7.06795592e+00 6.36390233e+00 1.47293618e+00 29 -2.14506205e+00 -2.97980462e+00 3.78868364e-01 30 1.67576573e+00 3.43415738e+00 2.78803767e-01 31 4.08335203e+00 -2.91159852e+00 2.83654206e+00 32 2.40004907e+00 4.23517298e+00 3.83174473e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==34965== Memcheck, a memory error detector ==34965== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==34965== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==34965== Command: python runner2.py EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000 ==34965== ==37014== Warning: invalid file descriptor 1048564 in syscall close() ==37014== Warning: invalid file descriptor 1048565 in syscall close() ==37014== Warning: invalid file descriptor 1048566 in syscall close() ==37014== Warning: invalid file descriptor 1048567 in syscall close() ==37014== Use --log-fd= to select an alternative log fd. ==37014== Warning: invalid file descriptor 1048568 in syscall close() ==37014== Warning: invalid file descriptor 1048569 in syscall close() ==37020== Warning: invalid file descriptor 1048564 in syscall close() ==37020== Warning: invalid file descriptor 1048565 in syscall close() ==37020== Warning: invalid file descriptor 1048566 in syscall close() ==37020== Warning: invalid file descriptor 1048567 in syscall close() ==37020== Use --log-fd= to select an alternative log fd. ==37020== Warning: invalid file descriptor 1048568 in syscall close() ==37020== Warning: invalid file descriptor 1048569 in syscall close() ==37116== Warning: invalid file descriptor 1048564 in syscall close() ==37116== Warning: invalid file descriptor 1048565 in syscall close() ==37116== Warning: invalid file descriptor 1048566 in syscall close() ==37116== Warning: invalid file descriptor 1048567 in syscall close() ==37116== Use --log-fd= to select an alternative log fd. ==37116== Warning: invalid file descriptor 1048568 in syscall close() ==37116== Warning: invalid file descriptor 1048569 in syscall close() ==37117== Warning: invalid file descriptor 1048564 in syscall close() ==37117== Warning: invalid file descriptor 1048565 in syscall close() ==37117== Warning: invalid file descriptor 1048566 in syscall close() ==37117== Warning: invalid file descriptor 1048567 in syscall close() ==37117== Use --log-fd= to select an alternative log fd. ==37117== Warning: invalid file descriptor 1048568 in syscall close() ==37117== Warning: invalid file descriptor 1048569 in syscall close() ==37125== Warning: invalid file descriptor 1048564 in syscall close() ==37125== Warning: invalid file descriptor 1048565 in syscall close() ==37125== Warning: invalid file descriptor 1048566 in syscall close() ==37125== Warning: invalid file descriptor 1048567 in syscall close() ==37125== Use --log-fd= to select an alternative log fd. ==37125== Warning: invalid file descriptor 1048568 in syscall close() ==37125== Warning: invalid file descriptor 1048569 in syscall close() ==37135== Warning: invalid file descriptor 1048564 in syscall close() ==37135== Warning: invalid file descriptor 1048565 in syscall close() ==37135== Warning: invalid file descriptor 1048566 in syscall close() ==37135== Warning: invalid file descriptor 1048567 in syscall close() ==37135== Use --log-fd= to select an alternative log fd. ==37135== Warning: invalid file descriptor 1048568 in syscall close() ==37135== Warning: invalid file descriptor 1048569 in syscall close() ==34965== ==34965== HEAP SUMMARY: ==34965== in use at exit: 1,718,292 bytes in 1,321 blocks ==34965== total heap usage: 33,156 allocs, 31,835 frees, 43,643,309 bytes allocated ==34965== ==34965== LEAK SUMMARY: ==34965== definitely lost: 0 bytes in 0 blocks ==34965== indirectly lost: 0 bytes in 0 blocks ==34965== possibly lost: 178,943 bytes in 97 blocks ==34965== still reachable: 1,539,349 bytes in 1,224 blocks ==34965== suppressed: 0 bytes in 0 blocks ==34965== Rerun with --leak-check=full to see details of leaked memory ==34965== ==34965== For counts of detected and suppressed errors, rerun with: -v ==34965== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16374 from 601) ================================================================================ 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.